[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/

2020-12-30 Thread Martin Mokrejs
commit: 7653e736bbdbd6d7373e8015b0b79e1855032f83
Author: Martin Mokrejs  gmail  com>
AuthorDate: Wed Dec 30 22:52:06 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Wed Dec 30 22:52:26 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7653e736

sci-biology/bowtie: version bump

the sci-biology/sra_sdk is not complete in Gentoo so bowtie cannot
use this optional dependency (yet)

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/bowtie/{bowtie-2.4.1.ebuild => bowtie-2.4.2.ebuild} | 9 -
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/sci-biology/bowtie/bowtie-2.4.1.ebuild 
b/sci-biology/bowtie/bowtie-2.4.2.ebuild
similarity index 86%
rename from sci-biology/bowtie/bowtie-2.4.1.ebuild
rename to sci-biology/bowtie/bowtie-2.4.2.ebuild
index a4d6837ba..3cd8c2cdc 100644
--- a/sci-biology/bowtie/bowtie-2.4.1.ebuild
+++ b/sci-biology/bowtie/bowtie-2.4.2.ebuild
@@ -14,13 +14,15 @@ LICENSE="GPL-3"
 SLOT="2"
 KEYWORDS="~amd64 ~x86"
 
-IUSE="examples cpu_flags_x86_sse2 +tbb"
+IUSE="examples cpu_flags_x86_sse2 +tbb" # sra
+# IUSE=sra Use sra-toolkit to download input datasets on the fly.
 
 RDEPEND="dev-lang/perl
tbb? ( dev-cpp/tbb )"
 DEPEND="${RDEPEND}
app-arch/unzip
sys-libs/readline"
+#  sra? ( sci-biology/sra_sdk )"
 
 S="${WORKDIR}/${PN}2-${PV}"
 
@@ -42,6 +44,7 @@ src_compile() {
EXTRA_FLAGS="${LDFLAGS}" \
RELEASE_FLAGS="${CXXFLAGS} -msse2" \
WITH_TBB="$(usex tbb 1 0)"
+   # USE_SRA="$(usex sra 1 0)"
 }
 
 src_install() {
@@ -58,3 +61,7 @@ src_install() {
doins -r example
fi
 }
+
+src_test(){
+   emake test
+}



[gentoo-commits] proj/sci:master commit in: sci-biology/bedops/

2020-12-18 Thread Martin Mokrejs
commit: 2a28ea64417794f6c09e39345fec05445ff8ae44
Author: Martin Mokrejs  gmail  com>
AuthorDate: Fri Dec 18 10:53:44 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Dec 18 10:54:07 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2a28ea64

sci-biology/bedops: fix install procedure

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/bedops/bedops-2.4.26.ebuild | 8 +++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/sci-biology/bedops/bedops-2.4.26.ebuild 
b/sci-biology/bedops/bedops-2.4.26.ebuild
index d281fbede..4ae167a08 100644
--- a/sci-biology/bedops/bedops-2.4.26.ebuild
+++ b/sci-biology/bedops/bedops-2.4.26.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -23,3 +23,9 @@ src_prepare(){
local PATCHES=("${FILESDIR}"/${P}-respect-cxxflags.patch)
epatch ${PATCHES[@]}
 }
+
+src_install(){
+   emake install
+   dobin bin/*
+   dodoc README.md
+}



[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

2020-12-12 Thread Martin Mokrejs
commit: f1b4f4489e2e9181bca1dde19fffb24a9155bef7
Author: Martin Mokrejs  gmail  com>
AuthorDate: Sat Dec 12 15:23:20 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sat Dec 12 15:23:38 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f1b4f448

sci-biology/pybedtools: document more dependencies

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 7 +++
 1 file changed, 7 insertions(+)

diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild 
b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
index 9edb8f366..a91de8cca 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
@@ -19,11 +19,18 @@ RESTRICT="test"
 # Tests reported to fail on Gentoo:
 # https://github.com/daler/pybedtools/issues/329
 
+# see requirements.txt
 RDEPEND="
sci-biology/bedtools
sci-biology/pysam
+   dev-python/numpy
+   dev-python/pandas
!minimal? ( sci-libs/htslib )
doc? ( dev-python/sphinx )"
+# optional-requirements.txt also lists:
+# ucsc-bigwigtobedgraph
+# ucsc-bedgraphtobigwig
+# ucsc-wigtobigwig
 DEPEND="${RDEPEND}
dev-python/cython[${PYTHON_USEDEP}]"
 



[gentoo-commits] proj/sci:master commit in: sci-biology/rtg-tools/

2020-12-10 Thread Martin Mokrejs
commit: f51d6ce27e5c393c5c28926cee6d87b89d0e699c
Author: Martin Mokrejs  gmail  com>
AuthorDate: Thu Dec 10 11:12:19 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Dec 10 11:13:08 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f51d6ce2

sci-biology/rtg-tools: install missing files

The ebuild still needs some cleanup IMO, especially the
rtg shell script which writes /etc/rtg.cfg and $bindir
needs a fix. But one can run the jar file directly.

Package-Manager: Portage-3.0.11, Repoman-3.0.2
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/rtg-tools/rtg-tools-.ebuild | 26 +++---
 1 file changed, 23 insertions(+), 3 deletions(-)

diff --git a/sci-biology/rtg-tools/rtg-tools-.ebuild 
b/sci-biology/rtg-tools/rtg-tools-.ebuild
index b658f7c17..4f146be70 100644
--- a/sci-biology/rtg-tools/rtg-tools-.ebuild
+++ b/sci-biology/rtg-tools/rtg-tools-.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -16,13 +16,13 @@ IUSE=""
 
 DEPEND="
>=virtual/jdk-1.8:*
-   dev-java/ant-core
+   >=dev-java/ant-core-1.9
dev-java/jython"
 RDEPEND="${DEPEND}
>=virtual/jre-1.8:*"
 
 src_compile(){
-   ant runalltests || die
+   ant zip-nojre || die
 }
 
 # "${S}"/lib/sam-2.9.1.jar
@@ -42,3 +42,23 @@ src_compile(){
 # "${S}"/testLib/hamcrest-core-1.3.jar
 # "${S}"/testLib/junit.jar
 # "${S}"/testLib/spelling.jar
+
+src_install(){
+   dobin installer/rtg
+   insinto /usr/share/"${PN}"
+   doins build/rtg-tools.jar
+   doins lib/gzipfix.jar
+   dodoc installer/resources/tools/RTGOperationsManual.pdf
+   doins -r installer/resources/tools/RTGOperationsManual
+   dodoc installer/resources/tools/scripts/README.txt
+   dodoc installer/ReleaseNotes.txt
+   # TODO
+   # extract more files from the generated rtg-tools-3.11-39691f9f-base.zip
+   # file or better the installer/resources/ source directory
+   #
+   # install installer/resources/common/scripts/rtg-bash-completion
+}
+
+src_test(){
+   ant runalltests || die
+}



[gentoo-commits] proj/sci:master commit in: sci-biology/RSeQC/

2020-10-18 Thread Martin Mokrejs
commit: af893929af04f870cdb56c83d35153eb8d8d1cdc
Author: Martin Mokrejs  gmail  com>
AuthorDate: Sun Oct 18 08:32:35 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Oct 18 08:34:07 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=af893929

sci-biology/RSeQC: version bump

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/RSeQC/{RSeQC-2.6.1.ebuild => RSeQC-4.0.0.ebuild} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/RSeQC/RSeQC-2.6.1.ebuild 
b/sci-biology/RSeQC/RSeQC-4.0.0.ebuild
similarity index 90%
rename from sci-biology/RSeQC/RSeQC-2.6.1.ebuild
rename to sci-biology/RSeQC/RSeQC-4.0.0.ebuild
index d3bbd9104..871aa946b 100644
--- a/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
+++ b/sci-biology/RSeQC/RSeQC-4.0.0.ebuild
@@ -9,7 +9,7 @@ inherit distutils-r1
 
 DESCRIPTION="Utilities for RNA-seq data quality control"
 HOMEPAGE="https://rseqc.sourceforge.net;
-SRC_URI="https://sourceforge.net/projects/rseqc/files/RSeQC-2.6.1.tar.gz
+SRC_URI="https://sourceforge.net/projects/rseqc/files/RSeQC-${PV}.tar.gz
https://sourceforge.net/projects/rseqc/files/other/fetchChromSizes;
 
 LICENSE="GPL-3"



[gentoo-commits] proj/sci:master commit in: sci-biology/hisat2/files/, sci-biology/hisat2/

2020-08-07 Thread Martin Mokrejs
commit: 18242e80e4a76451d4559ec3c788304525f34446
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Fri Aug  7 12:15:21 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Aug  7 12:15:21 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=18242e80

sci-biology/hisat2: version bump

Package-Manager: Portage-2.3.100, Repoman-2.3.22
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 ...S.patch => hisat2-2.2.1-respect_CXXFLAGS.patch} | 22 +-
 .../{hisat2-2.0.5.ebuild => hisat2-2.2.1.ebuild}   |  6 +++---
 2 files changed, 8 insertions(+), 20 deletions(-)

diff --git a/sci-biology/hisat2/files/hisat2-2.0.5-respect_CXXFLAGS.patch 
b/sci-biology/hisat2/files/hisat2-2.2.1-respect_CXXFLAGS.patch
similarity index 61%
rename from sci-biology/hisat2/files/hisat2-2.0.5-respect_CXXFLAGS.patch
rename to sci-biology/hisat2/files/hisat2-2.2.1-respect_CXXFLAGS.patch
index 26db123c8..4ca550c66 100644
--- a/sci-biology/hisat2/files/hisat2-2.0.5-respect_CXXFLAGS.patch
+++ b/sci-biology/hisat2/files/hisat2-2.2.1-respect_CXXFLAGS.patch
@@ -1,18 +1,6 @@
 hisat2-2.0.5/Makefile.ori  2017-03-01 11:35:36.430368298 +0100
-+++ hisat2-2.0.5/Makefile  2017-03-01 11:43:42.974034697 +0100
-@@ -23,9 +23,8 @@
- INC =
- GCC_PREFIX = $(shell dirname `which gcc`)
- GCC_SUFFIX =
--CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
--CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
--CXX = $(CPP)
-+CXX ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
-+CXXFLAGS ?= "-O3"
- HEADERS = $(wildcard *.h)
- BOWTIE_MM = 1
- BOWTIE_SHARED_MEM = 0
-@@ -134,30 +133,30 @@
+--- hisat2-2.2.1/Makefile.ori  2020-08-07 13:12:25.393396171 +0200
 hisat2-2.2.1/Makefile  2020-08-07 13:15:56.845080223 +0200
+@@ -152,30 +152,30 @@
  VERSION = $(shell cat VERSION)
  
  # Convert BITS=?? to a -m flag
@@ -43,8 +31,8 @@
 -SSE_FLAG=-msse2
 +SSE_FLAG?=-msse2
  
--DEBUG_FLAGS= -O0 -g3 $(BIToS_FLAG) $(SSE_FLAG)
-+DEBUG_FLAGS= -g3 -O0 $(CXXFLAGS) $(BIToS_FLAG) $(SSE_FLAG)
+-DEBUG_FLAGS= -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
++DEBUG_FLAGS= -g3 -O0 $(CXXFLAGS) $(BITS_FLAG) $(SSE_FLAG)
  DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
 -RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
 +RELEASE_FLAGS  = $(CXXFLAGS) $(BITS_FLAG) $(SSE_FLAG) -funroll-loops

diff --git a/sci-biology/hisat2/hisat2-2.0.5.ebuild 
b/sci-biology/hisat2/hisat2-2.2.1.ebuild
similarity index 89%
rename from sci-biology/hisat2/hisat2-2.0.5.ebuild
rename to sci-biology/hisat2/hisat2-2.2.1.ebuild
index d200a57ac..5532d2b71 100644
--- a/sci-biology/hisat2/hisat2-2.0.5.ebuild
+++ b/sci-biology/hisat2/hisat2-2.2.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{6,7,8} )
 
 inherit python-r1
 
@@ -11,7 +11,7 @@ DESCRIPTION="Align DNA reads to a population of genomes"
 HOMEPAGE="
https://ccb.jhu.edu/software/hisat2
https://github.com/infphilo/hisat2;
-SRC_URI="ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/${P}-source.zip;
+SRC_URI="https://cloud.biohpc.swmed.edu/index.php/s/fE9QCsX3NH4QwBi/download 
-> ${P}.zip"
 
 LICENSE="GPL-3+"
 SLOT="0"



[gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/

2020-05-15 Thread Martin Mokrejs
commit: f3a538b68e80b3fc42af81717f48a5cbfb283f45
Author: Martin Mokrejs  gmail  com>
AuthorDate: Fri May 15 19:30:28 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri May 15 19:30:47 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f3a538b6

sci-biology/SPAdes: version bump to 3.14.1

This is a bug-fix release, which includes:
- Fix for read filtering tool;
- Soft and hard-filtered transcripts are now copied to the output
  folder in rnaSPAdes;
- Minor fix in biosyntheticSPAdes pipeline;
- Minor fix in metaplasmidSPAdes contig output;
- Several usability fixes in `spades.py';
- Other minor bug-fixes.

Package-Manager: Portage-2.3.99, Repoman-2.3.22
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/SPAdes/{SPAdes-3.14.0.ebuild => SPAdes-3.14.1.ebuild} | 6 +-
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/sci-biology/SPAdes/SPAdes-3.14.0.ebuild 
b/sci-biology/SPAdes/SPAdes-3.14.1.ebuild
similarity index 87%
rename from sci-biology/SPAdes/SPAdes-3.14.0.ebuild
rename to sci-biology/SPAdes/SPAdes-3.14.1.ebuild
index d3c1e0a57..773ccf658 100644
--- a/sci-biology/SPAdes/SPAdes-3.14.0.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.14.1.ebuild
@@ -13,11 +13,7 @@ SRC_URI="
https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz
http://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html
http://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> 
${P}_rnaspades_manual.html
-   http://cab.spbu.ru/files/release${PV}/truspades_manual.html -> 
${P}_truspades_manual.html
-   http://spades.bioinf.spbau.ru/release3.11.1/dipspades_manual.html -> 
${P}_dipspades_manual.html"
-# DEPRECATED in 3.12.0: dipSPAdes pipeline for highly polymorphic diploid 
genomes
-#  (still present in the release but no longer supported)
-
+   http://cab.spbu.ru/files/release${PV}/truspades_manual.html -> 
${P}_truspades_manual.html"
 LICENSE="GPL-2"
 SLOT="0"
 KEYWORDS=""



[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

2020-05-06 Thread Martin Mokrejs
commit: 3a0d3cb989aa14f980ad867cb8b7d7db5284789f
Author: Martin Mokrejs  gmail  com>
AuthorDate: Wed May  6 18:27:40 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Wed May  6 18:28:05 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a0d3cb9

sci-biology/pybedtools: hopefully install generated HTML files

Package-Manager: Portage-2.3.95, Repoman-2.3.22
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 6 ++
 1 file changed, 6 insertions(+)

diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild 
b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
index 9d4dc23c0..440e644b7 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
@@ -29,3 +29,9 @@ src_compile(){
default
use doc && cd docs && emake html
 }
+
+src_install(){
+   default
+   insinto /usr/share/doc/"${PN}"
+   doins -r docs/build/html
+}



[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

2020-05-06 Thread Martin Mokrejs
commit: e29df37c8b9b02f3749a57c2075bed05f0a71260
Author: Martin Mokrejs  gmail  com>
AuthorDate: Wed May  6 18:22:00 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Wed May  6 18:22:20 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e29df37c

sci-biology/pybedtools: respect minimal and doc USE flags

Installation of the to be generated doc pages is not tested
as I am blocked by bug #721306. Probably some dir needs to be
recursively installed.

Package-Manager: Portage-2.3.95, Repoman-2.3.22
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 7 +--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild 
b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
index cd444a09e..9d4dc23c0 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
@@ -14,15 +14,18 @@ 
SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.g
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
+IUSE="doc minimal"
 
 RDEPEND="
sci-biology/bedtools
-   sci-biology/pysam"
+   sci-biology/pysam
+   !minimal? ( sci-libs/htslib )
+   doc? ( dev-python/sphinx )"
 DEPEND="${RDEPEND}
dev-python/cython[${PYTHON_USEDEP}]"
 
 src_compile(){
python setup.py cythonize
default
+   use doc && cd docs && emake html
 }



[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

2020-05-06 Thread Martin Mokrejs
commit: ae5eb7ca6ede7e8579ade25afb8eb005c62ee35a
Author: Martin Mokrejs  gmail  com>
AuthorDate: Wed May  6 17:44:42 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Wed May  6 17:44:49 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ae5eb7ca

sci-biology/pybedtools: update homepage, explicitly run cythonize

Package-Manager: Portage-2.3.95, Repoman-2.3.22
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 13 ++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild 
b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
index d817a594f..cd444a09e 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 python3_{5,6,7,8} )
 inherit distutils-r1
 
 DESCRIPTION="Use BED and GFF files from python using BEDtools"
-HOMEPAGE="http://pythonhosted.org/pybedtools/;
+HOMEPAGE="https://daler.github.io/pybedtools;
 SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
 
 LICENSE="MIT"
@@ -16,6 +16,13 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
-RDEPEND="sci-biology/bedtools"
+RDEPEND="
+   sci-biology/bedtools
+   sci-biology/pysam"
 DEPEND="${RDEPEND}
dev-python/cython[${PYTHON_USEDEP}]"
+
+src_compile(){
+   python setup.py cythonize
+   default
+}



[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/

2020-02-28 Thread Martin Mokrejs
commit: 1f6479da30739c1e62b5df19384df7e5c2674e14
Author: Martin Mokrejs  gmail  com>
AuthorDate: Fri Feb 28 23:06:48 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Feb 28 23:07:25 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1f6479da

sci-biology/bowtie: version bump (bugfix release)

Package-Manager: Portage-2.3.87, Repoman-2.3.20
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/bowtie/{bowtie-2.4.0.ebuild => bowtie-2.4.1.ebuild} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/sci-biology/bowtie/bowtie-2.4.0.ebuild 
b/sci-biology/bowtie/bowtie-2.4.1.ebuild
similarity index 100%
rename from sci-biology/bowtie/bowtie-2.4.0.ebuild
rename to sci-biology/bowtie/bowtie-2.4.1.ebuild



[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/

2020-02-26 Thread Martin Mokrejs
commit: 731ea47715109fabdd7cc3944b6c522509619f56
Author: Martin Mokrejs  gmail  com>
AuthorDate: Wed Feb 26 08:48:45 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Wed Feb 26 08:49:28 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=731ea477

sci-biology/bowtie: version bump to 2.4.0, drop old 2.3.5

Package-Manager: Portage-2.3.87, Repoman-2.3.20
Signed-off-by: Martin Mokrejs  gmail.com>

 .../bowtie/bowtie-1.2.2_beta20190219.ebuild|  2 +-
 sci-biology/bowtie/bowtie-2.3.5-r1.ebuild  | 63 --
 .../{bowtie-2.3.5.1.ebuild => bowtie-2.4.0.ebuild} |  2 +-
 3 files changed, 2 insertions(+), 65 deletions(-)

diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild 
b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
index fcf0b4516..f7a1b92d4 100644
--- a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
+++ b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6

diff --git a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild 
b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
deleted file mode 100644
index 2a6fc04eb..0
--- a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/;
-SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
-SRC_URI="https://github.com/BenLangmead/${PN}2/releases/download/v${PV}/${PN}2-${PV}-source.zip;
-
-LICENSE="GPL-3"
-SLOT="2"
-KEYWORDS="~amd64 ~x86"
-
-IUSE="examples cpu_flags_x86_sse2 +tbb"
-
-RDEPEND="dev-lang/perl
-   tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
-   app-arch/unzip
-   sys-libs/readline"
-
-S="${WORKDIR}/${PN}2-${PV}"
-
-DOCS=( AUTHORS NEWS TUTORIAL )
-HTML_DOCS=( doc/{manual.html,style.css} )
-#PATCHES=( "${FILESDIR}/${P}-fix-c++14.patch" ) # needs 2.3.4.3 update
-PATCHES=( "${FILESDIR}"/bowtie-2.3.5-fix-interleaved.patch
-   "${FILESDIR}"/bowtie-2.3.5-fix-fifo.patch )
-
-pkg_pretend() {
-   if ! use cpu_flags_x86_sse2 ; then
-   eerror "This package requires a CPU supporting the SSE2 
instruction set."
-   die "SSE2 support missing"
-   fi
-}
-
-src_compile() {
-   emake \
-   CC="$(tc-getCC)" \
-   CPP="$(tc-getCXX)" \
-   CXX="$(tc-getCXX)" \
-   EXTRA_FLAGS="${LDFLAGS}" \
-   RELEASE_FLAGS="${CXXFLAGS} -msse2" \
-   WITH_TBB="$(usex tbb 1 0)"
-}
-
-src_install() {
-   dobin ${PN}2 ${PN}2-*
-
-   exeinto /usr/libexec/${PN}2
-   doexe scripts/*
-
-   newman MANUAL ${PN}2.1
-   einstalldocs
-
-   if use examples; then
-   insinto /usr/share/${PN}2
-   doins -r example
-   fi
-}

diff --git a/sci-biology/bowtie/bowtie-2.3.5.1.ebuild 
b/sci-biology/bowtie/bowtie-2.4.0.ebuild
similarity index 97%
rename from sci-biology/bowtie/bowtie-2.3.5.1.ebuild
rename to sci-biology/bowtie/bowtie-2.4.0.ebuild
index c2fef8667..a4d6837ba 100644
--- a/sci-biology/bowtie/bowtie-2.3.5.1.ebuild
+++ b/sci-biology/bowtie/bowtie-2.4.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6



[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/

2020-02-20 Thread Martin Mokrejs
commit: 05629a9dc997950a1bf3dfa002307decc492e4b7
Author: Martin Mokrejs  gmail  com>
AuthorDate: Thu Feb 20 15:15:16 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Feb 20 15:16:22 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=05629a9d

sci-biology/abyss: version bump

Package-Manager: Portage-2.3.87, Repoman-2.3.20
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/abyss/{abyss-2.2.3.ebuild => abyss-2.2.4.ebuild} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/abyss/abyss-2.2.3.ebuild 
b/sci-biology/abyss/abyss-2.2.4.ebuild
similarity index 97%
rename from sci-biology/abyss/abyss-2.2.3.ebuild
rename to sci-biology/abyss/abyss-2.2.4.ebuild
index 5e80a0a3c..c81bf292e 100644
--- a/sci-biology/abyss/abyss-2.2.3.ebuild
+++ b/sci-biology/abyss/abyss-2.2.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6



[gentoo-commits] proj/sci:master commit in: sci-biology/nwalign3/, sci-biology/nwalign/

2020-01-24 Thread Martin Mokrejs
commit: 406aa4f9dc9deee2defa3b66c779d69da1a30eec
Author: Martin Mokrejs  gmail  com>
AuthorDate: Fri Jan 24 17:34:50 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Jan 24 17:50:46 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=406aa4f9

sci-biology/nwalign: Improve pkg description, clarify python2_7 need
sci-biology/nwalign3: python3 version of sci-biology/nwalign

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/nwalign/nwalign-0.3.1.ebuild   | 12 +++-
 sci-biology/nwalign3/metadata.xml  | 15 +++
 .../nwalign3-0.1.2.ebuild} | 18 ++
 3 files changed, 32 insertions(+), 13 deletions(-)

diff --git a/sci-biology/nwalign/nwalign-0.3.1.ebuild 
b/sci-biology/nwalign/nwalign-0.3.1.ebuild
index d419002fd..06285c366 100644
--- a/sci-biology/nwalign/nwalign-0.3.1.ebuild
+++ b/sci-biology/nwalign/nwalign-0.3.1.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 PYTHON_COMPAT=( python2_7 )
 
-inherit python-single-r1
+inherit distutils-r1 
 
-DESCRIPTION="Needleman-Wunsch global sequence alignment in python/cython"
+DESCRIPTION="Needleman-Wunsch global sequence alignment in python2"
 HOMEPAGE="https://pypi.python.org/pypi/nwalign;
 SRC_URI="mirror://pypi/n/${PN}/${P}.tar.gz"
 
@@ -16,5 +16,7 @@ SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""
 
-DEPEND=""
+DEPEND="
+   dev-python/numpy
+   dev-python/cython"
 RDEPEND="${DEPEND}"

diff --git a/sci-biology/nwalign3/metadata.xml 
b/sci-biology/nwalign3/metadata.xml
new file mode 100644
index 0..ad73a59be
--- /dev/null
+++ b/sci-biology/nwalign3/metadata.xml
@@ -0,0 +1,15 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+   
+   mmokr...@gmail.com
+   Martin Mokrejs
+   
+   
+   sci-biol...@gentoo.org
+   Gentoo Biology Project
+   
+   
+   nwalign
+   
+

diff --git a/sci-biology/nwalign/nwalign-0.3.1.ebuild 
b/sci-biology/nwalign3/nwalign3-0.1.2.ebuild
similarity index 52%
copy from sci-biology/nwalign/nwalign-0.3.1.ebuild
copy to sci-biology/nwalign3/nwalign3-0.1.2.ebuild
index d419002fd..6f523bc7f 100644
--- a/sci-biology/nwalign/nwalign-0.3.1.ebuild
+++ b/sci-biology/nwalign3/nwalign3-0.1.2.ebuild
@@ -1,20 +1,22 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{6,7,8} )
 
-inherit python-single-r1
+inherit distutils-r1
 
-DESCRIPTION="Needleman-Wunsch global sequence alignment in python/cython"
-HOMEPAGE="https://pypi.python.org/pypi/nwalign;
+DESCRIPTION="Needleman-Wunsch global sequence alignment in python3"
+HOMEPAGE="https://github.com/briney/nwalign3;
 SRC_URI="mirror://pypi/n/${PN}/${P}.tar.gz"
 
 LICENSE="BSD"
 SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
 IUSE=""
 
-DEPEND=""
+DEPEND="
+   dev-python/numpy
+   dev-python/cython"
 RDEPEND="${DEPEND}"



[gentoo-commits] proj/sci:master commit in: sci-biology/nwalign/

2020-01-24 Thread Martin Mokrejs
commit: 7d09a68f938a752bf97adf9e4cafe473848318d4
Author: Martin Mokrejs  gmail  com>
AuthorDate: Fri Jan 24 17:51:54 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Jan 24 17:54:14 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7d09a68f

sci-biology/nwalign: drop python2-only package, use nwalign3 instead

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/nwalign/metadata.xml | 15 ---
 sci-biology/nwalign/nwalign-0.3.1.ebuild | 22 --
 2 files changed, 37 deletions(-)

diff --git a/sci-biology/nwalign/metadata.xml b/sci-biology/nwalign/metadata.xml
deleted file mode 100644
index e593c9312..0
--- a/sci-biology/nwalign/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-   
-   mmokr...@fold.natur.cuni.cz
-       Martin Mokrejs
-   
-   
-   sci-biol...@gentoo.org
-   Gentoo Biology Project
-   
-   
-   nwalign
-   
-

diff --git a/sci-biology/nwalign/nwalign-0.3.1.ebuild 
b/sci-biology/nwalign/nwalign-0.3.1.ebuild
deleted file mode 100644
index 06285c366..0
--- a/sci-biology/nwalign/nwalign-0.3.1.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 
-
-DESCRIPTION="Needleman-Wunsch global sequence alignment in python2"
-HOMEPAGE="https://pypi.python.org/pypi/nwalign;
-SRC_URI="mirror://pypi/n/${PN}/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="
-   dev-python/numpy
-   dev-python/cython"
-RDEPEND="${DEPEND}"



[gentoo-commits] proj/sci:master commit in: sci-biology/pysam/, sci-biology/pysamstats/

2020-01-10 Thread Martin Mokrejs
commit: b1ad15e7a10105fb9f0905ea5aac0835a62b46f3
Author: Martin Mokrejs  gmail  com>
AuthorDate: Fri Jan 10 16:32:20 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Jan 10 16:52:47 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b1ad15e7

sci-biology/pysamstats: version bump
sci-biology/pysam: version bump

I am not sure if the path pysam-0.12-fix-buildsystem.patch is still
needed or not. Nevertheless, the modules do not import properly into
python so the ebuild needs more work.

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/pysam/metadata.xml | 12 ++
 sci-biology/pysam/pysam-0.15.3.ebuild  | 46 ++
 ...stats-0.24.2.ebuild => pysamstats-1.1.2.ebuild} |  9 +++--
 3 files changed, 64 insertions(+), 3 deletions(-)

diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml
new file mode 100644
index 0..6182254bd
--- /dev/null
+++ b/sci-biology/pysam/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+  
+sci-biol...@gentoo.org
+Gentoo Biology Project
+  
+  
+pysam
+pysam-developers/pysam
+  
+

diff --git a/sci-biology/pysam/pysam-0.15.3.ebuild 
b/sci-biology/pysam/pysam-0.15.3.ebuild
new file mode 100644
index 0..4224df0be
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.15.3.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_6 )
+
+inherit distutils-r1
+
+DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping 
format"
+HOMEPAGE="
+   https://github.com/pysam-developers/pysam
+   https://pypi.org/project/pysam/;
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS=""
+
+# current code wraps 3rd-party code from htslib-1.9, samtools-1.9 and 
bcftools-1.9
+RDEPEND="=sci-libs/htslib-1.9*:="
+DEPEND="${RDEPEND}
+   dev-python/cython[${PYTHON_USEDEP}]
+   dev-python/setuptools[${PYTHON_USEDEP}]"
+
+python_prepare_all() {
+   # unbundle htslib
+   export HTSLIB_MODE="external"
+   export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include
+   export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir)
+   rm -r htslib || die
+
+   # prevent setup.py from adding RPATHs
+   sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \
+   -i cy_build.py || die
+   sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
+   -i setup.py || die
+
+   distutils-r1_python_prepare_all
+}
+
+src_compile() {
+   # TODO
+   # empty compile, as the build system runs the whole build again in 
install
+   :
+}

diff --git a/sci-biology/pysamstats/pysamstats-0.24.2.ebuild 
b/sci-biology/pysamstats/pysamstats-1.1.2.ebuild
similarity index 77%
rename from sci-biology/pysamstats/pysamstats-0.24.2.ebuild
rename to sci-biology/pysamstats/pysamstats-1.1.2.ebuild
index d6e1350a4..06bb7c69b 100644
--- a/sci-biology/pysamstats/pysamstats-0.24.2.ebuild
+++ b/sci-biology/pysamstats/pysamstats-1.1.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -17,6 +17,9 @@ SLOT="0"
 KEYWORDS="" # needs working pysam, see bug #645060
 IUSE=""
 
-DEPEND="dev-python/cython
-   >=sci-biology/pysam-0.8.4"
+DEPEND="
+   dev-python/cython
+   dev-python/numpy
+   dev-python/pytables
+   >=sci-biology/pysam-0.15.1"
 RDEPEND="${DEPEND}"



[gentoo-commits] proj/sci:master commit in: sci-biology/tigmint/

2020-01-10 Thread Martin Mokrejs
commit: 61199804d047b3bb60a69643a79263d4d9f9ff6c
Author: Martin Mokrejs  gmail  com>
AuthorDate: Fri Jan 10 16:13:53 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Jan 10 16:13:58 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=61199804

sci-biology/tigmint: fix package name

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/tigmint/tigmint-1.1.0.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/tigmint/tigmint-1.1.0.ebuild 
b/sci-biology/tigmint/tigmint-1.1.0.ebuild
index 66a1f3460..7e2d6d143 100644
--- a/sci-biology/tigmint/tigmint-1.1.0.ebuild
+++ b/sci-biology/tigmint/tigmint-1.1.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -21,7 +21,7 @@ RDEPEND="${DEPEND}
sci-biology/bwa
sci-biology/bedtools
sci-biology/samtools:0
-   sci-biology/seqtools
+   sci-biology/seqtk
dev-util/makefile2graph
media-gfx/graphviz
dev-vcs/git



[gentoo-commits] proj/sci:master commit in: sci-biology/sga/

2020-01-10 Thread Martin Mokrejs
commit: 8171b99830c37a7ceb1fed36d3cf8f2eb70d6d98
Author: Martin Mokrejs  gmail  com>
AuthorDate: Fri Jan 10 16:12:25 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Jan 10 16:12:42 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=8171b998

sci-biology/sga: fix typo

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/sga/sga-.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/sga/sga-.ebuild b/sci-biology/sga/sga-.ebuild
index 8ec029f94..52f7bb69c 100644
--- a/sci-biology/sga/sga-.ebuild
+++ b/sci-biology/sga/sga-.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -38,7 +38,7 @@ src_compile(){
#
# other unreviewed patches:
# https://github.com/jts/sga/issues/96
-   cd src || die "Try -atd=g++-98, try gcc-5 or -std=c++03"
+   cd src || die "Try -std=g++-98, try gcc-5 or -std=c++03"
default
 }
 



[gentoo-commits] proj/sci:master commit in: sci-biology/samstat/

2020-01-10 Thread Martin Mokrejs
commit: b4fcf5069fd98b11d2a5aa6fb452d7d3ba5a1e05
Author: Martin Mokrejs  gmail  com>
AuthorDate: Fri Jan 10 16:08:09 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Jan 10 16:08:46 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b4fcf506

sci-biology/samstat: add missing dependency

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/samstat/samstat-1.5.1.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/samstat/samstat-1.5.1.ebuild 
b/sci-biology/samstat/samstat-1.5.1.ebuild
index 1ea4ffdde..af0f76cb2 100644
--- a/sci-biology/samstat/samstat-1.5.1.ebuild
+++ b/sci-biology/samstat/samstat-1.5.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -14,5 +14,5 @@ SLOT="0"
 KEYWORDS="~amd64"
 IUSE=""
 
-DEPEND=""
+DEPEND="sci-biology/samtools"
 RDEPEND="${DEPEND}"



[gentoo-commits] proj/sci:master commit in: sci-biology/NGSEPcore/, sci-biology/NGSEPcore/files/

2020-01-10 Thread Martin Mokrejs
commit: 0495ef801513cebc129bbcd392d955e86dea2fc9
Author: Martin Mokrejs  gmail  com>
AuthorDate: Fri Jan 10 15:55:18 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Jan 10 15:57:51 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0495ef80

sci-biology/NGSEPcore: cleanup the ebuild

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild   | 23 --
 .../files/NGSEPcore_drop_utf8_chars.patch  | 81 ++
 .../files/NGSEPcore_fix_compilation.patch  |  0
 3 files changed, 97 insertions(+), 7 deletions(-)

diff --git a/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild 
b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild
index 3f844bf16..24445eb0d 100644
--- a/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild
+++ b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -6,7 +6,8 @@ EAPI=7
 inherit java-pkg-2 java-ant-2
 
 DESCRIPTION="NGSEP (CNV and indel discovery)"
-HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home;
+HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home
+   https://github.com/NGSEP/NGSEPcore;
 
SRC_URI="https://sourceforge.net/projects/ngsep/files/SourceCode/NGSEPcore_${PV}.tar.gz

https://sourceforge.net/projects/ngsep/files/training/UserManualNGSEP_V330.pdf 
-> ${P}_UserManual.pdf
https://sourceforge.net/projects/ngsep/files/training/Tutorial.txt -> 
${P}_Tutorial.txt
@@ -17,21 +18,29 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
-DEPEND="dev-java/htsjdk"
+DEPEND="
+   dev-java/htsjdk
+   dev-java/jsci-bin"
 RDEPEND="${DEPEND}"
 
 S="${WORKDIR}/${PN}_${PV}"
 
+PATCHES=( "${FILESDIR}"/NGSEPcore_drop_utf8_chars.patch 
"${FILESDIR}"/NGSEPcore_fix_compilation.patch )
+
 src_prepare(){
-   rm -f *.jar lib/htsjdk-1.129.jar || die
+   rm lib/htsjdk-1.129.jar || die
+   rm lib/jsci-core.jar || die
default
 }
 
 src_compile(){
-   make -j1
+   emake -j1
 }
 
 src_install(){
-   java-pkg_dojar *.jar
-   dodoc "$DISTDIR}"/${P}_user_manual.pdf
+   java-pkg_dojar *.jar lib/*.jar
+   dodoc "${DISTDIR}"/${P}_UserManual.pdf \
+   "${DISTDIR}"/${P}_Tutorial.txt \
+   "${DISTDIR}"/${P}_QuickStart.txt \
+   README.txt
 }

diff --git a/sci-biology/NGSEPcore/files/NGSEPcore_drop_utf8_chars.patch 
b/sci-biology/NGSEPcore/files/NGSEPcore_drop_utf8_chars.patch
new file mode 100644
index 0..eb61747be
--- /dev/null
+++ b/sci-biology/NGSEPcore/files/NGSEPcore_drop_utf8_chars.patch
@@ -0,0 +1,81 @@
+From 5161e22e7730e2637376402718ed7048f838054a Mon Sep 17 00:00:00 2001
+From: jorge 
+Date: Thu, 28 Mar 2019 16:24:24 -0500
+Subject: [PATCH] Fixed encoding and manual compilation issues
+
+---
+ makefile | 2 +-
+ src/ngsep/discovery/TillingPoolsIndividualGenotyper.java | 5 ++---
+ src/ngsep/simulation/TillingPopulationSimulator.java | 2 +-
+ src/ngsep/variants/CalledSNV.java| 2 +-
+ 4 files changed, 5 insertions(+), 6 deletions(-)
+
+diff --git a/makefile b/makefile
+index 517895d..0532725 100755
+--- a/makefile
 b/makefile
+@@ -11,7 +11,7 @@ compile:
+ copy: 
+   cp -f src/ngsep/transcriptome/ProteinTranslatorDefaultBundle.properties 
bin/ngsep/transcriptome/
+   cp -f src/ngsep/main/CommandsDescriptor.xml bin/ngsep/main/
+-  cp -f src/ngsep/assembly/GenomesAlignerLinearVisualizer.js 
bin/ngsep/assembly/
++  cp -f src/ngsep/genome/GenomesAlignerLinearVisualizer.js 
bin/ngsep/genome/
+ 
+ jar: 
+   mkdir dist
+diff --git a/src/ngsep/discovery/TillingPoolsIndividualGenotyper.java 
b/src/ngsep/discovery/TillingPoolsIndividualGenotyper.java
+index c8c3d42..2e7a7bf 100644
+--- a/src/ngsep/discovery/TillingPoolsIndividualGenotyper.java
 b/src/ngsep/discovery/TillingPoolsIndividualGenotyper.java
+@@ -19,7 +19,6 @@
+ import ngsep.main.CommandsDescriptor;
+ import ngsep.main.ProgressNotifier;
+ import ngsep.sequences.QualifiedSequenceList;
+-import ngsep.simulation.TillingPopulationSimulator;
+ import ngsep.variants.CalledGenomicVariant;
+ import ngsep.variants.CalledGenomicVariantImpl;
+ import ngsep.variants.GenomicVariant;
+@@ -31,7 +30,7 @@
+ 
+ public class TillingPoolsIndividualGenotyper {
+ 
+-  private Logger log = 
Logger.getLogger(TillingPopulationSimulator.class.getName());
++  private Logger log = 
Logger.getLogger(TillingPoolsIndividualGenotyper.class.getName());
+   private ProgressNotifier progressNotifier=null;
+   
+   private static HashMap> poolConfiguration;
+@@ -111,7 +110,7 @@ publ

[gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/

2020-01-06 Thread Martin Mokrejs
commit: 84bb511d7a904b2e151faa1f9224dd91a196349f
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Jan  6 17:13:56 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Jan  6 17:13:56 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=84bb511d

sci-biology/SPAdes: version bump

- BiosyntheticSPAdes pipeline for identifying Biosynthetic Gene Clusters (BGCs)
- Hybrid transcriptome assembly (Illumina RNA-Seq + Iso-seq / ONT RNA)
- Plasmid assembly from metagenomic datasets
- New --isolate option that improves assembly quality of standard datasets with
  high coverage
- New standalone tools for read filtration based on k-mer coverage and
  estimating number of unique k-mers in reads
- Improved SPAligner tool for read-to-graph alignment
- Major performance improvements and memory consumption reduction in graph
  construction, simplification procedures and throughout the whole pipeline
- Several bug-fixes.

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/SPAdes/SPAdes-3.13.0.ebuild   | 2 +-
 sci-biology/SPAdes/{SPAdes-3.13.0.ebuild => SPAdes-3.14.0.ebuild} | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/SPAdes/SPAdes-3.13.0.ebuild 
b/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
index 00ccc4f27..d3c1e0a57 100644
--- a/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6

diff --git a/sci-biology/SPAdes/SPAdes-3.13.0.ebuild 
b/sci-biology/SPAdes/SPAdes-3.14.0.ebuild
similarity index 98%
copy from sci-biology/SPAdes/SPAdes-3.13.0.ebuild
copy to sci-biology/SPAdes/SPAdes-3.14.0.ebuild
index 00ccc4f27..d3c1e0a57 100644
--- a/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.14.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6



[gentoo-commits] proj/sci:master commit in: sci-biology/RAILS/

2020-01-02 Thread Martin Mokrejs
commit: 4a5df3568fcb228f465287849d51a18cea1bc76a
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Thu Jan  2 08:36:48 2020 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Jan  2 08:36:48 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4a5df356

sci-biology/RAILS: version bump

The minimap2-based wrapper script won't work as we do not have minimap2
in Gentoo Linux yet.

Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 .../RAILS/{RAILS-1.4.1.ebuild => RAILS-1.5.1.ebuild}   | 14 +-
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/sci-biology/RAILS/RAILS-1.4.1.ebuild 
b/sci-biology/RAILS/RAILS-1.5.1.ebuild
similarity index 54%
rename from sci-biology/RAILS/RAILS-1.4.1.ebuild
rename to sci-biology/RAILS/RAILS-1.5.1.ebuild
index 9360c6040..df5f0ea4a 100644
--- a/sci-biology/RAILS/RAILS-1.4.1.ebuild
+++ b/sci-biology/RAILS/RAILS-1.5.1.ebuild
@@ -1,11 +1,11 @@
-# Copyright 2018 Gentoo Authors
+# Copyright 2018-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-DESCRIPTION="Cobbler and RAILS scaffolding tools"
+DESCRIPTION="Cobbler and RAILS scaffolding tools acting on SAM streams"
 HOMEPAGE="https://github.com/bcgsc/RAILS;
-SRC_URI="https://github.com/bcgsc/RAILS/archive/v1.4.1.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/bcgsc/RAILS/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-3+"
 SLOT="0"
@@ -15,12 +15,16 @@ IUSE=""
 DEPEND=""
 RDEPEND="${DEPEND}
dev-lang/perl
-   sci-biology/samtools"
+   sci-biology/samtools
+   sci-biology/bwa
+"
+# bin/runRAILSminimap.sh calls minimap2 but one can stream the SAM data 
directly
 BDEPEND=""
 
 src_prepare(){
# remove hardcoded PATHs
-   sed -e 's@^\.\./@@g' -e 's@^export PATH=/gsc/btl/linuxbrew@#&1@' -i 
bin/runRAILS.sh || die
+   # https://github.com/bcgsc/RAILS/issues/8
+   sed -e 's@^\.\./@@g' -e 's@^export PATH=/gsc/btl/linuxbrew@#&1@' -i 
bin/*.sh || die
default
 }
 



[gentoo-commits] proj/sci:master commit in: sci-libs/libmaus2/

2019-12-30 Thread Martin Mokrejs
commit: 14d6fe3e3263ff60126348989714159e9731e2a5
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Dec 30 15:37:44 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Dec 30 15:37:44 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=14d6fe3e

sci-libs/libmaus2: point to libmaus2 and to gitlab

Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-libs/libmaus2/metadata.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-libs/libmaus2/metadata.xml b/sci-libs/libmaus2/metadata.xml
index 80f68639f..4b4685854 100644
--- a/sci-libs/libmaus2/metadata.xml
+++ b/sci-libs/libmaus2/metadata.xml
@@ -15,6 +15,6 @@ BAM sequence alignment files input/output (simple and 
collating)
 and many lower level support classes.
 

-   gt1/libmaus
+   german.tischler/libmaus2

 



[gentoo-commits] proj/sci:master commit in: sci-biology/biobambam2/

2019-12-30 Thread Martin Mokrejs
commit: 5b51e6e70104d94d1a287add2206c31eca040da2
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Dec 30 15:33:25 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Dec 30 15:33:25 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5b51e6e7

sci-biology/biobambam2: version bump to 2.0.146

Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/biobambam2/biobambam2-2.0.146.ebuild | 29 
 1 file changed, 29 insertions(+)

diff --git a/sci-biology/biobambam2/biobambam2-2.0.146.ebuild 
b/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
new file mode 100644
index 0..1921fe3b7
--- /dev/null
+++ b/sci-biology/biobambam2/biobambam2-2.0.146.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools
+
+release_data="20191030105216"
+
+DESCRIPTION="Tools for bam file processing (libmaus2)"
+HOMEPAGE="https://gitlab.com/german.tischler/biobambam2
+   https://github.com/gt1/biobambam2;
+SRC_URI="https://gitlab.com/german.tischler/${PN}/-/archive/${PV}-release-${release_data}/${P}-release-${release_data}.tar.gz
 -> ${P}.tar.gz"
+
+LICENSE="GPL-3 MIT"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+   !sci-biology/biobambam
+   >=sci-libs/libmaus2-2.0.683"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${P}-release-${release_data}"
+
+src_configure(){
+   econf --with-libmaus2="${EPREFIX}"
+}



[gentoo-commits] proj/sci:master commit in: sci-libs/libmaus2/

2019-12-30 Thread Martin Mokrejs
commit: 08a272766f1feb9206762a4c51839c55a9c7637d
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Dec 30 15:20:32 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Dec 30 15:20:32 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=08a27276

sci-libs/libmaus2: version bump to 2.0.689

Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-libs/libmaus2/libmaus2-2.0.689.ebuild | 45 +++
 1 file changed, 45 insertions(+)

diff --git a/sci-libs/libmaus2/libmaus2-2.0.689.ebuild 
b/sci-libs/libmaus2/libmaus2-2.0.689.ebuild
new file mode 100644
index 0..50b82d5aa
--- /dev/null
+++ b/sci-libs/libmaus2/libmaus2-2.0.689.ebuild
@@ -0,0 +1,45 @@
+# Copyright 2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools
+
+release_data="20191120141844"
+DESCRIPTION="Library for biobambam2"
+HOMEPAGE="https://github.com/gt1/libmaus;
+SRC_URI="https://gitlab.com/german.tischler/${PN}/-/archive/${PV}-release-${release_data}/${P}-release-${release_data}.tar.gz
 -> ${P}.tar.gz"
+
+LICENSE="BSD-2 GPL-2 GPL-3 MIT ZLIB" # BUG: incomplete list of licenses, see 
AUTHORS
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2"
+
+DEPEND="
+   !sci-libs/libmaus
+   >=sci-libs/io_lib-1.14.11
+   app-arch/snappy
+   sci-libs/fftw
+   sci-libs/hdf5
+   net-libs/gnutls
+   dev-libs/nettle"
+# --with-daligner
+# --with-irods
+# old github.com release tarballs
+# S="${WORKDIR}"/libmaus2-master-27828cd78121d5e4b19c263c5527e462360f5901
+# current gitlab.com release tarballs
+S="${WORKDIR}/${P}-release-${release_data}"
+
+src_configure(){
+   local CONFIG_OPTS
+   use cpu_flags_x86_ssse3 && CONFIG_OPTS+=( --enable-ssse3 )
+   ( use cpu_flags_x86_sse4_1 || use cpu_flags_x86_sse4_2 ) && 
CONFIG_OPTS+=( --enable-sse4 )
+   econf --with-snappy --with-io_lib $CONFIG_OPTS \
+   --with-lzma --with-gnutls --with-nettle --with-hdf5 --with-gmp 
--with-fftw
+}
+
+pkg_postinst(){
+   einfo "The io_lib, snappy dependencies are not strictly needed"
+   einfo "but were forced for optimal libmaus2 performance."
+   einfo "igzip is only used if gzip level is set to 11."
+}



[gentoo-commits] proj/sci:master commit in: sci-libs/libmaus2/

2019-12-30 Thread Martin Mokrejs
commit: 6a52a6c327152d555ec8699271d8d4445a27f285
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Dec 30 15:14:45 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Dec 30 15:14:45 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6a52a6c3

sci-libs/libmaus2: update the ebuild for gitlab.com site

Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-libs/libmaus2/libmaus2-2.0.587.ebuild | 8 ++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/sci-libs/libmaus2/libmaus2-2.0.587.ebuild 
b/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
index 1c61df056..593fe083f 100644
--- a/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
+++ b/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
@@ -5,9 +5,10 @@ EAPI=7
 
 inherit autotools
 
+release_data="20190122104826"
 DESCRIPTION="Library for biobambam2"
 HOMEPAGE="https://github.com/gt1/libmaus;
-SRC_URI="https://gitlab.com/german.tischler/libmaus2/-/archive/master/${P}.tar.gz;
+SRC_URI="https://gitlab.com/german.tischler/${PN}/-/archive/${PV}-release-${release_data}/${P}-release-${release_data}.tar.gz
 -> ${P}.tar.gz"
 
 LICENSE="BSD-2 GPL-2 GPL-3 MIT ZLIB" # BUG: incomplete list of licenses, see 
AUTHORS
 SLOT="0"
@@ -24,7 +25,10 @@ DEPEND="
dev-libs/nettle"
 # --with-daligner
 # --with-irods
-S="${WORKDIR}"/libmaus2-master-27828cd78121d5e4b19c263c5527e462360f5901
+# old github.com release tarballs
+# S="${WORKDIR}"/libmaus2-master-27828cd78121d5e4b19c263c5527e462360f5901
+# current gitlab.com release tarballs
+S="${WORKDIR}/${P}-release-${release_data}"
 
 src_configure(){
local CONFIG_OPTS



[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

2019-12-29 Thread Martin Mokrejs
commit: f54702e57e98ae5f4bf7f867f40dd3ea29157f19
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sun Dec 29 11:39:28 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Dec 29 11:39:28 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f54702e5

sci-biology/pybedtools: upgrade from 0.6.9 to 0.8.0

0.6.9 was not fully python3 ready, due to
  
https://stackoverflow.com/questions/40367569/dictionary-not-writable-generic-old-setup-py
  at least

Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 .../{pybedtools-0.6.9.ebuild => pybedtools-0.8.0.ebuild}  | 8 
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-biology/pybedtools/pybedtools-0.6.9.ebuild 
b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
similarity index 70%
rename from sci-biology/pybedtools/pybedtools-0.6.9.ebuild
rename to sci-biology/pybedtools/pybedtools-0.8.0.ebuild
index f0d497802..d817a594f 100644
--- a/sci-biology/pybedtools/pybedtools-0.6.9.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python2_7 python3_{5,6,7,8} )
 
 inherit distutils-r1
 
-DESCRIPTION="Wrapper for Aaron Quinlan's BEDtools, plus other useful methods 
for working"
+DESCRIPTION="Use BED and GFF files from python using BEDtools"
 HOMEPAGE="http://pythonhosted.org/pybedtools/;
 SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
 



[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/

2019-12-23 Thread Martin Mokrejs
commit: 37d6c90ece12854ac4ae220e0d95bc88ec3af1b9
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Dec 23 15:38:01 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Dec 23 15:38:01 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=37d6c90e

sci-biology/bowtie: version bump

Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/bowtie/bowtie-2.3.5.1.ebuild   | 60 ++
 .../bowtie/files/bowtie-2.3.5-fix-fifo.patch   | 15 --
 .../files/bowtie-2.3.5-fix-interleaved.patch   | 15 --
 3 files changed, 60 insertions(+), 30 deletions(-)

diff --git a/sci-biology/bowtie/bowtie-2.3.5.1.ebuild 
b/sci-biology/bowtie/bowtie-2.3.5.1.ebuild
new file mode 100644
index 0..c2fef8667
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.3.5.1.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/;
+SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
+SRC_URI="https://github.com/BenLangmead/${PN}2/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="2"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="examples cpu_flags_x86_sse2 +tbb"
+
+RDEPEND="dev-lang/perl
+   tbb? ( dev-cpp/tbb )"
+DEPEND="${RDEPEND}
+   app-arch/unzip
+   sys-libs/readline"
+
+S="${WORKDIR}/${PN}2-${PV}"
+
+DOCS=( AUTHORS NEWS TUTORIAL )
+HTML_DOCS=( doc/{manual.html,style.css} )
+
+pkg_pretend() {
+   if ! use cpu_flags_x86_sse2 ; then
+   eerror "This package requires a CPU supporting the SSE2 
instruction set."
+   die "SSE2 support missing"
+   fi
+}
+
+src_compile() {
+   emake \
+   CC="$(tc-getCC)" \
+   CPP="$(tc-getCXX)" \
+   CXX="$(tc-getCXX)" \
+   EXTRA_FLAGS="${LDFLAGS}" \
+   RELEASE_FLAGS="${CXXFLAGS} -msse2" \
+   WITH_TBB="$(usex tbb 1 0)"
+}
+
+src_install() {
+   dobin ${PN}2 ${PN}2-*
+
+   exeinto /usr/libexec/${PN}2
+   doexe scripts/*
+
+   newman MANUAL ${PN}2.1
+   einstalldocs
+
+   if use examples; then
+   insinto /usr/share/${PN}2
+   doins -r example
+   fi
+}

diff --git a/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch 
b/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch
deleted file mode 100644
index 136bb1e69..0
--- a/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-https://github.com/BenLangmead/bowtie2/commit/d7eab7cf6b7e238047044cf61acc662b05c772c4
-
-diff --git a/pat.cpp b/pat.cpp
-index 453ba69..6d862f8 100644
 a/pat.cpp
-+++ b/pat.cpp
-@@ -494,7 +494,7 @@ void CFilePatternSource::open() {
- 
-   is_fifo = S_ISFIFO(st.st_mode) != 0;
- #endif
--  if (pp_.format != BAM || is_fifo || 
is_gzipped_file(fd)) {
-+  if (pp_.format != BAM && (is_fifo || 
is_gzipped_file(fd))) {
-   zfp_ = gzdopen(fd, "r");
-   compressed_ = true;
-   } else {

diff --git a/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch 
b/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch
deleted file mode 100644
index 45d6a0f96..0
--- a/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-https://github.com/BenLangmead/bowtie2/commit/753df9deca210db54e1ecc94f946b413876e456e
-
-diff --git bowtie-2.3.5/bt2_search.cpp b/bt2_search.cpp
-index 1d53741..c59e39c 100644
 bowtie-2.3.5/bt2_search.cpp
-+++ bowtie-2.3.5/bt2_search.cpp
-@@ -1673,7 +1673,7 @@ static void parseOptions(int argc, const char **argv) {
-<< "sequences must be specified with -1 and -2." << endl;
-   throw 1;
-   }
--  if(interleaved && (format != FASTA || format != FASTQ)) {
-+  if(interleaved && (format != FASTA && format != FASTQ)) {
-   cerr << "Error: --interleaved only works in combination with 
FASTA (-f) and FASTQ (-q) formats." << endl;
-   throw 1;
-   }



[gentoo-commits] proj/sci:master commit in: sci-biology/staden/

2019-10-22 Thread Martin Mokrejs
commit: cad3d25dae697461e1a6d295f2bdf99e9c2f626a
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Tue Oct 22 10:51:46 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Oct 22 10:51:46 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=cad3d25d

sci-biology/staden: sourceforge moved SVN repo URL

Also, somehow I cannot set "${S}" to src because svn would checkout the
source tree there, so one would need ./src/src to access configure.in.
Overwriting "${S}" inside each function helps.

Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/staden/staden-.ebuild | 16 +---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/sci-biology/staden/staden-.ebuild 
b/sci-biology/staden/staden-.ebuild
index 0253c9eb5..4be43217f 100644
--- a/sci-biology/staden/staden-.ebuild
+++ b/sci-biology/staden/staden-.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -9,8 +9,7 @@ inherit autotools-utils flag-o-matic fortran-2 multilib 
subversion
 
 DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools 
(Spin)"
 HOMEPAGE="http://sourceforge.net/projects/staden/;
-SRC_URI=""
-ESVN_REPO_URI="https://staden.svn.sourceforge.net/svnroot/staden/staden/trunk/src;
+ESVN_REPO_URI="https://svn.code.sf.net/p/${PN}/code/${PN}/trunk;
 
 LICENSE="staden"
 SLOT="0"
@@ -42,6 +41,7 @@ RDEPEND="${DEPEND}
 AUTOTOOLS_IN_SOURCE_BUILD=1
 
 src_prepare() {
+   cd "${WORKDIR}"/"${P}"/src || die
sed \
-e 's:svnversion:false:' \
-i configure.in || die
@@ -50,6 +50,8 @@ src_prepare() {
 }
 
 src_configure() {
+   cd "${WORKDIR}"/"${P}"/src || die
+   S="${WORKDIR}"/"${P}"/src
local myeconfargs=()
use X && myeconfargs+=( --with-x )
myeconfargs+=(
@@ -62,7 +64,15 @@ src_configure() {
sed -e "s/^SVNVERS.*/SVNVERS = "${ESVN_REVISION}"/" -i system.mk || die
 }
 
+src_compile(){
+   cd "${WORKDIR}"/"${P}"/src || die
+   S="${WORKDIR}"/"${P}"/src
+   default
+}
+
 src_install() {
+   cd "${WORKDIR}"/"${P}"/src || die
+   S="${WORKDIR}"/"${P}"/src
autotools-utils_src_install SVN_VERSION="${ESVN_REVISION}"
cat >> "${T}"/99staden <<- EOF
STADENROOT="${EPREFIX}"/usr/share/staden



[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/

2019-09-28 Thread Martin Mokrejs
commit: 08f6cb388ea7db562f4f6a32e9cef76dfd62caff
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sat Sep 28 13:05:52 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sat Sep 28 13:05:52 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=08f6cb38

sci-biology/abyss: version bump to 2.2.3

Release version 2.2.3
Revert memory consumption of Bloom filters to pre 2.2.0 behaviour.
ABySS will now share the specified memory among all Bloom filters
instead of just the counting Bloom filter.
Fix gcc-9 compilation warnings

Release version 2.2.2
Fix abyss-overlap for 32-bit systems

Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/abyss/{abyss-2.2.2.ebuild => abyss-2.2.3.ebuild} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/sci-biology/abyss/abyss-2.2.2.ebuild 
b/sci-biology/abyss/abyss-2.2.3.ebuild
similarity index 100%
rename from sci-biology/abyss/abyss-2.2.2.ebuild
rename to sci-biology/abyss/abyss-2.2.3.ebuild



[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/

2019-08-20 Thread Martin Mokrejs
commit: 982e84f44b14e71d4bae96aab4d246a3f0ec0f6f
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Tue Aug 20 13:22:28 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Aug 20 13:22:28 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=982e84f4

sci-biology/abyss: version bump

Package-Manager: Portage-2.3.71, Repoman-2.3.17
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/abyss/{abyss-2.2.1.ebuild => abyss-2.2.2.ebuild} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/sci-biology/abyss/abyss-2.2.1.ebuild 
b/sci-biology/abyss/abyss-2.2.2.ebuild
similarity index 100%
rename from sci-biology/abyss/abyss-2.2.1.ebuild
rename to sci-biology/abyss/abyss-2.2.2.ebuild



[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/

2019-08-15 Thread Martin Mokrejs
commit: 581b836c34e32d3e201b8cfc7a4377514d16e2e3
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Thu Aug 15 07:51:31 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Aug 15 07:51:31 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=581b836c

sci-biology/abyss: update LICENSE, version bump

Upstream released abyss 3 years ago under GPL-3, now also another
part of the code is under GPL-3.

https://github.com/bcgsc/abyss/issues/295

Package-Manager: Portage-2.3.69, Repoman-2.3.16
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/abyss/{abyss-2.1.5.ebuild => abyss-2.2.1.ebuild} | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/abyss/abyss-2.1.5.ebuild 
b/sci-biology/abyss/abyss-2.2.1.ebuild
similarity index 95%
rename from sci-biology/abyss/abyss-2.1.5.ebuild
rename to sci-biology/abyss/abyss-2.2.1.ebuild
index 66c216fab..5e80a0a3c 100644
--- a/sci-biology/abyss/abyss-2.1.5.ebuild
+++ b/sci-biology/abyss/abyss-2.2.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -9,7 +9,7 @@ DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, 
paired-end seque
 HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/;
 SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
 
-LICENSE="abyss"
+LICENSE="GPL-3"
 SLOT="0"
 IUSE="+mpi openmp misc-haskell"
 KEYWORDS="~amd64 ~x86"



[gentoo-commits] proj/sci:master commit in: sci-biology/BRAKER/

2019-07-18 Thread Martin Mokrejs
commit: c7a40f0c2955843da5c85d0abbeed58351547ce1
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Thu Jul 18 17:12:10 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Jul 18 17:12:10 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c7a40f0c

sci-biology/BRAKER: version bump

New HOMEPAGE, SRC_URI, layout of .tar.gz tarball

Package-Manager: Portage-2.3.69, Repoman-2.3.16
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 .../BRAKER/{BRAKER-2.1.0.ebuild => BRAKER-2.1.2.ebuild}   | 15 +++
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/sci-biology/BRAKER/BRAKER-2.1.0.ebuild 
b/sci-biology/BRAKER/BRAKER-2.1.2.ebuild
similarity index 79%
rename from sci-biology/BRAKER/BRAKER-2.1.0.ebuild
rename to sci-biology/BRAKER/BRAKER-2.1.2.ebuild
index 13d63d4b8..908e57e51 100644
--- a/sci-biology/BRAKER/BRAKER-2.1.0.ebuild
+++ b/sci-biology/BRAKER/BRAKER-2.1.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -8,9 +8,10 @@ inherit perl-module
 
 DESCRIPTION="Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS"
 # http://bioinf.uni-greifswald.de/bioinf/publications/pag2015.pdf
-HOMEPAGE="http://bioinf.uni-greifswald.de/bioinf/braker
+HOMEPAGE="https://github.com/Gaius-Augustus/BRAKER
+   http://bioinf.uni-greifswald.de/bioinf/braker
http://bioinf.uni-greifswald.de/augustus/downloads;
-SRC_URI="http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER_v"${PV}".tar.gz
 -> ${P}.tar.gz"
+SRC_URI="https://github.com/Gaius-Augustus/BRAKER/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
 # Example data for testing the BRAKER2 pipeline is available at
 # http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER2examples.tar.gz 
(1.1 GB).
 
@@ -29,14 +30,12 @@ RDEPEND="${DEPEND}
sci-biology/augustus"
#>=sci-biology/GeneMark_ET-bin-4.29"
 
-S="${WORKDIR}"/BRAKER_v"${PV}"
-
 src_install(){
perl_set_version
-   dobin *.pl
+   dobin scripts/*.pl
insinto ${VENDOR_LIB}/${PN}
-   doins *.pm
-   dodoc userguide.pdf
+   doins scripts/*.pm
+   dodoc docs/userguide.pdf
 }
 
 pkg_postinst(){



[gentoo-commits] proj/sci:master commit in: sci-biology/jellyfish/

2019-07-18 Thread Martin Mokrejs
commit: 149f20f4275c9b8530d623935f370a2edd84af8d
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Thu Jul 18 16:10:11 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Jul 18 16:10:11 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=149f20f4

sci-biology/jellyfish: version bump

Package-Manager: Portage-2.3.69, Repoman-2.3.16
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 .../jellyfish/{jellyfish-2.2.6-r1.ebuild => jellyfish-2.3.0.ebuild} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild 
b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
similarity index 97%
rename from sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
rename to sci-biology/jellyfish/jellyfish-2.3.0.ebuild
index 89f9fa231..eba4dcc9c 100644
--- a/sci-biology/jellyfish/jellyfish-2.2.6-r1.ebuild
+++ b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6



[gentoo-commits] proj/sci:master commit in: sci-biology/portrait/

2019-07-16 Thread Martin Mokrejs
commit: 2e1c2e4408aae4d87589293af913dfa588b679d3
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Tue Jul 16 21:53:39 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Jul 16 21:53:39 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2e1c2e44

sci-biology/portrait: Rewrite sed hackery (aka DOS2Unix)

Thanks to @mgorny for the hint.
Reported-by:  gentoo.org>
Closes: https://bugs.gentoo.org/689816
Package-Manager: Portage-2.3.69, Repoman-2.3.16
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/portrait/portrait-1.1.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/portrait/portrait-1.1.ebuild 
b/sci-biology/portrait/portrait-1.1.ebuild
index 424ccfcd6..d6e0c7e82 100644
--- a/sci-biology/portrait/portrait-1.1.ebuild
+++ b/sci-biology/portrait/portrait-1.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -22,7 +22,7 @@ RDEPEND="
 # was only tested with sci-libs/libsvm-2.84
 
 src_install(){
-   sed -e 's/
//' -i *.pl || die "Failed to convert from DOS line endings to Unix"
+   sed -e 's/\r//' -i *.pl || die "Failed to convert from DOS line endings 
to Unix"
sed -e 's#/home/rtarrial/prog#/usr/bin#' -i *.pl
dobin *.pl
dodoc README.txt



[gentoo-commits] proj/sci:master commit in: sci-libs/iRODS/

2019-07-07 Thread Martin Mokrejs
commit: 16978af8e7bb6fc105fd2079543e1b74cf93e8b3
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sun Jul  7 18:31:07 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Jul  7 18:31:07 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=16978af8

sci-libs/iRODS: drop the extraneous license file

It is just am ordinary 3-clause BSD license.

Package-Manager: Portage-2.3.67, Repoman-2.3.16
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-libs/iRODS/iRODS-4.2.0.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-libs/iRODS/iRODS-4.2.0.ebuild 
b/sci-libs/iRODS/iRODS-4.2.0.ebuild
index f2b5d1067..244962491 100644
--- a/sci-libs/iRODS/iRODS-4.2.0.ebuild
+++ b/sci-libs/iRODS/iRODS-4.2.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -9,7 +9,7 @@ DESCRIPTION="Integrated Rule Oriented Data System, a data 
management software"
 HOMEPAGE="https://irods.org;
 SRC_URI="https://github.com/irods/irods/archive/4.2.0.tar.gz -> ${P}.tar.gz"
 
-LICENSE="BSD-with-attribution"
+LICENSE="BSD"
 SLOT="0"
 KEYWORDS=""
 IUSE=""



[gentoo-commits] proj/sci:master commit in: licenses/

2019-07-07 Thread Martin Mokrejs
commit: dc2aff5fcf8052679743b41e978b130afc286edc
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sun Jul  7 18:31:34 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Jul  7 18:31:34 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=dc2aff5f

Drop the extraneous license file

It is just an ordinary 3-clause BSD license.

 licenses/BSD-3 | 26 --
 1 file changed, 26 deletions(-)

diff --git a/licenses/BSD-3 b/licenses/BSD-3
deleted file mode 100644
index 3e6ae8250..0
--- a/licenses/BSD-3
+++ /dev/null
@@ -1,26 +0,0 @@
-Copyright (c) 2009-2018, Broad Institute, Inc. All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-* Redistributions of source code must retain the above copyright notice, this
-  list of conditions and the following disclaimer.
-
-* Redistributions in binary form must reproduce the above copyright notice,
-  this list of conditions and the following disclaimer in the documentation
-  and/or other materials provided with the distribution.
-
-* Neither the name Broad Institute, Inc. nor the names of its
-  contributors may be used to endorse or promote products derived from
-  this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
-OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.



[gentoo-commits] proj/sci:master commit in: sci-biology/maker/

2019-07-01 Thread Martin Mokrejs
commit: 69bf257d740cc8fa15a30afdcfb3b22ed1a7db08
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Jul  1 08:15:27 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Jul  1 08:15:27 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=69bf257d

sci-biology/maker-3.01.02_beta: mpi_evaluator is already gone

The mpi_evaluator is not anymore in the distribution
tarball. When rm is called with no arguments it obviously
breaks. Drop the commands altogether.

Package-Manager: Portage-2.3.67, Repoman-2.3.16
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/maker/maker-3.01.02_beta.ebuild | 2 --
 1 file changed, 2 deletions(-)

diff --git a/sci-biology/maker/maker-3.01.02_beta.ebuild 
b/sci-biology/maker/maker-3.01.02_beta.ebuild
index d6ad845d1..dd8b088ac 100644
--- a/sci-biology/maker/maker-3.01.02_beta.ebuild
+++ b/sci-biology/maker/maker-3.01.02_beta.ebuild
@@ -119,8 +119,6 @@ src_compile(){
 src_install(){
cd "${WORKDIR}"/maker || die
rm -f bin/fasta_tool # is part of sci-biology/GAL
-   # drop development related accessory script requiring Parallel/MPIcar.pm
-   find . -name mpi_evaluator | xargs rm || die
mv bin/compare bin/compare_gff3_to_chado # rename as agreed by 
upstream, will be in maker-3 as well
dobin bin/*
perl_set_version



[gentoo-commits] proj/sci:master commit in: sci-biology/vague-bin/

2019-04-30 Thread Martin Mokrejs
commit: 72457ca425a702a0640f6bddeef66d3985d03ea5
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Tue Apr 30 18:40:23 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Apr 30 18:40:23 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=72457ca4

sci-biology/vague-bin: drop DEPEND on velvetk

It is gone from the tree.

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/vague-bin/vague-bin-1.0.5.ebuild | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild 
b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
index bbb594948..dc327b8d6 100644
--- a/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
+++ b/sci-biology/vague-bin/vague-bin-1.0.5.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -23,8 +23,7 @@ SLOT="0"
 
 RDEPEND="
>=virtual/jre-1.5:*
-   sci-biology/velvet
-   sci-biology/velvetk"
+   sci-biology/velvet"
 DEPEND=">=virtual/jdk-1.5:*"
 
 S="${WORKDIR}"/vague-${PV}



[gentoo-commits] proj/sci:master commit in: sci-physics/mc-tester/

2019-04-13 Thread Martin Mokrejs
commit: 55b203149488709cd3f2e362e3560c9ec614e2c9
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sat Apr 13 20:39:49 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sat Apr 13 20:39:49 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=55b20314

sci-physics/mc-tester: add missing SLOT (non-maintainer commit)

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-physics/mc-tester/mc-tester-1.25.0.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-physics/mc-tester/mc-tester-1.25.0.ebuild 
b/sci-physics/mc-tester/mc-tester-1.25.0.ebuild
index 6126cde65..d651961b9 100644
--- a/sci-physics/mc-tester/mc-tester-1.25.0.ebuild
+++ b/sci-physics/mc-tester/mc-tester-1.25.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -17,7 +17,7 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="doc examples hepmc"
 
-RDEPEND="sci-physics/root
+RDEPEND="sci-physics/root:=
hepmc? ( sci-physics/hepmc )
 "
 DEPEND="${RDEPEND}



[gentoo-commits] proj/sci:master commit in: sci-biology/chiron/

2019-04-13 Thread Martin Mokrejs
commit: e5ce549c694e952e624f1c4b2b751db1618294ec
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sat Apr 13 20:36:02 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sat Apr 13 20:36:02 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e5ce549c

sci-biology/chiron: Fix RDEPEND issue

RDEPEND uses the = operator with no revision:
  '=sci-libs/tensorflow-1.0.1';
if any revision is acceptable, use '~' instead;
if only -r0 then please append '-r0' to the dep

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/chiron/chiron-.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/chiron/chiron-.ebuild 
b/sci-biology/chiron/chiron-.ebuild
index cd99cb976..4294326ee 100644
--- a/sci-biology/chiron/chiron-.ebuild
+++ b/sci-biology/chiron/chiron-.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 PYTHON_COMPAT=( python2_7 pypy )
 
@@ -17,6 +17,6 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
-DEPEND="=sci-libs/tensorflow-1.0.1"
+DEPEND="~sci-libs/tensorflow-1.0.1"
 RDEPEND="${DEPEND}
dev-python/h5py"



[gentoo-commits] proj/sci:master commit in: sci-mathematics/dolfin/

2019-04-13 Thread Martin Mokrejs
commit: 444afbb71d21aef9221bc6142c9a7cf4ad676a73
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sat Apr 13 20:28:46 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sat Apr 13 20:28:46 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=444afbb7

sci-mathematics/dolfin: Fix RDEPEND.suspect

Non-maintainer commit fixing:

RDEPEND.suspect   2
 sci-mathematics/dolfin/dolfin-2016.2.0-r2.ebuild: 'dev-lang/swig:0='
 sci-mathematics/dolfin/dolfin-2017.1.0.ebuild: 'dev-lang/swig:0='

All swig ebuilds define only SLOT="0"

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-mathematics/dolfin/dolfin-2016.2.0-r2.ebuild | 4 ++--
 sci-mathematics/dolfin/dolfin-2017.1.0.ebuild| 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-mathematics/dolfin/dolfin-2016.2.0-r2.ebuild 
b/sci-mathematics/dolfin/dolfin-2016.2.0-r2.ebuild
index 4d5d8f716..169611161 100644
--- a/sci-mathematics/dolfin/dolfin-2016.2.0-r2.ebuild
+++ b/sci-mathematics/dolfin/dolfin-2016.2.0-r2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -23,7 +23,7 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}
 DEPEND="
${PYTHON_DEPS}
dev-cpp/eigen:3
-   dev-lang/swig:0=
+   dev-lang/swig
dev-libs/boost:=
dev-libs/libxml2:2
~dev-python/dijitso-${PV}[${PYTHON_USEDEP}]

diff --git a/sci-mathematics/dolfin/dolfin-2017.1.0.ebuild 
b/sci-mathematics/dolfin/dolfin-2017.1.0.ebuild
index 64e736315..b5b66a708 100644
--- a/sci-mathematics/dolfin/dolfin-2017.1.0.ebuild
+++ b/sci-mathematics/dolfin/dolfin-2017.1.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -23,7 +23,7 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}
 DEPEND="
${PYTHON_DEPS}
dev-cpp/eigen:3
-   dev-lang/swig:0=
+   dev-lang/swig
dev-libs/boost:=
dev-libs/libxml2:2
~dev-python/dijitso-${PV}[${PYTHON_USEDEP}]



[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/files/, sci-biology/ncbi-tools++/

2019-04-05 Thread Martin Mokrejs
commit: 903f1a13a0c2953d5f556ccdd996d72120188c56
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Fri Apr  5 15:24:06 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Apr  5 15:26:16 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=903f1a13

sci-biology/ncbi-tools++: set -rpath-link to temp build location

Add more regexps specifying which parts of the test suite should
not be compiled at all.

We have so far problems with say ncbi-tools++-18.0.0 libs installed
in ${EPREFIX}/usr/lib64/ncbi-tools++/ which get picked during linking
of a currently emerged package, like ncbi-tools++-22.0.0. That happens
due to LDPATH being set through

```
  echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN}
  doenvd "${S}/99${PN}"
```

which results in

```
$ cat /etc/env.d/99ncbi-tools++
LDPATH=/usr/lib64/ncbi-tools++
$
```

and later used during linking of a future version. Some symbols will be
resolved by ${EPREFIX}/usr/lib64/ncbi-tools++/ from older version,
some probably not. It is confusing to debug the errors popping up
during compilation/linking.

Aaron Ucko from NCBI proposed:

To avoid interference from old installations, please try passing
`LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib` to configure, no patches
(likely) needed.

@kiwifb François Bissey commented with:


LDPATH is used to generate the ld.so.conf.d files. So it is important
to have it to be able to find the libraries that are not in a standard
path. LDPATH is a Gentoo special. You need to regenerate the cache with
ldconfig after installing such a library and such a path.

...

$ /usr/bin/x86_64-pc-linux-gnu-g++ -std=gnu++11 -Wl,--verbose
  -Wl,-rpath,/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0
  -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -Wl,-O1
  -Wl,--as-needed -g speedtest.o
  -L/scratch/var/tmp/portage/sci-biology/ncbi-tools++-22.0.0/work/\
ncbi_cxx--22_0_0_build/lib
  -lprosplign -lxalgoalignutil -ltaxon1 -lxalgoseq -lxcleanup
  -lxobjedit -ltaxon3 -lvalid -lvalerr -lproteinkmer -lxblast
  -lxalgoblastdbindex -lcomposition_adjustment -lxalgodustmask
  -lxalgowinmask -lseqmasks_io -lseqdb -lblast_services -lxalnmgr
  -lxobjutil -lxobjread -lvariation -lcreaders -lsubmit -lxnetblastcli
  -lxnetblast -lblastdb -lscoremat -ltables -lxqueryparse -lxregexp
  -lncbi_xloader_genbank -lncbi_xreader_id1 -lncbi_xreader_id2
  -lncbi_xreader_cache -ldbapi_driver -lncbi_xreader -lxconnect
  -lid1 -lid2 -lxobjmgr -lgenome_collection -lseqedit -lseqsplit
  -lsubmit -lseqset -lseq -lseqcode -lsequtil -lpub -lmedline
  -lbiblio -lgeneral -lxser -lxutil -lxncbi -lxcompress -lz -lbz2
  -llzo2 -lz -lnsl -ldl -lpcre -llmdb -lpthread -ldw -ldl -lm
  -lpthread -o speedtest

It cannot find libmlacli.so. Note that there isn’t a `-lmlacli`
anywhere in the above line. It is searched for because you are
compiling an executable and executable cannot have unresolved
symbols. It must in the table of needed libraries for libxobjedit.so
libmlacli.so needed by /scratch/var/tmp/portage/sci-biology/\
  ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/lib/libxobjedit.so

Because there is no path or possibly a final path in libxobjedit.so
that library cannot be found.
Two solutions here:
1) add -lmlacli in the compilation line above
2) Precede the whole line with
LD_LIBRARY_PATH=/scratch/var/tmp/portage/sci-biology/\
  ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/lib

The LDPATH setting probably enabled you to find a previously
installed version of the library.

François

PS: You can pass that analysis upstream because -lmlacli should
probably be added by right.


Later François also wrote:


rpath are usually the preferred solution but it is not the end all
solution. Looking for LDPATH in your /etc/env.d/ may shock you.
In the case of ncbi, adding path is only one of the solution I
would consider. I don’t see why they need to install in
/usr/lib{,64}/ncbi-tools++ rather than just /usr/lib{,64} in
the first place. It is not even versioned to allow several versions
installed in parallel. It is not plugins or “modules” or other
special kinds of shared objects.

Possibly it is some language runtime - at best. Does it use names
that could collide easily with something else? May be some of them
should be prefixed then.


make[3]: Entering directory '/scratch/var/tmp/portage/sci-biology/\
  ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0_build/build/app/speedtest'
Updating dependency information for /scratch/var/tmp/portage/sci-biology/\
  ncbi-tools++-22.0.0/work/ncbi_cxx--22_0_0/src/app/speedtest/speedtest.cpp.
/usr/bin/x86_64-pc-linux-gnu-g++  -std=gnu++11 -c  -Wall -Wno-format-y2k
  -pthread -pipe -mpclmul -mpopcnt -march=native -ftree-vectorize -fPIC
  -g -D_DEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
  -D_MT -D_REENTRANT -D_THREAD_SAFE
  -I/scratch/var/tmp/portage/sci-biology/ncbi-tools++-22.0.0/work/\
ncbi_cxx--22_0_0_build/inc
 

[gentoo-commits] proj/sci:master commit in: sci-biology/velvetk/

2019-03-30 Thread Martin Mokrejs
commit: 52d9da4d866e95afa5270fb9533fa359df0a9957
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sat Mar 30 23:36:06 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sat Mar 30 23:36:06 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=52d9da4d

sci-biology/velvetk: drop faulty software per its author

From: Torsten S.
The velvetk.pl is faulty and should not be used.
Try `kmergenie` instead, or use the SPades Assembler.

 sci-biology/velvetk/metadata.xml| 12 
 sci-biology/velvetk/velvetk-20120606.ebuild | 24 
 2 files changed, 36 deletions(-)

diff --git a/sci-biology/velvetk/metadata.xml b/sci-biology/velvetk/metadata.xml
deleted file mode 100644
index 138cb7705..0
--- a/sci-biology/velvetk/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-   
-   mmokr...@fold.natur.cuni.cz
-       Martin Mokrejs
-   
-   
-   sci-biol...@gentoo.org
-   Gentoo Biology Project
-   
-

diff --git a/sci-biology/velvetk/velvetk-20120606.ebuild 
b/sci-biology/velvetk/velvetk-20120606.ebuild
deleted file mode 100644
index a2fdb7c25..0
--- a/sci-biology/velvetk/velvetk-20120606.ebuild
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit perl-module
-
-DESCRIPTION="Estimate the best k-mer size to use for your Velvet de novo 
assembly"
-HOMEPAGE="http://www.vicbioinformatics.com/software.velvetk.shtml;
-SRC_URI="http://www.vicbioinformatics.com/velvetk.pl;
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="dev-lang/perl"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"
-
-src_install(){
-   dobin "${DISTDIR}"/velvetk.pl
-}



[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/

2019-03-30 Thread Martin Mokrejs
commit: a6b601e64f7b9313fc7d7c2fec43d0f4d4d7ec1f
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sat Mar 30 06:42:42 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sat Mar 30 06:42:42 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a6b601e6

sci-biology/ncbi-tools++: document possible issue with builds

I have the following defined due to ncbi-tools++-18.0.0 installed
on my system:

/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/32:
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0:
/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/32:
/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0:
/usr/lib/llvm/7/lib32:
/usr/lib/llvm/7/lib64:
/usr/lib64/itcl4.1.1:
/usr/lib64/itk4.1.0:
/lib64:
/usr/lib64:
/usr/local/lib64:
/lib32:
/usr/lib32:
/usr/lib64/rust-1.29.2:
/usr/lib64/R/lib:
/usr/lib64/fltk:
/usr/lib64/ncbi-tools++:
/usr/lib64/staden:

grep: /etc: No such file or directory
grep: /etc/env.d: No such file or directory
/etc/env.d/99ncbi-tools++:LDPATH=/usr/lib64/ncbi-tools++
...

That in turn makes linker pick "${WORKDIR}"/ncbi_cxx--22_0_0_build/lib/*
files but later overrides some of them with /usr/lib64/ncbi-tools++/*,
depending on the ordering of -lXX arguments.

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 5 +++--
 sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 5 +++--
 sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild | 3 ++-
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild 
b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index 14e1fabda..68341a338 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -36,11 +36,12 @@ KEYWORDS="~amd64"
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 # sys-libs/db should be compiled with USE=cxx
+# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] 
then?
 DEPEND="
!sci-biology/sra_sdk
app-arch/cpio
berkdb? ( sys-libs/db:4.3[cxx] )
-   boost? ( dev-libs/boost )
+   boost? ( dev-libs/boost[tools] )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
mysql? ( virtual/mysql )

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild 
b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 3f1fc7bd1..c737392fd 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -35,11 +35,12 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 # sys-libs/db should be compiled with USE=cxx
+# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] 
then?
 DEPEND="
!sci-biology/sra_sdk
app-arch/cpio
berkdb? ( sys-libs/db:4.3[cxx] )
-   boost? ( dev-libs/boost )
+   boost? ( dev-libs/boost[tools] )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
mysql? ( virtual/mysql )

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild 
b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
index 585042f9f..971789fb4 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -35,11 +35,12 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 
 # sys-libs/db should be compiled with USE=cxx
+# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] 
then?
 DEPEND="
!sci-biology/sra_sdk
app-arch/cpio
berkdb? ( sys-libs/db:4.3[cxx] )
-   boost? ( dev-libs/boost )
+   boost? ( dev-libs/boost[tools] )
curl? ( net-misc/curl )
sqlite? ( >=dev-db/sqlite-3.6.6:3 )
mysql? ( virtual/mysql )



[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/

2019-03-29 Thread Martin Mokrejs
commit: 220946d413cfcfa399e3609f2b215eabdc8df3a8
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sat Mar 30 00:13:51 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sat Mar 30 00:13:51 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=220946d4

sci-biology/ncbi-tools++: version bump

It does not link if older version is installed because linker
picks up older version of libraries and obviously does not find
newly added functions.

Upstream says:
Please try either supplying an LD_RUN_PATH environment setting
or a -Wl,-rpath-link,... flag pointing at your build tree's lib
directory.  Also, please bear in mind that adding the old
installation's library directory to the central search path largely
defeats the purpose of making it a separate directory.

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 .../ncbi-tools++/ncbi-tools++-22.0.0.ebuild| 380 +
 1 file changed, 380 insertions(+)

diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild 
b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
new file mode 100644
index 0..585042f9f
--- /dev/null
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -0,0 +1,380 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
+
+MY_TAG="Mar_28_2019"
+MY_Y="${MY_TAG/*_/}"
+MY_PV="22_0_0"
+MY_P="ncbi_cxx--${MY_PV}"
+
+# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+
+DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+"
+HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit;
+# https://ncbi.github.io/cxx-toolkit/pages/release_notes
+SRC_URI="
+   
ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2019/${MY_TAG}/ncbi_cxx--${MY_PV}.tar.gz;
+#  http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz;
+
+# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz
+# see http://www.biostars.org/p/76551/ and 
http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html
+LICENSE="public-domain"
+SLOT="0"
+IUSE="
+   debug static-libs static threads pch
+   test wxwidgets odbc
+   berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif
+   glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python
+   sablotron sqlite tiff xerces xalan xml xpm xslt X"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+# sys-libs/db should be compiled with USE=cxx
+DEPEND="
+   !sci-biology/sra_sdk
+   app-arch/cpio
+   berkdb? ( sys-libs/db:4.3[cxx] )
+   boost? ( dev-libs/boost )
+   curl? ( net-misc/curl )
+   sqlite? ( >=dev-db/sqlite-3.6.6:3 )
+   mysql? ( virtual/mysql )
+   fltk? ( x11-libs/fltk )
+   opengl? ( virtual/opengl media-libs/glew:0= )
+   mesa? ( media-libs/mesa[osmesa] )
+   glut? ( media-libs/freeglut )
+   freetype? ( media-libs/freetype )
+   gnutls? ( net-libs/gnutls )
+   python? ( ${PYTHON_DEPS} )
+   cppunit? ( dev-util/cppunit )
+   icu? ( dev-libs/icu )
+   expat? ( dev-libs/expat )
+   sablotron? ( app-text/sablotron )
+   xml? ( dev-libs/libxml2 )
+   xslt? ( >=dev-libs/libxslt-1.1.14 )
+   xerces? ( dev-libs/xerces-c )
+   xalan? ( dev-libs/xalan-c )
+   muparser? ( dev-cpp/muParser )
+   hdf5? ( sci-libs/hdf5[cxx] )
+   gif? ( media-libs/giflib )
+   jpeg? ( virtual/jpeg:0= )
+   png? ( media-libs/libpng:0= )
+   tiff? ( media-libs/tiff:0= )
+   xpm? ( x11-libs/libXpm )
+   >=dev-libs/lzo-2.0
+   app-arch/bzip2
+   dev-libs/libpcre"
+# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC 
OEChem sge
+# Intentionally omitted USE flags:
+#   ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is 
currently broken.
+#  The default (heavily patched) embedded copy 
should work, or you can
+#  leave it off altogether -- the only public apps 
that make use of it are
+#  samples and tests, since NCBI's database 
servers are of course firewalled.
+
+# seems muParser is required, also glew is required. configure exits otherwise 
if these are explicitly passed to it (due to USE flag enabled)
+
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${MY_P}"
+
+src_prepare() {
+#  filter-ldflags -Wl,--as-needed
+#  append-ldflags -Wl,--no-undefined
+#  sed -i -e 's/-print-file-name=libstdc++.a//' \
+#  -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \
+#  src/build-

[gentoo-commits] proj/sci:master commit in: sci-biology/KaKs_Calculator/

2019-03-29 Thread Martin Mokrejs
commit: 21fc7bb7e17bc4bd4f44f8f80a357f260d3d3748
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sat Mar 30 00:04:54 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sat Mar 30 00:04:54 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=21fc7bb7

sci-biology/KaKs_Calculator: another attempt at SRC_URI

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild 
b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
index e6620b359..643352424 100644
--- a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
+++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
@@ -11,7 +11,7 @@ HOMEPAGE="https://code.google.com/p/kaks-calculator
https://www.sciencedirect.com/science/article/pii/S1672022910600083;
 SRC_URI="

https://netcologne.dl.sourceforge.net/project/kakscalculator2/${PN}${PV}.tar.gz 
-> ${P}.tar.gz
-   
https://raw.githubusercontent.com/WilsonSayresLab/AlignmentProcessor/master/"{$PN}"/"{$PN}${PV}"/"{$PN}${PV}"_manual.pdf
 -> ${P}_manual.pdf
+   
https://raw.githubusercontent.com/WilsonSayresLab/AlignmentProcessor/master/${PN}/${PN}${PV}/${PN}${PV}_manual.pdf
 -> ${P}_manual.pdf

https://s3.amazonaws.com/fumba.me/share+files/1-s2.0-S1672022907600072-main.pdf 
-> ${PN}-Zhang_et_al_2006.pdf"
 
 LICENSE="GPL-3"



[gentoo-commits] proj/sci:master commit in: sci-biology/KaKs_Calculator/

2019-03-29 Thread Martin Mokrejs
commit: 9434b7843e92befab076411b1b39764ff4a35738
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Fri Mar 29 23:58:06 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Mar 29 23:58:06 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9434b784

sci-biology/KaKs_Calculator: fix download URL

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild 
b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
index 5edd1323a..e6620b359 100644
--- a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
+++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
@@ -11,7 +11,7 @@ HOMEPAGE="https://code.google.com/p/kaks-calculator
https://www.sciencedirect.com/science/article/pii/S1672022910600083;
 SRC_URI="

https://netcologne.dl.sourceforge.net/project/kakscalculator2/${PN}${PV}.tar.gz 
-> ${P}.tar.gz
-   
https://github.com/WilsonSayresLab/AlignmentProcessor/blob/master/KaKs_Calculator/${PN}${PV}/${PN}${PV}_manual.pdf
 -> ${P}_manual.pdf
+   
https://raw.githubusercontent.com/WilsonSayresLab/AlignmentProcessor/master/"{$PN}"/"{$PN}${PV}"/"{$PN}${PV}"_manual.pdf
 -> ${P}_manual.pdf

https://s3.amazonaws.com/fumba.me/share+files/1-s2.0-S1672022907600072-main.pdf 
-> ${PN}-Zhang_et_al_2006.pdf"
 
 LICENSE="GPL-3"



[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/

2019-03-29 Thread Martin Mokrejs
commit: 346ebf0f53a5e272706bcb6ad909ad72a62bb4c7
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Fri Mar 29 23:28:32 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Mar 29 23:28:32 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=346ebf0f

sci-biology/bowtie: add another upstream patch

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/bowtie/bowtie-2.3.5-r1.ebuild |  3 ++-
 sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch  | 15 +++
 .../bowtie/files/bowtie-2.3.5-fix-interleaved.patch   |  2 ++
 3 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild 
b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
index f79dcb9cb..2a6fc04eb 100644
--- a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
+++ b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
@@ -27,7 +27,8 @@ S="${WORKDIR}/${PN}2-${PV}"
 DOCS=( AUTHORS NEWS TUTORIAL )
 HTML_DOCS=( doc/{manual.html,style.css} )
 #PATCHES=( "${FILESDIR}/${P}-fix-c++14.patch" ) # needs 2.3.4.3 update
-PATCHES=( "${FILESDIR}"/bowtie-2.3.5-fix-interleaved.patch )
+PATCHES=( "${FILESDIR}"/bowtie-2.3.5-fix-interleaved.patch
+   "${FILESDIR}"/bowtie-2.3.5-fix-fifo.patch )
 
 pkg_pretend() {
if ! use cpu_flags_x86_sse2 ; then

diff --git a/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch 
b/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch
new file mode 100644
index 0..136bb1e69
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch
@@ -0,0 +1,15 @@
+https://github.com/BenLangmead/bowtie2/commit/d7eab7cf6b7e238047044cf61acc662b05c772c4
+
+diff --git a/pat.cpp b/pat.cpp
+index 453ba69..6d862f8 100644
+--- a/pat.cpp
 b/pat.cpp
+@@ -494,7 +494,7 @@ void CFilePatternSource::open() {
+ 
+   is_fifo = S_ISFIFO(st.st_mode) != 0;
+ #endif
+-  if (pp_.format != BAM || is_fifo || 
is_gzipped_file(fd)) {
++  if (pp_.format != BAM && (is_fifo || 
is_gzipped_file(fd))) {
+   zfp_ = gzdopen(fd, "r");
+   compressed_ = true;
+   } else {

diff --git a/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch 
b/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch
index b2f24a7fa..45d6a0f96 100644
--- a/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch
+++ b/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch
@@ -1,3 +1,5 @@
+https://github.com/BenLangmead/bowtie2/commit/753df9deca210db54e1ecc94f946b413876e456e
+
 diff --git bowtie-2.3.5/bt2_search.cpp b/bt2_search.cpp
 index 1d53741..c59e39c 100644
 --- bowtie-2.3.5/bt2_search.cpp



[gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker/, sci-biology/repeatmasker/files/

2019-03-29 Thread Martin Mokrejs
commit: 80e24faa006c5883307c0dadd31cab8cecd8
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Fri Mar 29 16:24:12 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Mar 29 16:24:12 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=80e2

sci-biology/repeatmasker: rewamp configuration code

The changes are partly based on https://github.com/gentoo/sci/pull/580
from Michael Schubert but it seems we could figure out the paths
to binaries automatically using `which`.

Block between the USE options and allow only a single to be enabled,
that is what configure requires, otherwise it enters a loop.

The hmmer is the default in configure and preferred.

Tested with `USE="hmmer -wublast -phrap -rmblast"` and other
combinations while only one is allowed.

If users have wublast/abblast/rmblast/crossmatch in the PATHS we just
pick it.

`which` returns a '.' (dot) if a binary was not found, we need to zap it
otherwise configure enters a loop.

In the end, one can get:

Add a Search Engine:
   1. CrossMatch: [ Configured ]
   2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Configured ]
   3. WUBlast/ABBlast (required by DupMasker): [ Un-configured ]
   4. HMMER3.1 & DFAM: [ Configured, Default ]

   5. Done

properly written into

/usr/lib64/perl5/vendor_perl/5.28.0/RepeatMaskerConfig.pm

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 .../files/repeatmasker-4.0.6__configure.patch  |   4 +-
 sci-biology/repeatmasker/metadata.xml  |   6 +
 .../repeatmasker/repeatmasker-4.0.6-r3.ebuild  | 111 
 .../repeatmasker/repeatmasker-4.0.6-r4.ebuild  | 142 +
 .../repeatmasker/repeatmasker-4.0.8-r1.ebuild  | 111 
 .../repeatmasker/repeatmasker-4.0.8-r2.ebuild  | 142 +
 6 files changed, 292 insertions(+), 224 deletions(-)

diff --git a/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch 
b/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch
index e4042190f..c1e0cfb55 100644
--- a/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch
+++ b/sci-biology/repeatmasker/files/repeatmasker-4.0.6__configure.patch
@@ -1,5 +1,5 @@
 configure.ori  2015-11-24 20:56:46.0 +0100
-+++ configure  2015-11-24 20:59:58.0 +0100
+--- RepeatMasker/configure.ori 2015-11-24 20:56:46.0 +0100
 RepeatMasker/configure 2015-11-24 20:59:58.0 +0100
 @@ -253,17 +253,16 @@
close INVERS;
  }

diff --git a/sci-biology/repeatmasker/metadata.xml 
b/sci-biology/repeatmasker/metadata.xml
index 8417d1580..de382fa16 100644
--- a/sci-biology/repeatmasker/metadata.xml
+++ b/sci-biology/repeatmasker/metadata.xml
@@ -5,4 +5,10 @@
sci-biol...@gentoo.org
Gentoo Biology Project

+   
+   Use cross_match search engine as 
default
+   Use RM-BLAST search engine as 
default
+   Use HMMER search engine as default
+   Use wublast or abblast search engine as 
default
+   
 

diff --git a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild 
b/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
deleted file mode 100644
index d41784eb7..0
--- a/sci-biology/repeatmasker/repeatmasker-4.0.6-r3.ebuild
+++ /dev/null
@@ -1,111 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils perl-module
-
-MY_PV=${PV//\./-}
-
-DESCRIPTION="Screen DNA sequences for interspersed repeats and low complexity 
DNA"
-HOMEPAGE="http://repeatmasker.org/;
-SRC_URI="http://www.repeatmasker.org/RepeatMasker-open-${MY_PV}.tar.gz;
-
-LICENSE="OSL-2.1"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=dev-lang/perl-5.8"
-RDEPEND="
-   dev-perl/Text-Soundex
-   sci-biology/phrap
-   <=sci-biology/repeatmasker-libraries-20160829
-   sci-biology/rmblast
-   !sci-biology/trf
-   >=sci-biology/trf-bin-4.0.4
-"
-
-S="${WORKDIR}/RepeatMasker"
-
-PATCHES=( "${FILESDIR}"/"${P}"__configure.patch )
-
-src_configure() {
-   sed \
-   -e "s#/usr/bin/which#which#g" \
-   -e "s#/usr/bin/perl#perl#g" \
-   -i "${S}"/configure || die
-   perl_set_version
-   insinto ${VENDOR_LIB}
-   sed -e "s#/usr/perl5/lib/#${VENDOR_LIB}/#g" -i "${S}"/configure || die
-   # The below is wrong as it causes:
-   # Enter path [ 
/var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/work/RepeatMasker ]:
-   #  -- Building monolithic RM database...sh: 
/var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/image///usr/share/repeatmasker/Libraries/RepeatMasker.lib:

[gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker-libraries/

2019-03-29 Thread Martin Mokrejs
commit: 192396a3084735738acce2fbb93475b5da28078e
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Fri Mar 29 13:30:44 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Mar 29 13:30:44 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=192396a3

sci-biology/repeatmasker-libraries: dohtml has been banned for EAPI 7

This slipped through repoman checks.

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 .../repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild   | 2 +-
 .../repeatmasker-libraries/repeatmasker-libraries-20160829.ebuild   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git 
a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild 
b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild
index 160d8c62d..4b1222536 100644
--- a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild
+++ b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild
@@ -33,5 +33,5 @@ src_install() {
insinto /usr/share/repeatmasker/Libraries
doins "${S}"/RepeatMaskerLib.embl
dodoc README
-   dohtml README.html
+   dodoc README.html
 }

diff --git 
a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20160829.ebuild 
b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20160829.ebuild
index 2fb5b1002..98521c4ba 100644
--- a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20160829.ebuild
+++ b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20160829.ebuild
@@ -33,5 +33,5 @@ src_install() {
insinto /usr/share/repeatmasker/Libraries
doins "${S}"/RepeatMaskerLib.embl
dodoc README
-   dohtml README.html
+   dodoc README.html
 }



[gentoo-commits] proj/sci:master commit in: sci-biology/augustus/

2019-03-29 Thread Martin Mokrejs
commit: 7e11364f3429ea8e4662a5c245c23e53a498326c
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Fri Mar 29 13:07:02 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Mar 29 13:07:02 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7e11364f

sci-biology/augustus: fix typo in a comment line

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/augustus/augustus-3.3.2.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/augustus/augustus-3.3.2.ebuild 
b/sci-biology/augustus/augustus-3.3.2.ebuild
index 2326d9c92..a959252a0 100644
--- a/sci-biology/augustus/augustus-3.3.2.ebuild
+++ b/sci-biology/augustus/augustus-3.3.2.ebuild
@@ -103,7 +103,7 @@ src_install() {
 
use man && doman mansrc/*.1
 
-   # install stuff not compiled but not written into bin/
+   # install stuff compiled but not written into bin/
# https://github.com/Gaius-Augustus/Augustus/issues/14
dobin auxprogs/utrrnaseq/Debug/utrrnaseq
dodoc auxprogs/utrrnaseq/doc/reference.pdf



[gentoo-commits] proj/sci:master commit in: sci-biology/augustus/

2019-03-29 Thread Martin Mokrejs
commit: dad62d03f97e438406e58011f360195638297858
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Fri Mar 29 13:05:38 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Mar 29 13:05:38 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=dad62d03

sci-biology/augustus: adjust to current LICENSE, use ${PV}

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/augustus/augustus-3.3.2.ebuild | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/sci-biology/augustus/augustus-3.3.2.ebuild 
b/sci-biology/augustus/augustus-3.3.2.ebuild
index f28fb4e93..2326d9c92 100644
--- a/sci-biology/augustus/augustus-3.3.2.ebuild
+++ b/sci-biology/augustus/augustus-3.3.2.ebuild
@@ -8,12 +8,12 @@ inherit eutils toolchain-funcs
 DESCRIPTION="Eukaryotic gene predictor"
 HOMEPAGE="http://bioinf.uni-greifswald.de/augustus
https://github.com/Gaius-Augustus/Augustus;
-SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/3.3.2.tar.gz -> 
${P}.tar.gz"
+SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/${PV}.tar.gz -> 
${P}.tar.gz"
 
-LICENSE="GPL-3"
+# LICENSE="GPL-3"
 # temporary drop in licensing scheme, see 
http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/HISTORY.TXT
 # 
http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/LICENCE.TXT
-# LICENSE="Artistic"
+LICENSE="Artistic"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE="bam2wig examples man mysql sqlite"



[gentoo-commits] proj/sci:master commit in: sci-biology/augustus/

2019-03-29 Thread Martin Mokrejs
commit: f291cafdf1bac38dea4e9781f08ee7cc171a6dc4
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Fri Mar 29 13:00:21 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Mar 29 13:00:21 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f291cafd

sci-biology/augustus: version bump, fix awful Makefile's

Do not require static libraries. Only bamtools are really needed.
htslib is not needed. For bam2wig samtools-0.2 series is needed.

I decided to blindly install some of the binaries created but not
copied into `./bin/`.

`src/Makefile` will gladly define mysql and sqlite together, probably
a non-sense. We force mysql as we check for it first. Not sure if
sqlite should be preferred.

I documented in the augustus-3.3.2.ebuild other "forgotten" files,
like gbrowse.conf and a template for gff2ps.

I dropped `-O3` but left in `-ggdb` in the `CXXFLAGS`.

https://github.com/Gaius-Augustus/Augustus/issues/14
https://github.com/Gaius-Augustus/Augustus/issues/50
https://github.com/Gaius-Augustus/Augustus/issues/51
https://github.com/Gaius-Augustus/Augustus/issues/52
https://github.com/Gaius-Augustus/Augustus/issues/53

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/augustus/augustus-3.3.2.ebuild | 115 +
 sci-biology/augustus/augustus-3.3.ebuild   |  70 --
 sci-biology/augustus/metadata.xml  |   4 +
 3 files changed, 119 insertions(+), 70 deletions(-)

diff --git a/sci-biology/augustus/augustus-3.3.2.ebuild 
b/sci-biology/augustus/augustus-3.3.2.ebuild
new file mode 100644
index 0..f28fb4e93
--- /dev/null
+++ b/sci-biology/augustus/augustus-3.3.2.ebuild
@@ -0,0 +1,115 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Eukaryotic gene predictor"
+HOMEPAGE="http://bioinf.uni-greifswald.de/augustus
+   https://github.com/Gaius-Augustus/Augustus;
+SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/3.3.2.tar.gz -> 
${P}.tar.gz"
+
+LICENSE="GPL-3"
+# temporary drop in licensing scheme, see 
http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/HISTORY.TXT
+# 
http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/LICENCE.TXT
+# LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="bam2wig examples man mysql sqlite"
+
+RDEPEND="
+   bam2wig? ( sci-biology/samtools:0.1-legacy )
+   sci-biology/bamtools
+   >=sci-mathematics/lpsolve-5.5
+   sci-libs/gsl
+   sci-libs/suitesparse
+   sqlite? ( dev-db/sqlite:3 )
+   mysql? ( dev-db/mysql++ )
+   >=dev-libs/boost-1.49.0
+   sys-libs/zlib"
+DEPEND="${RDEPEND}
+   sys-devel/flex"
+S="${WORKDIR}/Augustus-${PV}"
+
+src_prepare() {
+   # TODO: do we need anything from the 2.5.5 patch?
+   # epatch "${FILESDIR}"/${P}-sane-build.patch
+   default
+   tc-export CC CXX
+   # lets respect upstream's wish and keep -ggdb
+   sed -e 's#-ggdb -O3#-ggdb#' -i src/Makefile || die
+   sed -e 's#TOOLDIR=$(HOME)/tools#TOOLDIR='"${EPREFIX}/usr/include#" \
+   -i auxprogs/bam2wig/Makefile || die
+   sed -e "s#INCLUDES=#INCLUDES=-I${EPREFIX}/usr/include/bam-0.1-legacy #" 
\
+   -i auxprogs/bam2wig/Makefile || die
+   # https://github.com/Gaius-Augustus/Augustus/issues/53
+   sed -e 's#$(SAMTOOLS)/libbam.a $(HTSLIB)/libhts.a -lcurses -lm -lz 
-lpthread -lcurl -lssl -lcrypto#-lbam-0.1-legacy#' -i auxprogs/bam2wig/Makefile 
|| die
+   sed -e 's#-lbz2 -llzma##' -i auxprogs/bam2wig/Makefile || die
+   # enable comparative gene prediction (CGP, needs c++11 compiler),
+   #this needs sci-mathematics/lpsolve
+   sed -e 's/^# COMPGENEPRED/COMPGENEPRED/' -i common.mk || die
+   # enable compressed gzip input
+   sed -e 's/^#ZIPINPUT/ZIPINPUT/' -i common.mk || die
+   # comparative (multi-species, CGP) AUGUSTUS with MySQL or SQLite
+   #supposedly pick only either a single-one
+   if use mysql; then
+   sed -e 's/^#MYSQL/MYSQL/' -i common.mk || die
+   elif use sqlite; then
+   # comparative (mutli-species, CGP) AUGUSTUS with SQLite
+   sed -e 's/^# SQLITE/SQLITE/' -i common.mk || die
+   fi
+   # respect $EPREFIX in all Makefile's
+   find . -name Makefile | while read f; do \
+   sed -s "s#/usr/include#${EPREFIX}/usr/include#g" -i $f || die;
+   done
+}
+
+src_compile() {
+   emake clean && default
+
+   # compile stuff not compiled by default
+   # https://github.com/Gaius-Augustus/Augustus/issues/52
+   cd auxprogs/aln2wig || die
+   emake
+}
+
+src_ins

[gentoo-commits] proj/sci:master commit in: sci-biology/tablet/

2019-03-28 Thread Martin Mokrejs
commit: 6ff12313344e3b1b686430875f4b866c67ab8d4f
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Thu Mar 28 22:06:49 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Mar 28 22:06:49 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6ff12313

sci-biology/tablet: fix indentation

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/tablet/tablet-.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/tablet/tablet-.ebuild 
b/sci-biology/tablet/tablet-.ebuild
index 5cebde785..e9ae6890d 100644
--- a/sci-biology/tablet/tablet-.ebuild
+++ b/sci-biology/tablet/tablet-.ebuild
@@ -51,7 +51,7 @@ src_install() {
java-pkg_dojar lib/samtools-linux64.jar
fi
if [ "${ABI}" == "x86" ]; then
-   java-pkg_dojar lib/samtools-linux32.jar
+   java-pkg_dojar lib/samtools-linux32.jar
fi
java-pkg_dojar lib/htsjdk*.jar # is htsjdk-2.11.0 in tablet-1.17.08.17
java-pkg_dojar lib/sqlite-jdbc*.jar



[gentoo-commits] proj/sci:master commit in: media-libs/avbin-bin/

2019-03-28 Thread Martin Mokrejs
commit: 48bbbf86c8400201906bf06220d53015b1d4d347
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Thu Mar 28 22:05:53 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Mar 28 22:05:53 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=48bbbf86

media-libs/avbin-bin: non-maintainer commit

Trying to get rids of FATAL errors reported by Travis.CI.

Use `if [ "${ABI}" == "amd64" ]; then`
instead of
`if use amd64; then`

Also bump to EAPI7.

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 media-libs/avbin-bin/avbin-bin-8.1.ebuild | 11 ++-
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/media-libs/avbin-bin/avbin-bin-8.1.ebuild 
b/media-libs/avbin-bin/avbin-bin-8.1.ebuild
index 13eb02661..d46f511f8 100644
--- a/media-libs/avbin-bin/avbin-bin-8.1.ebuild
+++ b/media-libs/avbin-bin/avbin-bin-8.1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 DESCRIPTION="A thin wrapper around FFmpeg"
 HOMEPAGE="http://avbin.github.io/;
@@ -15,13 +15,14 @@ KEYWORDS="-* ~amd64 ~x86"
 IUSE=""
 
 pkg_setup(){
-   if use amd64; then
+   if [ "${ABI}" == "amd64" ]; then
S="${WORKDIR}"/avbin-linux-x86-64-v${PV}
-   elif use x86; then
+   elif [ "${ABI}" == "x86" ]; then
S="${WORKDIR}"/avbin-linux-x86-32-v${PV}
fi
 }
+
 src_install() {
ln -s libavbin.so.${PV} libavbin.so || die
-   dolib libavbin.so*
+   dolib.so libavbin.so*
 }



[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/

2019-03-28 Thread Martin Mokrejs
commit: 83b76a8c9aab16e157cd482e5ac3508d30bc52a5
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Thu Mar 28 21:54:30 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Mar 28 21:54:30 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=83b76a8c

sci-biology/ncbi-blast+: emphasize alternative building from sources

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild 
b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index c91a5d490..ca3e682ac 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
@@ -288,7 +288,7 @@ src_configure() {
--prefix="${EPREFIX}/usr" \
--libdir=/usr/lib64 \
--with-flat-makefile \
-   ${myconf[@]} || die
+   ${myconf[@]} || die "Maybe try new 
src/build-system/cmake/cmake-configure instead?"
 #--without-debug \
 #  --with-bin-release \
 #  --with-bincopy \



[gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker-libraries/

2019-03-28 Thread Martin Mokrejs
commit: ead7d4aa498db6ff8dd487d0b5b159061964af09
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Thu Mar 28 21:51:08 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Mar 28 21:51:08 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ead7d4aa

sci-biology/repeatmasker-libraries: finish version bump, EAPI7, add KEYWORDS

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 .../repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild   | 4 ++--
 .../repeatmasker-libraries/repeatmasker-libraries-20160829.ebuild   | 4 ++--
 .../repeatmasker-libraries/repeatmasker-libraries-20181026.ebuild   | 6 +++---
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git 
a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild 
b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild
index ff9bbd89d..160d8c62d 100644
--- a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild
+++ b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="A special version of RepBase used by RepeatMasker"
 HOMEPAGE="http://repeatmasker.org/;

diff --git 
a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20160829.ebuild 
b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20160829.ebuild
index a30389e54..2fb5b1002 100644
--- a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20160829.ebuild
+++ b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20160829.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="A special version of RepBase used by RepeatMasker"
 HOMEPAGE="http://repeatmasker.org/;

diff --git 
a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20181026.ebuild 
b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20181026.ebuild
index d7b1821bd..5ea9ee4b5 100644
--- a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20181026.ebuild
+++ b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20181026.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 DESCRIPTION="A special version of RepBase used by RepeatMasker"
 HOMEPAGE="http://repeatmasker.org/;
@@ -9,7 +9,7 @@ SRC_URI="RepBaseRepeatMaskerEdition-${PV}.tar.gz"
 
 LICENSE="all-rights-reserved"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 DEPEND=""



[gentoo-commits] proj/sci:master commit in: sci-biology/maker/

2019-03-28 Thread Martin Mokrejs
commit: d174cca6d660563e4d1ac95875628d8b4ec94867
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Thu Mar 28 21:46:20 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Mar 28 21:46:20 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d174cca6

sci-biology/maker: some progress with the ebuild, empty KEYWORDS

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 .../{maker-2.31.8.ebuild => maker-2.31.10.ebuild}  | 32 ++
 ...ker-2.31.8.ebuild => maker-3.01.02_beta.ebuild} | 16 +++
 2 files changed, 37 insertions(+), 11 deletions(-)

diff --git a/sci-biology/maker/maker-2.31.8.ebuild 
b/sci-biology/maker/maker-2.31.10.ebuild
similarity index 80%
copy from sci-biology/maker/maker-2.31.8.ebuild
copy to sci-biology/maker/maker-2.31.10.ebuild
index e5c791ab2..b7dc780a9 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-2.31.10.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -21,6 +21,10 @@ IUSE="mpi"
 
 # http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm # bug 
#566360
 # http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm
+#
+# MAKER does not work with MVAPICH2.
+# It can work with Intel MPI and OpenMPI with some command line modification.
+# It always works with MPICH, but MPICH may not be able to scale to more than 
~100 CPUs.
 DEPEND="
mpi? ( sys-cluster/mpich2 || ( sys-cluster/openmpi ) )
dev-perl/DBI
@@ -104,12 +108,14 @@ pkg_nofetch() {
 src_compile(){
perl Build.PL || die
./Build install || die
+   ./Build installdeps || die
 }
 
-# If you move it, then the executables won’t be able to locate dependencies in 
the …/maker/data,
-# …/maker/lib, and …/maker/perl directories. You should really either add the 
location of
-# …/maker/bin to you PATH environmental variable or at most soft link the 
executables somewhere
-# else using the ‘ln -s’ command.
+# If you move it, then the executables won't able to locate dependencies
+# in the /maker/data, /maker/lib, /maker/perl directories. You should
+# really either add the location of /maker/bin to you PATH environmental
+# variable or at most soft link the executables somewhere
+# else using the 'ln -s' command.
 src_install(){
cd "${WORKDIR}"/maker || die
rm -f bin/fasta_tool # is part of sci-biology/GAL
@@ -121,11 +127,25 @@ src_install(){
insinto "${VENDOR_LIB}"/MAKER # uppercase, not "${PN}"
doins perl/lib/MAKER/*.pm
doman perl/man/*.3pm
+   #
+   # FIXME: find equivalent perl packages for lib/* contents, for example 
lib/GI.pm
+   # You do not have write access to install missing Modules.
+   # I can try and install these locally (i.e. only for MAKER)
+   # in the .../maker/perl/lib directory, or you can run
+   # './Build installdeps' as root or using sudo and try again.
+   # Do want MAKER to try and build a local installation? [N ]N 
+   # 
+   # 
+   # WARNING: You do not appear to have write access to install missing
+   # Modules. Please run './Build installdeps' as root or using sudo.
+   # 
+   # Do you want to continue anyway? [N ]N 
+   # 
+   doins -r lib/*
insinto "${VENDOR_LIB}"/Parallel/Application
doins perl/lib/Parallel/Application/*.pm
insinto /usr/share/"${PN}"/data
doins data/*
-   # FIXME: find equivalent perl packages for lib/* contents, for example 
lib/GI.pm
dodoc README INSTALL
insinto /usr/share/"${PN}"/GMOD/Apollo
doins GMOD/Apollo/gff3.tiers

diff --git a/sci-biology/maker/maker-2.31.8.ebuild 
b/sci-biology/maker/maker-3.01.02_beta.ebuild
similarity index 87%
rename from sci-biology/maker/maker-2.31.8.ebuild
rename to sci-biology/maker/maker-3.01.02_beta.ebuild
index e5c791ab2..d6ad845d1 100644
--- a/sci-biology/maker/maker-2.31.8.ebuild
+++ b/sci-biology/maker/maker-3.01.02_beta.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -21,6 +21,10 @@ IUSE="mpi"
 
 # http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm # bug 
#566360
 # http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm
+#
+# MAKER does not work with MVAPICH2.
+# It can work with Intel MPI and OpenMPI with some command line modification.
+# It always works with MPICH, but MPICH may not be able to scale to more than 
~100 CPUs.
 DEPEND="
mpi? ( sys-cluster/mpich2 || ( sys-cluster/openmpi ) )
dev-perl/DBI
@@ -93,6 +97,7 @@ S="${WORKDIR}"/maker/src
 pkg_

[gentoo-commits] proj/sci:master commit in: sci-biology/NGSTools/

2019-03-28 Thread Martin Mokrejs
commit: 6d35d6134317057345c6c80f77d35fa937083219
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Thu Mar 28 21:41:36 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Mar 28 21:41:36 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6d35d613

sci-biology/NGSTools: renamed into NGSEPcore and NGSEPplugin

 sci-biology/NGSTools/NGSTools-2.0.5.ebuild | 20 
 sci-biology/NGSTools/metadata.xml  | 15 ---
 2 files changed, 35 deletions(-)

diff --git a/sci-biology/NGSTools/NGSTools-2.0.5.ebuild 
b/sci-biology/NGSTools/NGSTools-2.0.5.ebuild
deleted file mode 100644
index 862983fec..0
--- a/sci-biology/NGSTools/NGSTools-2.0.5.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2 eutils
-
-S="${PV/-/_}"
-
-DESCRIPTION="Next Generation Sequencing Eclipse Plugin (CNV and indel 
discovery), aka NGSEP"
-HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home;
-SRC_URI="http://sourceforge.net/projects/ngsep/files/SourceCode/NGSTools_2.0.5.tar.gz;
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-util/eclipse-sdk"
-RDEPEND="${DEPEND}"

diff --git a/sci-biology/NGSTools/metadata.xml 
b/sci-biology/NGSTools/metadata.xml
deleted file mode 100644
index 642261079..0
--- a/sci-biology/NGSTools/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-   
-   mmokr...@fold.natur.cuni.cz
-   Martin Mokrejs
-   
-   
-   sci-biol...@gentoo.org
-   Gentoo Biology Project
-   
-   
-   ngsep
-   
-



[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/

2019-03-27 Thread Martin Mokrejs
commit: 2b44f30b60c65d2485250cb71e7dabe10a2694a6
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Wed Mar 27 22:45:47 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Wed Mar 27 22:45:47 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2b44f30b

sci-biology/bowtie: patch --interleaved, add KEYWORDS

Do not unset contents of CFLAGS and CXXFLAGS.
Thanks to ch4rr0 at
https://github.com/BenLangmead/bowtie2/issues/239

Add deemed patch from
https://github.com/BenLangmead/bowtie2/issues/240

Added KEYWORDS.

Closes: https://bugs.gentoo.org/649824
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 .../bowtie/{bowtie-2.3.5.ebuild => bowtie-2.3.5-r1.ebuild}  |  5 ++---
 sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch | 13 +
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/sci-biology/bowtie/bowtie-2.3.5.ebuild 
b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
similarity index 94%
rename from sci-biology/bowtie/bowtie-2.3.5.ebuild
rename to sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
index dd4d8be66..f79dcb9cb 100644
--- a/sci-biology/bowtie/bowtie-2.3.5.ebuild
+++ b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
@@ -12,7 +12,7 @@ 
SRC_URI="https://github.com/BenLangmead/${PN}2/releases/download/v${PV}/${PN}2-$
 
 LICENSE="GPL-3"
 SLOT="2"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
 
 IUSE="examples cpu_flags_x86_sse2 +tbb"
 
@@ -27,6 +27,7 @@ S="${WORKDIR}/${PN}2-${PV}"
 DOCS=( AUTHORS NEWS TUTORIAL )
 HTML_DOCS=( doc/{manual.html,style.css} )
 #PATCHES=( "${FILESDIR}/${P}-fix-c++14.patch" ) # needs 2.3.4.3 update
+PATCHES=( "${FILESDIR}"/bowtie-2.3.5-fix-interleaved.patch )
 
 pkg_pretend() {
if ! use cpu_flags_x86_sse2 ; then
@@ -40,8 +41,6 @@ src_compile() {
CC="$(tc-getCC)" \
CPP="$(tc-getCXX)" \
CXX="$(tc-getCXX)" \
-   CFLAGS="" \
-   CXXFLAGS="" \
EXTRA_FLAGS="${LDFLAGS}" \
RELEASE_FLAGS="${CXXFLAGS} -msse2" \
WITH_TBB="$(usex tbb 1 0)"

diff --git a/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch 
b/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch
new file mode 100644
index 0..b2f24a7fa
--- /dev/null
+++ b/sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch
@@ -0,0 +1,13 @@
+diff --git bowtie-2.3.5/bt2_search.cpp b/bt2_search.cpp
+index 1d53741..c59e39c 100644
+--- bowtie-2.3.5/bt2_search.cpp
 bowtie-2.3.5/bt2_search.cpp
+@@ -1673,7 +1673,7 @@ static void parseOptions(int argc, const char **argv) {
+<< "sequences must be specified with -1 and -2." << endl;
+   throw 1;
+   }
+-  if(interleaved && (format != FASTA || format != FASTQ)) {
++  if(interleaved && (format != FASTA && format != FASTQ)) {
+   cerr << "Error: --interleaved only works in combination with 
FASTA (-f) and FASTQ (-q) formats." << endl;
+   throw 1;
+   }



[gentoo-commits] proj/sci:master commit in: sci-biology/NGSEPplugin/

2019-03-27 Thread Martin Mokrejs
commit: d17dc3cdafd776660dcedd72f13ad798d0d55e24
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Wed Mar 27 16:23:53 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Wed Mar 27 16:23:53 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d17dc3cd

sci-biology/NGSEPplugin: some progress with the package

Still does not work.

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/NGSEPplugin/NGSEPplugin-3.3.1.ebuild | 35 
 sci-biology/NGSEPplugin/metadata.xml | 15 ++
 2 files changed, 50 insertions(+)

diff --git a/sci-biology/NGSEPplugin/NGSEPplugin-3.3.1.ebuild 
b/sci-biology/NGSEPplugin/NGSEPplugin-3.3.1.ebuild
new file mode 100644
index 0..ec13ffa46
--- /dev/null
+++ b/sci-biology/NGSEPplugin/NGSEPplugin-3.3.1.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="NGSEP with Eclipse Plugin (CNV and indel discovery)"
+HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home;
+SRC_URI="https://sourceforge.net/projects/ngsep/files/SourceCode/NGSEPplugin_${PV}.tar.gz;
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="
+   >=virtual/jdk-1.7:*
+   dev-java/jcommon
+   dev-util/eclipse-sdk
+   dev-java/htsjdk
+   sci-biology/NGSEPcore"
+RDEPEND="${DEPEND}
+   >=virtual/jre-1.7:*"
+
+S="${WORKDIR}/${PN}_${PV}"
+
+src_prepare(){
+   rm -f lib/NGSEPcore_3.3.1.jar lib/SortSam.jar lib/jcommon-1.0.17.jar 
lib/xchart-2.4.2.jar || die
+   default
+}
+
+src_install(){
+   java-pkg_dojar *.jar
+}

diff --git a/sci-biology/NGSEPplugin/metadata.xml 
b/sci-biology/NGSEPplugin/metadata.xml
new file mode 100644
index 0..642261079
--- /dev/null
+++ b/sci-biology/NGSEPplugin/metadata.xml
@@ -0,0 +1,15 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+   
+   mmokr...@fold.natur.cuni.cz
+   Martin Mokrejs
+   
+   
+   sci-biol...@gentoo.org
+   Gentoo Biology Project
+   
+   
+   ngsep
+   
+



[gentoo-commits] proj/sci:master commit in: sci-biology/NGSEPcore/

2019-03-27 Thread Martin Mokrejs
commit: 26f7eab8fcc5e6148f85e81a876d1362c28c8e4f
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Wed Mar 27 16:23:05 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Wed Mar 27 16:23:05 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=26f7eab8

sci-biology/NGSEPcore: some improvements with the package

Still unfinished work.

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild | 37 
 sci-biology/NGSEPcore/metadata.xml   | 15 +++
 2 files changed, 52 insertions(+)

diff --git a/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild 
b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild
new file mode 100644
index 0..3f844bf16
--- /dev/null
+++ b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="NGSEP (CNV and indel discovery)"
+HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home;
+SRC_URI="https://sourceforge.net/projects/ngsep/files/SourceCode/NGSEPcore_${PV}.tar.gz
+   
https://sourceforge.net/projects/ngsep/files/training/UserManualNGSEP_V330.pdf 
-> ${P}_UserManual.pdf
+   https://sourceforge.net/projects/ngsep/files/training/Tutorial.txt -> 
${P}_Tutorial.txt
+   https://sourceforge.net/projects/ngsep/files/training/QuickStart.txt -> 
${P}_QuickStart.txt"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-java/htsjdk"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${PN}_${PV}"
+
+src_prepare(){
+   rm -f *.jar lib/htsjdk-1.129.jar || die
+   default
+}
+
+src_compile(){
+   make -j1
+}
+
+src_install(){
+   java-pkg_dojar *.jar
+   dodoc "$DISTDIR}"/${P}_user_manual.pdf
+}

diff --git a/sci-biology/NGSEPcore/metadata.xml 
b/sci-biology/NGSEPcore/metadata.xml
new file mode 100644
index 0..642261079
--- /dev/null
+++ b/sci-biology/NGSEPcore/metadata.xml
@@ -0,0 +1,15 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+   
+   mmokr...@fold.natur.cuni.cz
+   Martin Mokrejs
+   
+   
+   sci-biol...@gentoo.org
+   Gentoo Biology Project
+   
+   
+   ngsep
+   
+



[gentoo-commits] proj/sci:master commit in: sci-biology/bamql/

2019-03-25 Thread Martin Mokrejs
commit: f96c7ec91d0add7dfef7af06a4d81bc97cf0b7d9
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Mar 25 23:56:31 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Mar 25 23:56:31 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f96c7ec9

sci-biology/bamql: switch to `$(use_enable ...)`

https://github.com/gentoo/sci/issues/907#issuecomment-476420962

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/bamql/bamql-1.6.1.ebuild | 6 ++
 sci-biology/bamql/bamql-.ebuild  | 6 ++
 2 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/sci-biology/bamql/bamql-1.6.1.ebuild 
b/sci-biology/bamql/bamql-1.6.1.ebuild
index dacad6029..f11a50278 100644
--- a/sci-biology/bamql/bamql-1.6.1.ebuild
+++ b/sci-biology/bamql/bamql-1.6.1.ebuild
@@ -30,8 +30,6 @@ src_prepare(){
 }
 
 src_configure(){
-   local myeconfargs=()
-   use static-libs && myeconfargs+=( "--enable-static=yes" ) || \
-   myeconfargs+=( "--enable-static=no" )
-   econf ${myeconfargs[@]}
+   econf \
+   $(use_enable static-libs static)
 }

diff --git a/sci-biology/bamql/bamql-.ebuild 
b/sci-biology/bamql/bamql-.ebuild
index cda5043a7..288aef6bc 100644
--- a/sci-biology/bamql/bamql-.ebuild
+++ b/sci-biology/bamql/bamql-.ebuild
@@ -30,8 +30,6 @@ src_prepare(){
 }
 
 src_configure(){
-   local myeconfargs=()
-   use static-libs && myeconfargs+=( "--enable-static=yes" ) || \
-   myeconfargs+=( "--enable-static=no" )
-   econf ${myeconfargs[@]}
+   econf \
+   $(use_enable static-libs static)
 }



[gentoo-commits] proj/sci:master commit in: sci-biology/bamql/, sci-biology/bamql/files/

2019-03-25 Thread Martin Mokrejs
commit: 732c892485ba23fb419d064b28cba2b0dd982f90
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Mar 25 23:52:45 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Mar 25 23:52:45 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=732c8924

sci-biology/bamql: remove dependency on llvm static libs

Thanks for the patch and guidance to François Bissey:
https://github.com/gentoo/sci/issues/907

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/bamql/bamql-1.6.1.ebuild   | 12 ++-
 sci-biology/bamql/bamql-.ebuild| 12 ++-
 .../bamql-1.6.1_drop_enable_static_llvm.patch  | 23 ++
 3 files changed, 37 insertions(+), 10 deletions(-)

diff --git a/sci-biology/bamql/bamql-1.6.1.ebuild 
b/sci-biology/bamql/bamql-1.6.1.ebuild
index 146793318..dacad6029 100644
--- a/sci-biology/bamql/bamql-1.6.1.ebuild
+++ b/sci-biology/bamql/bamql-1.6.1.ebuild
@@ -22,14 +22,16 @@ DEPEND="
dev-libs/libpcre"
 RDEPEND="${DEPEND}"
 
+PATCHES=( "${FILESDIR}"/bamql-1.6.1_drop_enable_static_llvm.patch )
+
 src_prepare(){
-   eautoreconf
default
+   eautoreconf
 }
 
 src_configure(){
-   local mycmakeargs=()
-   use static-libs && mycmakeargs+=( "--enable-static=yes" 
"--enable-static-llvm=yes" ) || \
-   mycmakeargs+=( "--enable-static=no" "--enable-static-llvm=no" )
-   econf ${mycmakeargs[@]}
+   local myeconfargs=()
+   use static-libs && myeconfargs+=( "--enable-static=yes" ) || \
+   myeconfargs+=( "--enable-static=no" )
+   econf ${myeconfargs[@]}
 }

diff --git a/sci-biology/bamql/bamql-.ebuild 
b/sci-biology/bamql/bamql-.ebuild
index e9730e73b..cda5043a7 100644
--- a/sci-biology/bamql/bamql-.ebuild
+++ b/sci-biology/bamql/bamql-.ebuild
@@ -22,14 +22,16 @@ DEPEND="
dev-libs/libpcre"
 RDEPEND="${DEPEND}"
 
+PATCHES=( "${FILESDIR}"/bamql-1.6.1_drop_enable_static_llvm.patch )
+
 src_prepare(){
-   eautoreconf
default
+   eautoreconf
 }
 
 src_configure(){
-   local mycmakeargs=()
-   use static-libs && mycmakeargs+=( "--enable-static=yes" 
"--enable-static-llvm=yes" ) || \
-   mycmakeargs+=( "--enable-static=no" "--enable-static-llvm=no" )
-   econf ${mycmakeargs[@]}
+   local myeconfargs=()
+   use static-libs && myeconfargs+=( "--enable-static=yes" ) || \
+   myeconfargs+=( "--enable-static=no" )
+   econf ${myeconfargs[@]}
 }

diff --git a/sci-biology/bamql/files/bamql-1.6.1_drop_enable_static_llvm.patch 
b/sci-biology/bamql/files/bamql-1.6.1_drop_enable_static_llvm.patch
new file mode 100644
index 0..e76d245c8
--- /dev/null
+++ b/sci-biology/bamql/files/bamql-1.6.1_drop_enable_static_llvm.patch
@@ -0,0 +1,23 @@
+--- bamql-1.6.1/m4/ax_llvm.m4.old  2019-03-25 23:17:05.190272994 +0100
 bamql-1.6.1/m4/ax_llvm.m4  2019-03-25 23:16:10.698775171 +0100
+@@ -28,7 +28,6 @@
+ 
+ AC_DEFUN([AX_LLVM],
+ [
+-AC_ARG_ENABLE([static-llvm], AS_HELP_STRING([--enable-static-llvm], [compiled 
against the static LLVM libraries, instead of the shared library.]), 
[enable_static_llvm=yes])
+ AC_ARG_WITH([llvm-config],
+   AS_HELP_STRING([--with-llvm-config@<:@=FILE@:>@], [ the name or or 
complete path to the llvm-config script for llvm (optional)]),
+   [
+@@ -53,11 +52,7 @@
+   [$1]_LIBDIR="$($ac_llvm_config_path --libdir)"
+   LLVM_VERSION="$($ac_llvm_config_path --version | cut -f 1-2 -d 
.)"
+   LLVM_COMPONENTS="$2"
+-  if test "x$enable_static_llvm" != "xyes" ; then
+-  [$1]_LIBS="$($ac_llvm_config_path --libs --system-libs 
--link-static $LLVM_COMPONENTS | tr '\n' ' ')"
+-  else
+-  [$1]_LIBS="$($ac_llvm_config_path --libs --link-shared 
$LLVM_COMPONENTS | tr '\n' ' ')"
+-  fi
++  [$1]_LIBS="$($ac_llvm_config_path --libs $LLVM_COMPONENTS | tr 
'\n' ' ')"
+ 
+   AC_REQUIRE([AC_PROG_CXX])
+   CPPFLAGS_SAVED="$CPPFLAGS"



[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-blast+/

2019-03-25 Thread Martin Mokrejs
commit: 868fbe5eeaa38a05f1ae2775a286b8d2ae651572
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Mar 25 12:15:59 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Mar 25 12:15:59 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=868fbe5e

sci-biology/ncbi-blast+: EAPI7 bump, remove unused variable

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild| 8 
 sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild| 8 
 sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild | 6 +++---
 .../{ncbi-blast+-2.6.0.ebuild => ncbi-blast+-2.8.1.ebuild}   | 9 +
 4 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild 
b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index dd6f3444f..d6c529b57 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -1,13 +1,12 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 PYTHON_COMPAT=( python2_7 )
 
 inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
 
-MY_PV="2.2.30"
 MY_P="ncbi-blast-${PV}+-src"
 # workdir/ncbi-blast-2.2.30+-src
 # 
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
@@ -134,6 +133,7 @@ src_prepare() {
# Temporarily disabling eautoconf because we patch configure via 
${P}-support-autoconf-2.60.patch
# eautoconf # keep it disabled until we can ensure 2.59 is installed
# beware 12.0.0. and previous required autoconf-2.59, a patch for 
12.0.0 brings autoconf-2.60 support
+   default
 }
 
 # possibly place modified contents of ${W}/src/build-system/config.site.ncbi 
and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
@@ -279,7 +279,7 @@ src_configure() {
--prefix="${EPREFIX}/usr" \
--libdir=/usr/lib64 \
--with-flat-makefile \
-   ${myconf[@]} || die
+   ${myconf[@]} || die "gcc 7 or newer were not used by upstream 
hence unsupported"
 #--without-debug \
 #  --with-bin-release \
 #  --with-bincopy \

diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild 
b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index 4622ac976..40d060bf5 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -1,13 +1,12 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 PYTHON_COMPAT=( python2_7 )
 
 inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
 
-MY_PV="2.2.30"
 MY_P="ncbi-blast-${PV}+-src"
 # workdir/ncbi-blast-2.2.30+-src
 # 
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
@@ -137,6 +136,7 @@ src_prepare() {
# Temporarily disabling eautoconf because we patch configure via 
${P}-support-autoconf-2.60.patch
# eautoconf # keep it disabled until we can ensure 2.59 is installed
# beware 12.0.0. and previous required autoconf-2.59, a patch for 
12.0.0 brings autoconf-2.60 support
+   default
 }
 
 # possibly place modified contents of ${W}/src/build-system/config.site.ncbi 
and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site
@@ -282,7 +282,7 @@ src_configure() {
--prefix="${EPREFIX}/usr" \
--libdir=/usr/lib64 \
--with-flat-makefile \
-   ${myconf[@]} || die
+   ${myconf[@]} || die "gcc 7 or newer were not used by upstream 
hence unsupported"
 #--without-debug \
 #  --with-bin-release \
 #  --with-bincopy \

diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild 
b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index 6adbefad3..0a826b779 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -1,13 +1,12 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 PYTHON_COMPAT=( python2_7 )
 
 inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
 
-MY_PV="2.3.0"
 MY_P="ncbi-blast-${PV}+-src"
 # workdir/ncbi-blast-2.2.30+-src
 # 
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz
@@ -138,6 +137,7 @@ src_prepare() {
# Temporarily disabling eautoconf because we 

[gentoo-commits] proj/sci:master commit in: sci-biology/tablet/

2019-03-25 Thread Martin Mokrejs
commit: b7426d8f1df55eb09a50815dc95882363bb44895
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Mar 25 11:56:28 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Mar 25 11:56:28 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b7426d8f

sci-biology/tablet: still installs a mix of our and bundled jars

We have only dev-java/htdjdk-2.3.0 in the tree as newer versions
use gradle. The tablet-1.17.08.17 lacks the lib/htsjdk-2.0.11.jar
so we cannot install it. Use sci-biology/tablet-bin instead.

https://github.com/cropgeeks/tablet/issues/6

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/tablet/tablet-1.17.08.17.ebuild | 29 +
 sci-biology/tablet/tablet-.ebuild   | 17 ++---
 2 files changed, 35 insertions(+), 11 deletions(-)

diff --git a/sci-biology/tablet/tablet-1.17.08.17.ebuild 
b/sci-biology/tablet/tablet-1.17.08.17.ebuild
index 08a272961..158caba78 100644
--- a/sci-biology/tablet/tablet-1.17.08.17.ebuild
+++ b/sci-biology/tablet/tablet-1.17.08.17.ebuild
@@ -16,7 +16,7 @@ if [ "$PV" == "" ]; then
KEYWORDS=""
 else
SRC_URI="https://github.com/cropgeeks/tablet/archive/${PV}.tar.gz -> 
${P}.tar.gz"
-   KEYWORDS=""
+   KEYWORDS="" # lacks lib/htsjdk-2.0.11.jar
 fi
 
 LICENSE="BSD-2"
@@ -29,11 +29,17 @@ DEPEND="${PYTHON_DEPS}
>=virtual/jdk-1.8:*"
 RDEPEND="${PYTHON_DEPS}
>=virtual/jre-1.8:*
-   >=dev-java/commons-compress-1.4.1"
-# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, 
htsjdk-2.11.0.jar
-# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not 
sci-biology/samtools either
-
-S="${WORKDIR}"
+   >=dev-java/commons-compress-1.4.1
+   dev-java/htsjdk"
+# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar
+# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3
+# samtools-linux64.jar is not sci-biology/samtools but 0.1.12a (r862)
+# needs htsjdk-2.0.11.jar
+
+src_compile(){
+   mkdir -p classes || die
+   ant jar || die
+}
 
 src_install() {
java-pkg_dojar lib/tablet.jar
@@ -41,8 +47,15 @@ src_install() {
java-pkg_dojar lib/tablet-resources.jar
java-pkg_dojar lib/flamingo.jar
java-pkg_dojar lib/scri-commons.jar
-   java-pkg_dojar lib/samtools*.jar
-   java-pkg_dojar lib/htsjdk*.jar # is htsjdk-2.11.0 in tablet-1.17.08.17
+   java-pkg_dojar lib/samtools-all.jar
+   if [ "${ABI}" == "amd64" ]; then
+   java-pkg_dojar lib/samtools-linux64.jar
+   fi
+   if [ "${ABI}" == "x86" ]; then
+   java-pkg_dojar lib/samtools-linux32.jar
+   fi
+   # is the tar.gz tarball missing by mistake lib/htsjdk*.jar ?
+   # java-pkg_dojar lib/htsjdk*.jar # is htsjdk-2.11.0 in tablet-1.17.08.17
java-pkg_dojar lib/sqlite-jdbc*.jar
 
echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet

diff --git a/sci-biology/tablet/tablet-.ebuild 
b/sci-biology/tablet/tablet-.ebuild
index 01759c6b4..5cebde785 100644
--- a/sci-biology/tablet/tablet-.ebuild
+++ b/sci-biology/tablet/tablet-.ebuild
@@ -31,9 +31,14 @@ RDEPEND="${PYTHON_DEPS}
>=virtual/jre-1.8:*
>=dev-java/commons-compress-1.4.1"
 # contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, 
htsjdk-2.11.0.jar
-# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not 
sci-biology/samtools
+# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3
+# samtools-linux64.jar is not sci-biology/samtools but 0.1.12a (r862)
 
 #S="${WORKDIR}"
+src_compile(){
+   mkdir -p classes || die
+   ant jar || die
+}
 
 src_install() {
java-pkg_dojar lib/tablet.jar
@@ -41,8 +46,14 @@ src_install() {
java-pkg_dojar lib/tablet-resources.jar
java-pkg_dojar lib/flamingo.jar
java-pkg_dojar lib/scri-commons.jar
-   java-pkg_dojar lib/samtools*.jar
-   java-pkg_dojar lib/htsjdk*.jar
+   java-pkg_dojar lib/samtools-all.jar
+   if [ "${ABI}" == "amd64" ]; then
+   java-pkg_dojar lib/samtools-linux64.jar
+   fi
+   if [ "${ABI}" == "x86" ]; then
+   java-pkg_dojar lib/samtools-linux32.jar
+   fi
+   java-pkg_dojar lib/htsjdk*.jar # is htsjdk-2.11.0 in tablet-1.17.08.17
java-pkg_dojar lib/sqlite-jdbc*.jar
 
echo "PATH=${EPREFIX}/usr/share/${PN}" > 99Tablet



[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/

2019-03-25 Thread Martin Mokrejs
commit: a12a2d7f3f65eb66e44d3fc907f4b24e85ef201a
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Mar 25 11:50:28 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Mar 25 11:50:28 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a12a2d7f

dev-java/htsjdk: drop old 2.1.0 version

 dev-java/htsjdk/htsjdk-2.1.0.ebuild | 47 -
 1 file changed, 47 deletions(-)

diff --git a/dev-java/htsjdk/htsjdk-2.1.0.ebuild 
b/dev-java/htsjdk/htsjdk-2.1.0.ebuild
deleted file mode 100644
index c94f79781..0
--- a/dev-java/htsjdk/htsjdk-2.1.0.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats"
-HOMEPAGE="https://samtools.github.io/htsjdk/;
-SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> 
${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="dev-java/commons-jexl:2
-   dev-java/commons-compress:0
-   dev-java/commons-logging:0"
-
-DEPEND=">=virtual/jdk-1.8
-   ${CDEPEND}"
-RDEPEND=">=virtual/jre-1.8
-   ${CDEPEND}"
-
-EANT_BUILD_TARGET="all"
-EANT_NEEDS_TOOLS="true"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging"
-
-java_prepare() {
-   default
-   rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die
-}
-
-src_install() {
-   cd dist || die
-
-   for i in *.jar; do
-   java-pkg_newjar $i ${i/-[0-9]*.jar/.jar}
-   done
-
-   use source && java-pkg_dosrc "${S}"/src/java/*
-   use doc && java-pkg_dojavadoc "${S}"/javadoc
-}



[gentoo-commits] proj/sci:master commit in: sci-biology/gffread/files/, sci-biology/gffread/

2019-03-25 Thread Martin Mokrejs
commit: e55065dc88a894edab65609ffdd4e275cdcd4bd0
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Mar 25 11:49:49 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Mar 25 11:49:49 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e55065dc

sci-biology/gffread: bump to 0.11.0, drop old patch, use sed hackery

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/gffread/files/Makefile.patch   | 39 --
 ...gffread-0.9.12.ebuild => gffread-0.11.0.ebuild} | 25 +++---
 2 files changed, 20 insertions(+), 44 deletions(-)

diff --git a/sci-biology/gffread/files/Makefile.patch 
b/sci-biology/gffread/files/Makefile.patch
deleted file mode 100644
index 35e6b088e..0
--- a/sci-biology/gffread/files/Makefile.patch
+++ /dev/null
@@ -1,39 +0,0 @@
 gffread-0.9.12/Makefile2018-06-26 09:52:26.024747027 +0200
-+++ gffread-0.9.12/Makefile2018-06-26 09:52:41.845177021 +0200
-@@ -1,4 +1,4 @@
--GCLDIR := ../gclib
-+GCLDIR := ../gclib-0.10.2
- SEARCHDIRS := -I. -I${GCLDIR}
- 
- SYSTYPE := $(shell uname)
-@@ -10,7 +10,7 @@
- MARCH = 
- endif
- 
--CC  := g++
-+CXX  ?= g++
- 
- BASEFLAGS  := -Wall -Wextra ${SEARCHDIRS} $(MARCH) -D_FILE_OFFSET_BITS=64 \
- -D_LARGEFILE_SOURCE -D_REENTRANT -fno-strict-aliasing -fno-exceptions 
-fno-rtti
-@@ -26,15 +26,17 @@
- GCC45OPTMAIN :=
- 
- ifeq ($(findstring release,$(MAKECMDGOALS)),release)
--  CFLAGS := -O2 -DNDEBUG $(BASEFLAGS)
-+  CXXFLAGS ?= -O2
-+  CXXFLAGS += -DNDEBUG $(BASEFLAGS)
-   LDFLAGS :=
- else
--  CFLAGS := -g -DDEBUG $(BASEFLAGS)
--  LDFLAGS := -g
-+  CXXFLAGS ?= -g
-+  CXXFLAGS += -DDEBUG $(BASEFLAGS)
-+  LDFLAGS ?= -g
- endif
- 
- %.o : %.cpp
--  ${CC} ${CFLAGS} -c $< -o $@
-+  ${CXX} ${CXXFLAGS} -c $< -o $@
- 
- # C/C++ linker
- 

diff --git a/sci-biology/gffread/gffread-0.9.12.ebuild 
b/sci-biology/gffread/gffread-0.11.0.ebuild
similarity index 50%
rename from sci-biology/gffread/gffread-0.9.12.ebuild
rename to sci-biology/gffread/gffread-0.11.0.ebuild
index fc60b9a81..bfedb57a5 100644
--- a/sci-biology/gffread/gffread-0.9.12.ebuild
+++ b/sci-biology/gffread/gffread-0.11.0.ebuild
@@ -1,20 +1,35 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
+
+inherit toolchain-funcs
 
 DESCRIPTION="GFF/GTF utility providing format conversions, filter/extract 
regions from FASTA"
 HOMEPAGE="http://ccb.jhu.edu/software/stringtie/gff.shtml
https://github.com/gpertea/gffread;
 SRC_URI="https://github.com/gpertea/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
-   https://github.com/gpertea/gclib/archive/v0.10.2.tar.gz -> 
gclib-0.10.2.tar.gz"
+   https://github.com/gpertea/gclib/archive/v${PV}.tar.gz -> 
gclib-${PV}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}"
 
-PATCHES=( "${FILESDIR}"/Makefile.patch )
+src_prepare(){
+   src_unpack "${DISTDIR}"/gclib-${PV}.tar.gz
+   default
+   sed -e "s/-g -O3/${CXXFLAGS}/" -i Makefile || die
+   cd .. && ln -s gclib-"${PV}" gclib || die
+}
+
+src_compile(){
+   emake release
+}
+
+src_install(){
+   dobin gffread
+}



[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/

2019-03-25 Thread Martin Mokrejs
commit: 922b05adcf80432d8e8212128b90b456b8ad3fc5
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Mar 25 11:20:55 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Mar 25 11:20:55 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=922b05ad

sci-biology/bowtie: update SRC_URI and hash for 2.3.5

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/bowtie/{bowtie-2.3.4.3.ebuild => bowtie-2.3.5.ebuild} | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-biology/bowtie/bowtie-2.3.4.3.ebuild 
b/sci-biology/bowtie/bowtie-2.3.5.ebuild
similarity index 93%
rename from sci-biology/bowtie/bowtie-2.3.4.3.ebuild
rename to sci-biology/bowtie/bowtie-2.3.5.ebuild
index eea3059cf..dd4d8be66 100644
--- a/sci-biology/bowtie/bowtie-2.3.4.3.ebuild
+++ b/sci-biology/bowtie/bowtie-2.3.5.ebuild
@@ -8,6 +8,7 @@ inherit toolchain-funcs
 DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
 HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/;
 
SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
+SRC_URI="https://github.com/BenLangmead/${PN}2/releases/download/v${PV}/${PN}2-${PV}-source.zip;
 
 LICENSE="GPL-3"
 SLOT="2"



[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/

2019-03-25 Thread Martin Mokrejs
commit: 6d3f8d736bf1a9653f516c3e959a97948c61f843
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Mar 25 11:08:21 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Mar 25 11:08:21 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6d3f8d73

dev-java/htsjdk: 2.3.0 which was the last using Apache ant

Bump to EAPI7

Building does not work since sandbox has now no network access.

Downloading https://services.gradle.org/distributions/gradle-5.2.1-bin.zip

Exception in thread "main" java.net.SocketException: Network
is unreachable (connect failed)

htsjdk calls some `gradlew` wrapper so the recent ebuilds
need more work to use dev-java/gradle-bin package.

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 dev-java/htsjdk/htsjdk-2.1.0.ebuild   | 4 ++--
 dev-java/htsjdk/{htsjdk-2.5.1.ebuild => htsjdk-2.19.0.ebuild} | 7 ---
 dev-java/htsjdk/{htsjdk-2.2.2.ebuild => htsjdk-2.3.0.ebuild}  | 4 ++--
 dev-java/htsjdk/htsjdk-.ebuild| 7 ---
 4 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/dev-java/htsjdk/htsjdk-2.1.0.ebuild 
b/dev-java/htsjdk/htsjdk-2.1.0.ebuild
index fc2dd6e8a..c94f79781 100644
--- a/dev-java/htsjdk/htsjdk-2.1.0.ebuild
+++ b/dev-java/htsjdk/htsjdk-2.1.0.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 JAVA_PKG_IUSE="doc source"
 

diff --git a/dev-java/htsjdk/htsjdk-2.5.1.ebuild 
b/dev-java/htsjdk/htsjdk-2.19.0.ebuild
similarity index 91%
rename from dev-java/htsjdk/htsjdk-2.5.1.ebuild
rename to dev-java/htsjdk/htsjdk-2.19.0.ebuild
index 755a6fa1f..349e56673 100644
--- a/dev-java/htsjdk/htsjdk-2.5.1.ebuild
+++ b/dev-java/htsjdk/htsjdk-2.19.0.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 JAVA_PKG_IUSE="doc source"
 
@@ -18,7 +18,8 @@ KEYWORDS=""
 
 CDEPEND="dev-java/commons-jexl:2
dev-java/commons-compress:0
-   dev-java/commons-logging:0"
+   dev-java/commons-logging:0
+   dev-java/gradle-bin:*"
 
 DEPEND=">=virtual/jdk-1.8
${CDEPEND}"

diff --git a/dev-java/htsjdk/htsjdk-2.2.2.ebuild 
b/dev-java/htsjdk/htsjdk-2.3.0.ebuild
similarity index 95%
rename from dev-java/htsjdk/htsjdk-2.2.2.ebuild
rename to dev-java/htsjdk/htsjdk-2.3.0.ebuild
index fc2dd6e8a..c94f79781 100644
--- a/dev-java/htsjdk/htsjdk-2.2.2.ebuild
+++ b/dev-java/htsjdk/htsjdk-2.3.0.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 JAVA_PKG_IUSE="doc source"
 

diff --git a/dev-java/htsjdk/htsjdk-.ebuild 
b/dev-java/htsjdk/htsjdk-.ebuild
index b4a3c1441..2123bbc55 100644
--- a/dev-java/htsjdk/htsjdk-.ebuild
+++ b/dev-java/htsjdk/htsjdk-.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 JAVA_PKG_IUSE="doc source"
 
@@ -18,7 +18,8 @@ KEYWORDS=""
 
 CDEPEND="dev-java/commons-jexl:2
dev-java/commons-compress:0
-   dev-java/commons-logging:0"
+   dev-java/commons-logging:0
+   dev-java/gradle-bin:*"
 
 DEPEND=">=virtual/jdk-1.8
${CDEPEND}"



[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/

2019-03-25 Thread Martin Mokrejs
commit: 6520aa795d79c63f0566d8b1059acb95899f8f81
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Mar 25 09:40:18 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Mar 25 09:40:18 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6520aa79

sci-biology/tablet-bin: update license

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild | 14 +-
 1 file changed, 1 insertion(+), 13 deletions(-)

diff --git a/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild 
b/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
index 51f2d7921..fb89b4208 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
@@ -14,19 +14,7 @@ SRC_URI="
amd64? ( 
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x64_$(replace_all_version_separators
 _).sh -> ${P}.sh )
http://bioinf.hutton.ac.uk/tablet/additional/coveragestats.py;
 
-# Upstream says regarding source code unavailability:
-# Tablet uses a modified version of the BSD License which has been edited to
-# remove references to distribution and use in source forms. This means that
-# we are happy for you to distribute and use Tablet however you please, but we
-# do not (yet) want to make the source code publicly available.
-
-# The licence file itself is in the installer, and ends up on disk after
-# installation at /opt/Tablet/docs/tablet.html
-# The original BSD licence was modified to remove references to distribution
-# and use in source forms, because we cannot make the source code available
-# for Tablet.
-
-LICENSE="Tablet"
+LICENSE="BSD-2"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""



[gentoo-commits] proj/sci:master commit in: licenses/

2019-03-25 Thread Martin Mokrejs
commit: 3f67fa52b5fb5c0a3958751fe227032e7fe88cfa
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Mar 25 09:40:29 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Mar 25 09:40:29 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3f67fa52

Drop BSD-2 license of sci-biology/tablet

 licenses/Tablet | 10 --
 1 file changed, 10 deletions(-)

diff --git a/licenses/Tablet b/licenses/Tablet
deleted file mode 100644
index 296b09c7f..0
--- a/licenses/Tablet
+++ /dev/null
@@ -1,10 +0,0 @@
-Copyright (c) 2009-2014, Information & Computational Sciences, The James 
Hutton Institute.
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without 
modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this 
list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice, 
this list of conditions and the following disclaimer in the documentation 
and/or other materials provided with the distribution.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” 
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE 
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL 
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR 
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, 
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE 
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.



[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/

2019-03-25 Thread Martin Mokrejs
commit: ad4cf1cc47d4dadaec146d2515ae9645c062adcd
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Mar 25 09:30:59 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Mar 25 09:30:59 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ad4cf1cc

sci-biology/tablet-bin: use https for the new homepage

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild 
b/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
index 6934743b1..51f2d7921 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 )
 inherit java-pkg-2 python-r1
 
 DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
-HOMEPAGE="http://ics.hutton.ac.uk/tablet/;
+HOMEPAGE="https://ics.hutton.ac.uk/tablet;
 SRC_URI="
x86? ( 
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x86_$(replace_all_version_separators
 _).sh -> ${P}.sh )
amd64? ( 
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x64_$(replace_all_version_separators
 _).sh -> ${P}.sh )



[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/

2019-03-25 Thread Martin Mokrejs
commit: 9f62533afcb9014961a43534237d3a31a7aa4d00
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Mar 25 09:03:15 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Mar 25 09:03:15 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9f62533a

sci-biology/tablet-bin: version bump, ebuild cleanup

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 ...tablet-bin-1.16.09.06.ebuild => tablet-bin-1.17.08.17.ebuild} | 9 +
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild 
b/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
similarity index 93%
rename from sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
rename to sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
index 401515e00..6934743b1 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -10,8 +10,8 @@ inherit java-pkg-2 python-r1
 DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
 HOMEPAGE="http://ics.hutton.ac.uk/tablet/;
 SRC_URI="
-   x86? ( 
http://bioinf.hutton.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators
 _).sh -> ${P}.sh )
-   amd64? ( 
http://bioinf.hutton.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators
 _).sh -> ${P}.sh )
+   x86? ( 
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x86_$(replace_all_version_separators
 _).sh -> ${P}.sh )
+   amd64? ( 
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x64_$(replace_all_version_separators
 _).sh -> ${P}.sh )
http://bioinf.hutton.ac.uk/tablet/additional/coveragestats.py;
 
 # Upstream says regarding source code unavailability:
@@ -36,7 +36,8 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 DEPEND="${PYTHON_DEPS}
app-text/dos2unix
>=virtual/jdk-1.8:*"
-RDEPEND="${DEPEND}"
+RDEPEND="${DEPEND}
+   >=virtual/jre-1.8:*"
 # contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
 # sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not 
sci-biology/samtools either
 # replacing picard.jar with a symlink to picard.jar from sci-biology.picard 
does not help either



[gentoo-commits] proj/sci:master commit in: sci-biology/tablet/

2019-03-25 Thread Martin Mokrejs
commit: d54980d211f803108c958cd6b255827a0f9bd2a5
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Mar 25 09:25:31 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Mar 25 09:25:31 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d54980d2

sci-biology/tablet: drop old version

 sci-biology/tablet/tablet-1.15.09.01.ebuild | 51 -
 1 file changed, 51 deletions(-)

diff --git a/sci-biology/tablet/tablet-1.15.09.01.ebuild 
b/sci-biology/tablet/tablet-1.15.09.01.ebuild
deleted file mode 100644
index c0b67d139..0
--- a/sci-biology/tablet/tablet-1.15.09.01.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit java-pkg-2 java-ant-2 python-r1
-
-# [ "$PV" == "" ] && inherit subversion
-inherit subversion
-
-DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
-HOMEPAGE="http://bioinf.scri.ac.uk/tablet/;
-if [ "$PV" == "" ]; then
-   ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/;
-   KEYWORDS=""
-else
-   ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV};
-   KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="Tablet"
-SLOT="0"
-IUSE=""
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="${PYTHON_DEPS}
-   >=virtual/jdk-1.8:*"
-RDEPEND="${PYTHON_DEPS}
-   >=virtual/jre-1.8:*"
-# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
-# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not 
sci-biology/samtools either
-# replacing picard.jar with a symlink to picard.jar from sci-biology.picard 
does not help either
-
-S="${WORKDIR}"
-
-src_install() {
-   java-pkg_dojar lib/tablet.jar
-   java-pkg_dolauncher ${PN}
-   java-pkg_dojar lib/tablet-resources.jar
-   java-pkg_dojar lib/flamingo.jar
-   java-pkg_dojar lib/scri-commons.jar
-   java-pkg_dojar lib/samtools*.jar
-   java-pkg_dojar lib/picard*.jar
-   java-pkg_dojar lib/sqlite-jdbc*.jar
-
-   echo "PATH=${EPREFIX}/usr/share/${PN}/" > 99Tablet
-   doenvd 99Tablet
-}



[gentoo-commits] proj/sci:master commit in: sci-biology/tablet/

2019-03-25 Thread Martin Mokrejs
commit: b7d442c1ad60516bf1f2e25bdb4f7287ac29a0cd
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Mar 25 09:30:16 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Mar 25 09:30:16 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b7d442c1

sci-biology/tablet: update ebuild

New homepage, switch from svn to github, new license, switch
from picard to htsjdk

There is no ./classes/ so `ant build` does not work for me.

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 ...-1.16.09.06.ebuild => tablet-1.17.08.17.ebuild} | 25 ++--
 sci-biology/tablet/tablet-.ebuild  | 27 +++---
 2 files changed, 25 insertions(+), 27 deletions(-)

diff --git a/sci-biology/tablet/tablet-1.16.09.06.ebuild 
b/sci-biology/tablet/tablet-1.17.08.17.ebuild
similarity index 63%
rename from sci-biology/tablet/tablet-1.16.09.06.ebuild
rename to sci-biology/tablet/tablet-1.17.08.17.ebuild
index e72339d61..08a272961 100644
--- a/sci-biology/tablet/tablet-1.16.09.06.ebuild
+++ b/sci-biology/tablet/tablet-1.17.08.17.ebuild
@@ -1,26 +1,25 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 PYTHON_COMPAT=( python2_7 )
 
 inherit java-pkg-2 java-ant-2 python-r1
 
-# [ "$PV" == "" ] && inherit subversion
-inherit subversion
+[ "$PV" == "" ] && inherit git-r3
 
 DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
-HOMEPAGE="http://bioinf.scri.ac.uk/tablet/;
+HOMEPAGE="https://ics.hutton.ac.uk/tablet;
 if [ "$PV" == "" ]; then
-   ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/;
+   EGIT_REPO_URI="https://github.com/cropgeeks/tablet.git;
KEYWORDS=""
 else
-   ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV};
-   KEYWORDS="~amd64 ~x86"
+   SRC_URI="https://github.com/cropgeeks/tablet/archive/${PV}.tar.gz -> 
${P}.tar.gz"
+   KEYWORDS=""
 fi
 
-LICENSE="Tablet"
+LICENSE="BSD-2"
 SLOT="0"
 IUSE=""
 
@@ -29,10 +28,10 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 DEPEND="${PYTHON_DEPS}
>=virtual/jdk-1.8:*"
 RDEPEND="${PYTHON_DEPS}
-   >=virtual/jre-1.8:*"
-# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
+   >=virtual/jre-1.8:*
+   >=dev-java/commons-compress-1.4.1"
+# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, 
htsjdk-2.11.0.jar
 # sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not 
sci-biology/samtools either
-# replacing picard.jar with a symlink to picard.jar from sci-biology.picard 
does not help either
 
 S="${WORKDIR}"
 
@@ -43,7 +42,7 @@ src_install() {
java-pkg_dojar lib/flamingo.jar
java-pkg_dojar lib/scri-commons.jar
java-pkg_dojar lib/samtools*.jar
-   java-pkg_dojar lib/picard*.jar # is picard-1.113 in tablet-1.16.09.06
+   java-pkg_dojar lib/htsjdk*.jar # is htsjdk-2.11.0 in tablet-1.17.08.17
java-pkg_dojar lib/sqlite-jdbc*.jar
 
echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet

diff --git a/sci-biology/tablet/tablet-.ebuild 
b/sci-biology/tablet/tablet-.ebuild
index 467895e5d..01759c6b4 100644
--- a/sci-biology/tablet/tablet-.ebuild
+++ b/sci-biology/tablet/tablet-.ebuild
@@ -1,26 +1,25 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 PYTHON_COMPAT=( python2_7 )
 
 inherit java-pkg-2 java-ant-2 python-r1
 
-# [ "$PV" == "" ] && inherit subversion
-inherit subversion
+[ "$PV" == "" ] && inherit git-r3
 
 DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
-HOMEPAGE="http://bioinf.scri.ac.uk/tablet/;
+HOMEPAGE="https://ics.hutton.ac.uk/tablet;
 if [ "$PV" == "" ]; then
-   ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/trunk/;
+   EGIT_REPO_URI="https://github.com/cropgeeks/tablet.git;
KEYWORDS=""
 else
-   ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV};
+   SRC_URI="https://github.com/cropgeeks/tablet/archive/${PV}.tar.gz -> 
${P}.tar.gz"
KEYWORDS=""
 fi
 
-LICENSE="Tablet"
+LICENSE="BSD-2"
 SLOT="0"
 IUSE=""
 
@@ -29,12 +28,12 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}"
 DEPEND="${PYTHON_DEPS}
>=virtual/jdk-1.8:*"
 RDEPEND="${PYTHON_

[gentoo-commits] proj/sci:master commit in: sci-biology/MolBioLib/

2019-03-25 Thread Martin Mokrejs
commit: 487854338866a64efbd9ec434743f7ab7a23bccd
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Mar 25 08:52:33 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Mar 25 08:52:33 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=48785433

sci-biology/MolBioLib: fix RDEPEND.suspect at least

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/MolBioLib/MolBioLib-5.ebuild | 19 ++-
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/sci-biology/MolBioLib/MolBioLib-5.ebuild 
b/sci-biology/MolBioLib/MolBioLib-5.ebuild
index 681758724..ac54cfcaf 100644
--- a/sci-biology/MolBioLib/MolBioLib-5.ebuild
+++ b/sci-biology/MolBioLib/MolBioLib-5.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-DESCRIPTION="C++11 framework for rapid develop and deploy of bioinformatic 
tasks"
+DESCRIPTION="C++11 framework for bioinformatics tasks"
 HOMEPAGE="https://sourceforge.net/projects/molbiolib;
 
SRC_URI="https://sourceforge.net/projects/molbiolib/files/MolBioLib_public.version${PV}.tar.gz;
 
@@ -12,16 +12,16 @@ SLOT="0"
 KEYWORDS="" # does not build
 IUSE="doc"
 
-# contains bundled samtools-0.1.18 and bamtools (pezmaster31-bamtools-d553a62) 
which contains jsoncpp
-# also needs app-doc/doxygen
+# contains bundled samtools-0.1.18 and bamtools (pezmaster31-bamtools-d553a62)
+# which contains jsoncpp, also needs app-doc/doxygen
 DEPEND="
dev-lang/perl
sys-devel/gcc:*
sys-devel/clang:*
-   >=sci-biology/samtools-0.1.18:0
-   =sci-biology/samtools-0.1.18:0.1-legacy
+   

[gentoo-commits] proj/sci:master commit in: sci-biology/bamql/

2019-03-25 Thread Martin Mokrejs
commit: 47b0727a452b00a0552a3094eff49fc44a2ea9fe
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Mar 25 08:40:46 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Mar 25 08:40:46 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=47b0727a

sci-biology/bamql: bump to EAPI7

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/bamql/bamql-1.6.1.ebuild | 2 +-
 sci-biology/bamql/bamql-.ebuild  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/bamql/bamql-1.6.1.ebuild 
b/sci-biology/bamql/bamql-1.6.1.ebuild
index 535b31f44..146793318 100644
--- a/sci-biology/bamql/bamql-1.6.1.ebuild
+++ b/sci-biology/bamql/bamql-1.6.1.ebuild
@@ -1,7 +1,7 @@
 # Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit autotools eutils
 

diff --git a/sci-biology/bamql/bamql-.ebuild 
b/sci-biology/bamql/bamql-.ebuild
index 409804dc7..e9730e73b 100644
--- a/sci-biology/bamql/bamql-.ebuild
+++ b/sci-biology/bamql/bamql-.ebuild
@@ -1,7 +1,7 @@
 # Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit autotools git-r3
 



[gentoo-commits] proj/sci:master commit in: sci-biology/bamql/

2019-03-25 Thread Martin Mokrejs
commit: 87e5a20b2aa7f097ab01530ee9997b611e10808b
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Mar 25 08:25:37 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Mar 25 08:25:37 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=87e5a20b

sci-biology/bamql: bump to version with less greedy LLVM linking

The https://github.com/BoutrosLaboratory/bamql/blob/master/m4/ax_llvm.m4#L31
forces preference for static libs. The code was improved by Andre
Masella. Although the original code is based on ax_llvm.m4 which
is 4 versions behind current version at
http://git.savannah.gnu.org/gitweb/?p=autoconf-archive.git;a=blob_plain;f=m4/ax_llvm.m4
it does better job at the moment.

https://github.com/BoutrosLaboratory/bamql/issues/14#issuecomment-475947032

Many thanks to François Bissey (@kiwifb) and Andre Masella (@apmasell)
for discussion and Andre for the changes in
https://github.com/BoutrosLaboratory/bamql/commit/9441772
which enable use to overcome the requirement for static libs and
proceed with shared versions using:
  `--enable-static=no --enable-static-llvm=no`

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/bamql/{bamql-1.6.ebuild => bamql-1.6.1.ebuild} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/sci-biology/bamql/bamql-1.6.ebuild 
b/sci-biology/bamql/bamql-1.6.1.ebuild
similarity index 100%
rename from sci-biology/bamql/bamql-1.6.ebuild
rename to sci-biology/bamql/bamql-1.6.1.ebuild



[gentoo-commits] proj/sci:master commit in: sci-biology/bamql/

2019-03-23 Thread Martin Mokrejs
commit: 565f9b0c0ef3c2c6917d27a17495dbc279bc92de
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sat Mar 23 15:01:39 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sat Mar 23 15:01:39 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=565f9b0c

sci-biology/bamql: add IUSE="static-libs"

Provided one specifies `--enable-static=no --enable-static-llvm=no` the
patch in
https://github.com/BoutrosLaboratory/bamql/commit/94417720bc7653a90cd9edd932ba6ba52d7bb89b
is really needed (as these two args are enough to compile bamql-1.6 and
llvm with only shared libs).

See https://github.com/BoutrosLaboratory/bamql/issues/14

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/bamql/{bamql-1.5.ebuild => bamql-1.6.ebuild} | 15 +++
 sci-biology/bamql/bamql-.ebuild  | 11 +--
 2 files changed, 20 insertions(+), 6 deletions(-)

diff --git a/sci-biology/bamql/bamql-1.5.ebuild 
b/sci-biology/bamql/bamql-1.6.ebuild
similarity index 53%
rename from sci-biology/bamql/bamql-1.5.ebuild
rename to sci-biology/bamql/bamql-1.6.ebuild
index ef78e3753..535b31f44 100644
--- a/sci-biology/bamql/bamql-1.5.ebuild
+++ b/sci-biology/bamql/bamql-1.6.ebuild
@@ -1,19 +1,19 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-inherit autotools
+inherit autotools eutils
 
 DESCRIPTION="Extract reads from BAM files"
 HOMEPAGE="https://github.com/BoutrosLaboratory/bamql

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1162-y;
-SRC_URI="https://github.com/BoutrosLaboratory/bamql/archive/v1.5.tar.gz -> 
${P}.tar.gz"
+SRC_URI="https://github.com/BoutrosLaboratory/${PN}/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE=""
+IUSE="static-libs"
 
 DEPEND="
sys-devel/llvm:=
@@ -26,3 +26,10 @@ src_prepare(){
eautoreconf
default
 }
+
+src_configure(){
+   local mycmakeargs=()
+   use static-libs && mycmakeargs+=( "--enable-static=yes" 
"--enable-static-llvm=yes" ) || \
+   mycmakeargs+=( "--enable-static=no" "--enable-static-llvm=no" )
+   econf ${mycmakeargs[@]}
+}

diff --git a/sci-biology/bamql/bamql-.ebuild 
b/sci-biology/bamql/bamql-.ebuild
index 44a7d85f5..409804dc7 100644
--- a/sci-biology/bamql/bamql-.ebuild
+++ b/sci-biology/bamql/bamql-.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -13,7 +13,7 @@ EGIT_REPO_URI="https://github.com/BoutrosLaboratory/bamql.git;
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS=""
-IUSE=""
+IUSE="static-libs"
 
 DEPEND="
sys-devel/llvm:=
@@ -26,3 +26,10 @@ src_prepare(){
eautoreconf
default
 }
+
+src_configure(){
+   local mycmakeargs=()
+   use static-libs && mycmakeargs+=( "--enable-static=yes" 
"--enable-static-llvm=yes" ) || \
+   mycmakeargs+=( "--enable-static=no" "--enable-static-llvm=no" )
+   econf ${mycmakeargs[@]}
+}



[gentoo-commits] proj/sci:master commit in: sci-biology/CAT/files/, sci-biology/CAT/

2019-03-07 Thread Martin Mokrejs
commit: e75a3d6b5e82f3ca53ef356f21afe0369e82eac1
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Thu Mar  7 19:43:41 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Mar  7 19:43:41 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e75a3d6b

sci-biology/CAT: add missing -lstdc++ -lm and drop -w

Use proper env variables

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/CAT/CAT-1.3.ebuild|  9 ++---
 sci-biology/CAT/files/CAT-1.3_respect_env_variables.patch | 15 ++-
 2 files changed, 16 insertions(+), 8 deletions(-)

diff --git a/sci-biology/CAT/CAT-1.3.ebuild b/sci-biology/CAT/CAT-1.3.ebuild
index 2628c04a9..44d099524 100644
--- a/sci-biology/CAT/CAT-1.3.ebuild
+++ b/sci-biology/CAT/CAT-1.3.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-DESCRIPTION="Estimate codon usage bias and its statistical significance"
+DESCRIPTION="Codon usage bias (composition) and its statistical significance"
 HOMEPAGE="
http://bigd.big.ac.cn/tools/cat
http://cbb.big.ac.cn/Software
@@ -11,9 +11,9 @@ HOMEPAGE="
http://www.cbrc.kaust.edu.sa/CAT;
 SRC_URI="ftp://download.big.ac.cn/bigd/tools/${PN}${PV}.tar.gz -> ${P}.tar.gz"
 
-LICENSE="GPL-3"
+LICENSE="GPL-3+"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
 IUSE=""
 
 PATCHES=( "${FILESDIR}"/CAT-1.3_respect_env_variables.patch )
@@ -30,5 +30,8 @@ src_compile(){
 }
 
 src_install(){
+   dodoc README.TXT
+   newdoc doc/CAT-DOC.pdf "${PN}".pdf
+   cd src || die
dobin CAT
 }

diff --git a/sci-biology/CAT/files/CAT-1.3_respect_env_variables.patch 
b/sci-biology/CAT/files/CAT-1.3_respect_env_variables.patch
index 5dff3986c..9c32d8a1d 100644
--- a/sci-biology/CAT/files/CAT-1.3_respect_env_variables.patch
+++ b/sci-biology/CAT/files/CAT-1.3_respect_env_variables.patch
@@ -1,11 +1,16 @@
 CAT1.3/src/makefile2011-03-13 15:05:27.0 +0100
-+++ CAT1.3/src/makefile2019-03-07 20:08:29.988220775 +0100
-@@ -1,6 +1,6 @@
+--- CAT1.3/src/makefile.ori2011-03-13 15:05:27.0 +0100
 CAT1.3/src/makefile2019-03-07 20:31:27.147985682 +0100
+@@ -1,10 +1,10 @@
  PRGS = CAT 
 -CC = g++
 -CFLAGS = -O3
-+CC ?= g++
-+CFLAGS ?= -O3
++CXX ?= g++
++CXXFLAGS ?= -O3
  
  all:  $(PRGS) 
  
+ CAT: main_CAT.cpp CAT.cpp base.cpp
+-  $(CC) $(CFLAGS) -o  $@ main_CAT.cpp CAT.cpp base.cpp  -w
++  $(CXX) $(CXXFLAGS) -o  $@ main_CAT.cpp CAT.cpp base.cpp -lstdc++ -lm
+ install: CAT
+   install CAT ~/bin/



[gentoo-commits] proj/sci:master commit in: sci-biology/CAT/, sci-biology/CAT/files/

2019-03-07 Thread Martin Mokrejs
commit: 2b35fa3317ef51f0de6002b65efa23605ee5e0cb
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Thu Mar  7 19:20:38 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Mar  7 19:20:38 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2b35fa33

sci-biology/CAT: new package

Does not compile, probably requires some older C++ standard?

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/CAT/CAT-1.3.ebuild | 34 ++
 .../CAT/files/CAT-1.3_respect_env_variables.patch  | 11 +++
 sci-biology/CAT/metadata.xml   | 12 
 3 files changed, 57 insertions(+)

diff --git a/sci-biology/CAT/CAT-1.3.ebuild b/sci-biology/CAT/CAT-1.3.ebuild
new file mode 100644
index 0..2628c04a9
--- /dev/null
+++ b/sci-biology/CAT/CAT-1.3.ebuild
@@ -0,0 +1,34 @@
+# Copyright 2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Estimate codon usage bias and its statistical significance"
+HOMEPAGE="
+   http://bigd.big.ac.cn/tools/cat
+   http://cbb.big.ac.cn/Software
+   http://code.google.com/p/composition-analysis-toolkit
+   http://www.cbrc.kaust.edu.sa/CAT;
+SRC_URI="ftp://download.big.ac.cn/bigd/tools/${PN}${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+PATCHES=( "${FILESDIR}"/CAT-1.3_respect_env_variables.patch )
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND=""
+
+S="${WORKDIR}/${PN}${PV}"
+
+src_compile(){
+   cd src || die
+   emake
+}
+
+src_install(){
+   dobin CAT
+}

diff --git a/sci-biology/CAT/files/CAT-1.3_respect_env_variables.patch 
b/sci-biology/CAT/files/CAT-1.3_respect_env_variables.patch
new file mode 100644
index 0..5dff3986c
--- /dev/null
+++ b/sci-biology/CAT/files/CAT-1.3_respect_env_variables.patch
@@ -0,0 +1,11 @@
+--- CAT1.3/src/makefile2011-03-13 15:05:27.0 +0100
 CAT1.3/src/makefile2019-03-07 20:08:29.988220775 +0100
+@@ -1,6 +1,6 @@
+ PRGS = CAT 
+-CC = g++
+-CFLAGS = -O3
++CC ?= g++
++CFLAGS ?= -O3
+ 
+ all:  $(PRGS) 
+ 

diff --git a/sci-biology/CAT/metadata.xml b/sci-biology/CAT/metadata.xml
new file mode 100644
index 0..138cb7705
--- /dev/null
+++ b/sci-biology/CAT/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+   
+   mmokr...@fold.natur.cuni.cz
+   Martin Mokrejs
+   
+   
+   sci-biol...@gentoo.org
+   Gentoo Biology Project
+   
+



[gentoo-commits] proj/sci:master commit in: sci-biology/ParaAT/

2019-03-07 Thread Martin Mokrejs
commit: b89f5830731c5051879f16da515be37ad14eab10
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Thu Mar  7 18:47:51 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Mar  7 18:47:51 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b89f5830

sci-biology/ParaAT: add missing default in src_prepare()

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/ParaAT/ParaAT-1.0.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-biology/ParaAT/ParaAT-1.0.ebuild 
b/sci-biology/ParaAT/ParaAT-1.0.ebuild
index 9339b121e..d806d90eb 100644
--- a/sci-biology/ParaAT/ParaAT-1.0.ebuild
+++ b/sci-biology/ParaAT/ParaAT-1.0.ebuild
@@ -21,6 +21,7 @@ S="${WORKDIR}/${PN}${PV}"
 
 src_prepare(){
rm -f ._Epal2nal.pl ._ParaAT.pl
+   default
 }
 
 src_install(){



[gentoo-commits] proj/sci:master commit in: sci-biology/KaKs_Calculator/files/, sci-biology/KaKs_Calculator/

2019-03-07 Thread Martin Mokrejs
commit: 3ae295ae35d49fc7242ae20b64611ebccc0daec3
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Thu Mar  7 18:41:26 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Mar  7 18:41:26 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3ae295ae

sci-biology/KaKs_Calculator: new package

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 .../KaKs_Calculator/KaKs_Calculator-1.2.ebuild | 22 +++---
 .../KaKs_Calculator/KaKs_Calculator-2.0.ebuild | 48 ++
 ...Ks_Calculator-1.2_strlen_was_not_declared.patch | 11 +
 3 files changed, 75 insertions(+), 6 deletions(-)

diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild 
b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
index ccd592626..929117604 100644
--- a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
+++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild
@@ -1,24 +1,33 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
 inherit eutils toolchain-funcs
 
 DESCRIPTION="Calculate nonsynonymous (Ka) and synonymous (Ks) substitution 
rates"
-HOMEPAGE="https://code.google.com/p/kaks-calculator;
+HOMEPAGE="https://code.google.com/p/kaks-calculator
+   http://bigd.big.ac.cn/tools/kaks;
 SRC_URI="
-   
https://kaks-calculator.googlecode.com/files/KaKs_Calculator"${PV}".tar.gz
-   https://kaks-calculator.googlecode.com/files/parseFastaIntoAXT.pl;
+   
https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/kaks-calculator/KaKs_Calculator"${PV}".tar.gz
 -> ${P}.tar.gz
+   
https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/kaks-calculator/parseFastaIntoAXT.pl
+   
https://raw.githubusercontent.com/WilsonSayresLab/AlignmentProcessor/master/KaKs_Calculator/${PN}${PV}/KaKs_CalculatorDOC.pdf
 -> ${P}_manual.pdf
+   
https://s3.amazonaws.com/fumba.me/share+files/1-s2.0-S1672022907600072-main.pdf 
-> ${PN}-Zhang_et_al_2006.pdf"
 
 LICENSE="GPL-3"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
 IUSE=""
 
+PATCHES=( "${FILESDIR}/${PN}"-1.2_strlen_was_not_declared.patch )
+
+# ParaAT: A parallel tool for constructing multiple protein-coding DNA 
alignments
+# http://cbb.big.ac.cn/software
+# https://www.sciencedirect.com/science/article/pii/S0006291X12003518
 DEPEND="sci-biology/ParaAT"
 RDEPEND="
dev-lang/perl
+   sci-biology/paml
${DEPEND}"
 
 S="${WORKDIR}"/KaKs_Calculator"${PV}"
@@ -36,4 +45,5 @@ src_compile(){
 src_install(){
dobin "${DISTDIR}"/parseFastaIntoAXT.pl
dobin src/{KaKs_Calculator,AXTConvertor,ConPairs}
+   dodoc "${DISTDIR}"/${P}_manual.pdf 
"${DISTDIR}"/${PN}-Zhang_et_al_2006.pdf
 }

diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild 
b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
new file mode 100644
index 0..5edd1323a
--- /dev/null
+++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Calculate nonsynonymous (Ka) and synonymous (Ks) substitution 
rates"
+HOMEPAGE="https://code.google.com/p/kaks-calculator
+   https://sourceforge.net/projects/kakscalculator2/
+   https://www.sciencedirect.com/science/article/pii/S1672022910600083;
+SRC_URI="
+   
https://netcologne.dl.sourceforge.net/project/kakscalculator2/${PN}${PV}.tar.gz 
-> ${P}.tar.gz
+   
https://github.com/WilsonSayresLab/AlignmentProcessor/blob/master/KaKs_Calculator/${PN}${PV}/${PN}${PV}_manual.pdf
 -> ${P}_manual.pdf
+   
https://s3.amazonaws.com/fumba.me/share+files/1-s2.0-S1672022907600072-main.pdf 
-> ${PN}-Zhang_et_al_2006.pdf"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+PATCHES=( "${FILESDIR}/${PN}"-1.2_strlen_was_not_declared.patch )
+
+# ParaAT: A parallel tool for constructing multiple protein-coding DNA 
alignments
+# http://cbb.big.ac.cn/software
+# https://www.sciencedirect.com/science/article/pii/S0006291X12003518
+DEPEND="sci-biology/ParaAT"
+RDEPEND="
+   dev-lang/perl
+   sci-biology/paml
+   ${DEPEND}"
+
+S="${WORKDIR}"/KaKs_Calculator"${PV}"
+
+src_prepare(){
+   sed -e "s/^CC = g++/CC="$(tc-getCXX)"/; s/^CFLAGS/#CFLAGS/" -i 
src/makefile  || die
+   default
+}
+
+src_compile(){
+   cd src || die
+   default
+}
+
+src_install(){
+   do

[gentoo-commits] proj/sci:master commit in: sci-biology/ParaAT/

2019-03-07 Thread Martin Mokrejs
commit: 70ea861437459dc2b1637d75098132578282b6f0
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Thu Mar  7 18:39:01 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Mar  7 18:39:01 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=70ea8614

sci-biology/ParaAT: new package

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/ParaAT/ParaAT-1.0.ebuild | 29 +
 sci-biology/ParaAT/metadata.xml  | 12 
 2 files changed, 41 insertions(+)

diff --git a/sci-biology/ParaAT/ParaAT-1.0.ebuild 
b/sci-biology/ParaAT/ParaAT-1.0.ebuild
new file mode 100644
index 0..9339b121e
--- /dev/null
+++ b/sci-biology/ParaAT/ParaAT-1.0.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+DESCRIPTION="Create multiple protein-coding DNA alignments and 
back-Translation"
+HOMEPAGE="https://code.google.com/p/paraat
+   http://cbb.big.ac.cn/software
+   https://www.sciencedirect.com/science/article/pii/S0006291X12003518;
+SRC_URI="https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/paraat/${PN}${PV}.tar.gz
 -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="dev-lang/perl"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/${PN}${PV}"
+
+src_prepare(){
+   rm -f ._Epal2nal.pl ._ParaAT.pl
+}
+
+src_install(){
+   dobin *.pl
+   dodoc readme.txt
+}

diff --git a/sci-biology/ParaAT/metadata.xml b/sci-biology/ParaAT/metadata.xml
new file mode 100644
index 0..138cb7705
--- /dev/null
+++ b/sci-biology/ParaAT/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+   
+   mmokr...@fold.natur.cuni.cz
+   Martin Mokrejs
+   
+   
+   sci-biol...@gentoo.org
+   Gentoo Biology Project
+   
+



[gentoo-commits] proj/sci:master commit in: sci-biology/canu/files/, sci-biology/canu/

2019-02-20 Thread Martin Mokrejs
commit: a93d11e69bfb168131822a534931dae912b5fbe2
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Wed Feb 20 19:43:32 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Wed Feb 20 19:43:32 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a93d11e6

sci-biology/canu: respect CXXFLAGS

Package-Manager: Portage-2.3.61, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/canu/canu-.ebuild  |  35 ++-
 .../canu/files/canu-1.8_respect_CXXFLAGS.patch | 112 +
 2 files changed, 143 insertions(+), 4 deletions(-)

diff --git a/sci-biology/canu/canu-.ebuild 
b/sci-biology/canu/canu-.ebuild
index bef85d20f..2233e284a 100644
--- a/sci-biology/canu/canu-.ebuild
+++ b/sci-biology/canu/canu-.ebuild
@@ -1,9 +1,11 @@
 # Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=5
 
-inherit java-pkg-2 git-r3
+PYTHON_COMPAT=( python2_7 )
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit eutils java-pkg-2 perl-module multilib git-r3
 
 DESCRIPTION="Fork of a wgs-assembler for Oxfordnanopore and PacBio sequences"
 HOMEPAGE="http://canu.readthedocs.io/en/latest;
@@ -14,6 +16,8 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
 RDEPEND="
>=virtual/jre-1.8:*
dev-lang/perl
@@ -24,8 +28,21 @@ RDEPEND="
 DEPEND="${RDEPEND}
>=virtual/jdk-1.8:*
dev-java/ant-core
+   !sci-biology/wgs-assembler
"
 
+# Detected file collision(s):
+#  * sci-biology/wgs-assembler-8.3_rc2:0::science
+#  *   /usr/bin/bogart
+#  *   /usr/bin/bogus
+#  *   /usr/bin/fastqAnalyze
+#  *   /usr/bin/fastqSample
+#  *   /usr/bin/fastqSimulate
+#  *   /usr/bin/fastqSimulate-sort
+#  *   /usr/bin/meryl
+#  *   /usr/bin/overlapInCore
+#  *   /usr/bin/utgcns
+
 # Perl 5.12.0, or File::Path 2.08
 # Java SE 8
 # https://github.com/marbl/MHAP uses Apache maven
@@ -33,6 +50,10 @@ S="${WORKDIR}"/"${P}"
 
 # contains bundled mhap-2.1.3.jar, kmer, pbutgcns, FALCON
 
+src_prepare(){
+   epatch "${FILESDIR}"/canu-1.8_respect_CXXFLAGS.patch
+}
+
 src_compile(){
cd src || die
emake
@@ -42,9 +63,15 @@ src_install(){
# installs
#  /usr/bin
#  /usr/lib/libcanu.a
-   #  /usr/lib/site_perl/canu
+   #  /usr/lib64/perl5/vendor_perl/5.28.0/lib/site_perl/canu
#  /usr/share/java/classes/mhap-2.1.3.jar
rm -rf Linux-amd64/obj
insinto /usr
-   doins -r Linux-amd64/{bin,lib,share}
+   doins -r Linux-amd64/{bin,share}
+   insinto /usr/$(get_libdir)
+   dolib Linux-amd64/lib/libcanu.a
+   rm Linux-amd64/lib/libcanu.a || die
+   perl_set_version
+   insinto ${VENDOR_LIB}
+   doins -r Linux-amd64/lib
 }

diff --git a/sci-biology/canu/files/canu-1.8_respect_CXXFLAGS.patch 
b/sci-biology/canu/files/canu-1.8_respect_CXXFLAGS.patch
new file mode 100644
index 0..ac46e0ddd
--- /dev/null
+++ b/sci-biology/canu/files/canu-1.8_respect_CXXFLAGS.patch
@@ -0,0 +1,112 @@
+diff --git a/src/Makefile b/src/Makefile
+index e2770f5a0..3cdb81a4c 100644
+--- a/src/Makefile
 b/src/Makefile
+@@ -388,6 +388,22 @@ endif
+ #  and remove -fomit-frame-pointer from CXXFLAGS.  It added a bunch of 
complication and wasn't
+ #  really used.
+ 
++ifeq ($(BUILDOPTIMIZED), 1)
++else
++  CXXFLAGS ?= -g3
++endif
++
++ifeq ($(BUILDDEBUG), 1)
++else
++  ifeq (${OSTYPE}, FreeBSD)
++  ifeq (${MACHINETYPE}, amd64)
++CXXFLAGS ?= -O3 -funroll-loops -fexpensive-optimizations 
-finline-functions -fomit-frame-pointer
++  else
++CXXFLAGS ?= -O4 -funroll-loops -fexpensive-optimizations 
-finline-functions -fomit-frame-pointer
++  endif
++  endif
++endif
++
+ ifeq (${OSTYPE}, Linux)
+   CC?= gcc
+   CXX   ?= g++
+@@ -398,16 +414,6 @@ ifeq (${OSTYPE}, Linux)
+   CXXFLAGS  += -Wall -Wextra -Wno-write-strings -Wno-unused 
-Wno-char-subscripts -Wno-sign-compare -Wformat
+ 
+   BUILDSTACKTRACE ?= 1
+-
+-  ifeq ($(BUILDOPTIMIZED), 1)
+-  else
+-CXXFLAGS += -g3
+-  endif
+-
+-  ifeq ($(BUILDDEBUG), 1)
+-  else
+-CXXFLAGS += -O4 -funroll-loops -fexpensive-optimizations 
-finline-functions -fomit-frame-pointer
+-  endif
+ endif
+ 
+ 
+@@ -479,16 +485,6 @@ ifeq (${OSTYPE}, Darwin)
+ 
+   CXXFLAGS += -pthread -fPIC -m64 -Wall -Wextra -Wno-write-strings 
-Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wno-format-truncation 
-Wformat
+   LDFLAGS  += -pthread -lm
+-
+-  ifeq ($(BUILDOPTIMIZED), 1)
+-  else
+-CXXFLAGS += -g3
+-  endif
+-
+-  ifeq ($(BUILDDEBUG), 1)
+-  else
+-CXXFLAGS += -O4 -funroll-loops -fexpensive-optimizations 
-finline-functions -fomit-frame-pointer
+-  endif
+ endif
+ 
+ 
+@@ -519,16 +515,6 @@ ifeq (${MACHINETYPE}, amd64)
+ 
+   #  callgrind
+   #CXXFLAGS  += -g3 -Wa,--gstabs -save-t

[gentoo-commits] proj/sci:master commit in: sci-biology/canu/

2019-02-20 Thread Martin Mokrejs
commit: 44e3ae771a3aa414d91c4687cb707b2d16b32ff7
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Wed Feb 20 12:50:03 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Wed Feb 20 12:50:03 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=44e3ae77

sci-biology/canu: add live package of a new tool

Package-Manager: Portage-2.3.61, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/canu/canu-.ebuild | 50 +++
 sci-biology/canu/metadata.xml | 12 ++
 2 files changed, 62 insertions(+)

diff --git a/sci-biology/canu/canu-.ebuild 
b/sci-biology/canu/canu-.ebuild
new file mode 100644
index 0..bef85d20f
--- /dev/null
+++ b/sci-biology/canu/canu-.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit java-pkg-2 git-r3
+
+DESCRIPTION="Fork of a wgs-assembler for Oxfordnanopore and PacBio sequences"
+HOMEPAGE="http://canu.readthedocs.io/en/latest;
+EGIT_REPO_URI="https://github.com/marbl/canu.git;
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+RDEPEND="
+   >=virtual/jre-1.8:*
+   dev-lang/perl
+   virtual/perl-File-Path
+   sci-visualization/gnuplot
+   "
+# =sci-biology/mhap-2.1.3 if we unbundle it
+DEPEND="${RDEPEND}
+   >=virtual/jdk-1.8:*
+   dev-java/ant-core
+   "
+
+# Perl 5.12.0, or File::Path 2.08
+# Java SE 8
+# https://github.com/marbl/MHAP uses Apache maven
+S="${WORKDIR}"/"${P}"
+
+# contains bundled mhap-2.1.3.jar, kmer, pbutgcns, FALCON
+
+src_compile(){
+   cd src || die
+   emake
+}
+
+src_install(){
+   # installs
+   #  /usr/bin
+   #  /usr/lib/libcanu.a
+   #  /usr/lib/site_perl/canu
+   #  /usr/share/java/classes/mhap-2.1.3.jar
+   rm -rf Linux-amd64/obj
+   insinto /usr
+   doins -r Linux-amd64/{bin,lib,share}
+}

diff --git a/sci-biology/canu/metadata.xml b/sci-biology/canu/metadata.xml
new file mode 100644
index 0..138cb7705
--- /dev/null
+++ b/sci-biology/canu/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+   
+   mmokr...@fold.natur.cuni.cz
+   Martin Mokrejs
+   
+   
+   sci-biol...@gentoo.org
+   Gentoo Biology Project
+   
+



[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/

2019-02-19 Thread Martin Mokrejs
commit: b6846dd42e04e42c0103983272b6db0db248f75a
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Tue Feb 19 11:26:14 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Feb 19 11:26:14 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b6846dd4

sci-biology/bowtie: removing not working -1.2.2 ebuild

Package-Manager: Portage-2.3.61, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/bowtie/bowtie-1.2.2.ebuild | 77 --
 1 file changed, 77 deletions(-)

diff --git a/sci-biology/bowtie/bowtie-1.2.2.ebuild 
b/sci-biology/bowtie/bowtie-1.2.2.ebuild
deleted file mode 100644
index cae085bff..0
--- a/sci-biology/bowtie/bowtie-1.2.2.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit flag-o-matic toolchain-funcs
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/;
-SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
-
-LICENSE="Artistic"
-SLOT="1"
-KEYWORDS=""
-
-IUSE="examples +tbb"
-
-RDEPEND="tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
-   sci-biology/seqan:1.4
-   app-arch/unzip"
-
-DOCS=( AUTHORS NEWS TUTORIAL doc/README )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-PATCHES=(
-   "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
-   "${FILESDIR}/${P}-fix-Intel-compilation.patch"
-   "${FILESDIR}/${P}-unbundle-seqan.patch"
-)
-# other patches to be still considered
-#  "${FILESDIR}/${P}-fix-setBegin-call.patch"
-#  "${FILESDIR}/${P}-seqan-popcount.patch"
-#  "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch"
-#  "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch"
-#  "${FILESDIR}/${P}-spelling.patch"
-#  "${FILESDIR}/${P}-tbb-tinythread-missing.patch"
-#)
-
-src_prepare() {
-   default
-
-   # remove bundled libraries, use system seqan 1.4
-   rm -rf SeqAn-1.1/ third_party/ || die
-
-   # innocuous non-security flags, prevent log pollution
-   append-cxxflags \
-   -Wno-unused-local-typedefs \
-   -Wno-unused-but-set-variable \
-   -Wno-unused-variable
-}
-
-src_compile() {
-   emake \
-   CC="$(tc-getCC)" \
-   CPP="$(tc-getCXX)" \
-   CFLAGS="" \
-   CXXFLAGS="" \
-   EXTRA_FLAGS="${LDFLAGS}" \
-   RELEASE_FLAGS="${CXXFLAGS}" \
-   WITH_TBB="$(usex tbb 1 0)"
-}
-
-src_install() {
-   dobin ${PN} ${PN}-*
-
-   exeinto /usr/libexec/${PN}
-   doexe scripts/*
-
-   newman MANUAL ${PN}.1
-   einstalldocs
-
-   if use examples; then
-   insinto /usr/share/${PN}
-   doins -r genomes indexes
-   fi
-}



[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/

2019-02-19 Thread Martin Mokrejs
commit: 51f9e3636c1422b40200dcc11c4122f356cfe4de
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Tue Feb 19 11:24:18 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Feb 19 11:24:18 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=51f9e363

sci-biology/bowtie: removing - ebuild

Package-Manager: Portage-2.3.61, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/bowtie/bowtie-.ebuild | 81 ---
 1 file changed, 81 deletions(-)

diff --git a/sci-biology/bowtie/bowtie-.ebuild 
b/sci-biology/bowtie/bowtie-.ebuild
deleted file mode 100644
index d54d0a544..0
--- a/sci-biology/bowtie/bowtie-.ebuild
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit flag-o-matic toolchain-funcs git-r3
-
-DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
-HOMEPAGE="http://bowtie-bio.sourceforge.net/;
-EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git;
-EGIT_BRANCH="bug_fixes"
-
-LICENSE="Artistic"
-SLOT="1"
-KEYWORDS=""
-
-IUSE="examples +tbb"
-
-RDEPEND="tbb? ( dev-cpp/tbb )"
-DEPEND="${RDEPEND}
-   sci-biology/seqan:1.4
-   app-arch/unzip"
-
-DOCS=( AUTHORS NEWS TUTORIAL doc/README )
-HTML_DOCS=( doc/{manual.html,style.css} )
-
-PATCHES=( "${FILESDIR}/bowtie--fix-isa-return-type.patch" )
-# not needed
-# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by 
https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b
-#PATCHES=(
-#  "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
-#  "${FILESDIR}/${P}-fix-Intel-compilation.patch"
-#  "${FILESDIR}/${P}-unbundle-seqan.patch"
-#)
-# other patches to be still considered
-#  "${FILESDIR}/${P}-fix-setBegin-call.patch"
-#  "${FILESDIR}/${P}-seqan-popcount.patch"
-#  "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch"
-#  "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch"
-#  "${FILESDIR}/${P}-spelling.patch"
-#  "${FILESDIR}/${P}-tbb-tinythread-missing.patch"
-#)
-
-src_prepare() {
-   default
-
-   # remove bundled libraries, use system seqan 1.4
-   # rm -rf SeqAn-1.1/ third_party/ || die
-
-   # innocuous non-security flags, prevent log pollution
-   append-cxxflags \
-   -Wno-unused-local-typedefs \
-   -Wno-unused-but-set-variable \
-   -Wno-unused-variable
-}
-
-src_compile() {
-   emake \
-   CC="$(tc-getCC)" \
-   CPP="$(tc-getCXX)" \
-   CFLAGS="" \
-   CXXFLAGS="" \
-   EXTRA_FLAGS="${LDFLAGS}" \
-   RELEASE_FLAGS="${CXXFLAGS}" \
-   WITH_TBB="$(usex tbb 1 0)"
-}
-
-src_install() {
-   dobin ${PN} ${PN}-*
-
-   exeinto /usr/libexec/${PN}
-   doexe scripts/*
-
-   newman MANUAL ${PN}.1
-   einstalldocs
-
-   if use examples; then
-   insinto /usr/share/${PN}
-   doins -r genomes indexes
-   fi
-}



[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/

2019-02-19 Thread Martin Mokrejs
commit: 85794dc2e25580c628e007d4a528ffc2e24d4239
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Tue Feb 19 11:20:51 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Feb 19 11:20:51 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=85794dc2

sci-biology/bowtie: working 1.2.2 snapshot

This ebuild keeps the bundled SeqAn-1.1 sources (a library of
headers) and does not insist on system-wide installed
SeqAn-1.4 (for which too many patches are needed and I am unable
to evaluate/apply them all).

Package-Manager: Portage-2.3.61, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 .../bowtie/bowtie-1.2.2_beta20190219.ebuild| 81 ++
 sci-biology/bowtie/bowtie-.ebuild  | 81 ++
 .../files/bowtie-1.2.2-fix-isa-return-type.patch   | 22 ++
 3 files changed, 184 insertions(+)

diff --git a/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild 
b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
new file mode 100644
index 0..fcf0b4516
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-1.2.2_beta20190219.ebuild
@@ -0,0 +1,81 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit flag-o-matic toolchain-funcs git-r3
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/;
+EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git;
+EGIT_BRANCH="bug_fixes"
+COMMIT="f253e204f5ba4565d14ae1b300ea6cb10dfe4660"
+
+LICENSE="Artistic"
+SLOT="1"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="examples +tbb"
+
+RDEPEND="tbb? ( dev-cpp/tbb )"
+DEPEND="${RDEPEND}
+   app-arch/unzip"
+#  sci-biology/seqan:1.4"
+
+DOCS=( AUTHORS NEWS TUTORIAL doc/README )
+HTML_DOCS=( doc/{manual.html,style.css} )
+
+PATCHES=( "${FILESDIR}/bowtie-1.2.2-fix-isa-return-type.patch" )
+# not needed
+# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by 
https://github.com/BenLangmead/bowtie/commit/d8b661fb36c129cb9899fcd3689b3618036f8c7b
+#
+# still to be considered
+#PATCHES=(
+#  "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
+#  "${FILESDIR}/${P}-unbundle-seqan.patch"
+#  "${FILESDIR}/${P}-fix-setBegin-call.patch"
+#  "${FILESDIR}/${P}-seqan-popcount.patch"
+#  "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch"
+#  "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch"
+#  "${FILESDIR}/${P}-spelling.patch"
+#  "${FILESDIR}/${P}-tbb-tinythread-missing.patch"
+#)
+
+src_prepare() {
+   default
+
+   # remove bundled library of headers, use system seqan 1.4
+   # rm -rf SeqAn-1.1/ third_party/ || die
+
+   # innocuous non-security flags, prevent log pollution
+   append-cxxflags \
+   -Wno-unused-local-typedefs \
+   -Wno-unused-but-set-variable \
+   -Wno-unused-variable
+}
+
+src_compile() {
+   emake \
+   CC="$(tc-getCC)" \
+   CPP="$(tc-getCXX)" \
+   CFLAGS="" \
+   CXXFLAGS="" \
+   EXTRA_FLAGS="${LDFLAGS}" \
+   RELEASE_FLAGS="${CXXFLAGS}" \
+   WITH_TBB="$(usex tbb 1 0)"
+}
+
+src_install() {
+   dobin ${PN} ${PN}-*
+
+   exeinto /usr/libexec/${PN}
+   doexe scripts/*
+
+   newman MANUAL ${PN}.1
+   einstalldocs
+
+   if use examples; then
+   insinto /usr/share/${PN}
+   doins -r genomes indexes
+   fi
+}

diff --git a/sci-biology/bowtie/bowtie-.ebuild 
b/sci-biology/bowtie/bowtie-.ebuild
new file mode 100644
index 0..d54d0a544
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-.ebuild
@@ -0,0 +1,81 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit flag-o-matic toolchain-funcs git-r3
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/;
+EGIT_REPO_URI="https://github.com/BenLangmead/bowtie.git;
+EGIT_BRANCH="bug_fixes"
+
+LICENSE="Artistic"
+SLOT="1"
+KEYWORDS=""
+
+IUSE="examples +tbb"
+
+RDEPEND="tbb? ( dev-cpp/tbb )"
+DEPEND="${RDEPEND}
+   sci-biology/seqan:1.4
+   app-arch/unzip"
+
+DOCS=( AUTHORS NEWS TUTORIAL doc/README )
+HTML_DOCS=( doc/{manual.html,style.css} )
+
+PATCHES=( "${FILESDIR}/bowtie--fix-isa-return-type.patch" )
+# not needed
+# "${FILESDIR}/${P}-fix-Intel-compilation.patch", obsoleted by 
https://github.com/BenLangmead/bowtie/commit/d8b661fb36c1

[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/

2019-02-18 Thread Martin Mokrejs
commit: 3c65e999c45f956a48f434581ed74f27732c9c2a
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon Feb 18 13:44:27 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Feb 18 13:44:27 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3c65e999

sci-biology/bowtie: add some compile patches from Debian

Seems both bowtie1 and bowtie2 are bound too much to SeqAn-1.1
and need more patches for SeqAn-1.4. Per reports on github
it seems one should be able to compile bowtie-1.2.2 using
-std=c++03 (but not me).

Package-Manager: Portage-2.3.59, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/bowtie/bowtie-1.2.2.ebuild | 77 ++
 sci-biology/bowtie/bowtie-2.3.4.3.ebuild   | 62 +
 .../files/bowtie-1.2.2-_ContextLss-1.1-1.4.patch   | 17 +
 .../files/bowtie-1.2.2-fix-Intel-compilation.patch | 32 +
 .../bowtie/files/bowtie-1.2.2-unbundle-seqan.patch | 14 
 .../bowtie/files/bowtie-1.2.2-void2int.patch   | 16 +
 sci-biology/bowtie/metadata.xml| 16 +
 7 files changed, 234 insertions(+)

diff --git a/sci-biology/bowtie/bowtie-1.2.2.ebuild 
b/sci-biology/bowtie/bowtie-1.2.2.ebuild
new file mode 100644
index 0..cae085bff
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-1.2.2.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit flag-o-matic toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/;
+SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip"
+
+LICENSE="Artistic"
+SLOT="1"
+KEYWORDS=""
+
+IUSE="examples +tbb"
+
+RDEPEND="tbb? ( dev-cpp/tbb )"
+DEPEND="${RDEPEND}
+   sci-biology/seqan:1.4
+   app-arch/unzip"
+
+DOCS=( AUTHORS NEWS TUTORIAL doc/README )
+HTML_DOCS=( doc/{manual.html,style.css} )
+
+PATCHES=(
+   "${FILESDIR}/${P}-_ContextLss-1.1-1.4.patch"
+   "${FILESDIR}/${P}-fix-Intel-compilation.patch"
+   "${FILESDIR}/${P}-unbundle-seqan.patch"
+)
+# other patches to be still considered
+#  "${FILESDIR}/${P}-fix-setBegin-call.patch"
+#  "${FILESDIR}/${P}-seqan-popcount.patch"
+#  "${FILESDIR}/${P}-seqan-rename-ChunkPool.patch"
+#  "${FILESDIR}/${P}-seqan-rename-fill-to-resize.patch"
+#  "${FILESDIR}/${P}-spelling.patch"
+#  "${FILESDIR}/${P}-tbb-tinythread-missing.patch"
+#)
+
+src_prepare() {
+   default
+
+   # remove bundled libraries, use system seqan 1.4
+   rm -rf SeqAn-1.1/ third_party/ || die
+
+   # innocuous non-security flags, prevent log pollution
+   append-cxxflags \
+   -Wno-unused-local-typedefs \
+   -Wno-unused-but-set-variable \
+   -Wno-unused-variable
+}
+
+src_compile() {
+   emake \
+   CC="$(tc-getCC)" \
+   CPP="$(tc-getCXX)" \
+   CFLAGS="" \
+   CXXFLAGS="" \
+   EXTRA_FLAGS="${LDFLAGS}" \
+   RELEASE_FLAGS="${CXXFLAGS}" \
+   WITH_TBB="$(usex tbb 1 0)"
+}
+
+src_install() {
+   dobin ${PN} ${PN}-*
+
+   exeinto /usr/libexec/${PN}
+   doexe scripts/*
+
+   newman MANUAL ${PN}.1
+   einstalldocs
+
+   if use examples; then
+   insinto /usr/share/${PN}
+   doins -r genomes indexes
+   fi
+}

diff --git a/sci-biology/bowtie/bowtie-2.3.4.3.ebuild 
b/sci-biology/bowtie/bowtie-2.3.4.3.ebuild
new file mode 100644
index 0..eea3059cf
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.3.4.3.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/;
+SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip"
+
+LICENSE="GPL-3"
+SLOT="2"
+KEYWORDS=""
+
+IUSE="examples cpu_flags_x86_sse2 +tbb"
+
+RDEPEND="dev-lang/perl
+   tbb? ( dev-cpp/tbb )"
+DEPEND="${RDEPEND}
+   app-arch/unzip
+   sys-libs/readline"
+
+S="${WORKDIR}/${PN}2-${PV}"
+
+DOCS=( AUTHORS NEWS TUTORIAL )
+HTML_DOCS=( doc/{manual.html,style.css} )
+#PATCHES=( "${FILESDIR}/${P}-fix-c++14.patch" ) # needs 2.3.4.3 update
+
+pkg_pretend() {
+   if ! use cpu_flags_x86_sse2 ; then
+   eerror "This package requires a CPU supporting the SSE2 
instr

[gentoo-commits] proj/sci:master commit in: sci-biology/biobambam2/

2019-01-22 Thread Martin Mokrejs
commit: c136ed4c31ad6688ff68b7f14c8b56f5f8d2504c
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Tue Jan 22 15:35:05 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Jan 22 15:35:05 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c136ed4c

sci-biology/biobambam2: upstream moved from github to gitlab

Package-Manager: Portage-2.3.56, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/biobambam2/biobambam2-2.0.89.ebuild |  5 +++--
 sci-biology/biobambam2/biobambam2-.ebuild   | 11 ++-
 2 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/sci-biology/biobambam2/biobambam2-2.0.89.ebuild 
b/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
index f4d9679eb..3ebc9cae5 100644
--- a/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
+++ b/sci-biology/biobambam2/biobambam2-2.0.89.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -6,7 +6,8 @@ EAPI=7
 inherit autotools
 
 DESCRIPTION="Tools for bam file processing (libmaus2)"
-HOMEPAGE="https://github.com/gt1/biobambam2;
+HOMEPAGE="https://gitlab.com/german.tischler/biobambam2
+   https://github.com/gt1/biobambam2;
 
SRC_URI="https://github.com/gt1/biobambam2/archive/2.0.89-release-20180518145034.tar.gz;
 
 LICENSE="GPL-3 MIT"

diff --git a/sci-biology/biobambam2/biobambam2-.ebuild 
b/sci-biology/biobambam2/biobambam2-.ebuild
index e2fc6946a..59774ca56 100644
--- a/sci-biology/biobambam2/biobambam2-.ebuild
+++ b/sci-biology/biobambam2/biobambam2-.ebuild
@@ -1,13 +1,14 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
 inherit git-r3 autotools
 
-DESCRIPTION="Tools for bam file processing (libmaus2)"
-HOMEPAGE="https://github.com/gt1/biobambam2;
-EGIT_REPO_URI="https://github.com/gt1/biobambam2.git;
+DESCRIPTION="Tools for bam file processing (using libmaus2)"
+HOMEPAGE="https://gitlab.com/german.tischler/biobambam2
+   https://github.com/gt1/biobambam2;
+EGIT_REPO_URI="https://gitlab.com/german.tischler/biobambam2;
 
 LICENSE="GPL-3 MIT"
 SLOT="0"
@@ -16,7 +17,7 @@ IUSE=""
 
 DEPEND="
!sci-biology/biobambam
-   >=sci-libs/libmaus2-2.0.225"
+   >=sci-libs/libmaus2-2.0.555"
 RDEPEND="${DEPEND}"
 
 src_prepare() {



[gentoo-commits] proj/sci:master commit in: sci-libs/libmaus2/

2019-01-22 Thread Martin Mokrejs
commit: 458e1564c2fa03fefffd8a8f9dc8975d95f26c3f
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Tue Jan 22 15:17:58 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Jan 22 15:17:58 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=458e1564

sci-libs/libmaus2: upstream moved from github to gitlab

https://github.com/gt1/libmaus2/issues/28#issuecomment-456336598

Package-Manager: Portage-2.3.56, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 .../{libmaus2-2.0.499.ebuild => libmaus2-2.0.587.ebuild}  | 15 +++
 sci-libs/libmaus2/libmaus2-.ebuild| 11 +--
 2 files changed, 12 insertions(+), 14 deletions(-)

diff --git a/sci-libs/libmaus2/libmaus2-2.0.499.ebuild 
b/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
similarity index 70%
rename from sci-libs/libmaus2/libmaus2-2.0.499.ebuild
rename to sci-libs/libmaus2/libmaus2-2.0.587.ebuild
index cebe44161..1c61df056 100644
--- a/sci-libs/libmaus2/libmaus2-2.0.499.ebuild
+++ b/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -7,36 +7,35 @@ inherit autotools
 
 DESCRIPTION="Library for biobambam2"
 HOMEPAGE="https://github.com/gt1/libmaus;
-SRC_URI="https://github.com/gt1/libmaus2/archive/2.0.499-release-20180606122508.tar.gz;
+SRC_URI="https://gitlab.com/german.tischler/libmaus2/-/archive/master/${P}.tar.gz;
 
 LICENSE="BSD-2 GPL-2 GPL-3 MIT ZLIB" # BUG: incomplete list of licenses, see 
AUTHORS
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
 IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 cpu_flags_x86_sse4_2"
 
 DEPEND="
!sci-libs/libmaus
-   sci-libs/io_lib
+   >=sci-libs/io_lib-1.14.11
app-arch/snappy
-   sci-biology/seqan
sci-libs/fftw
sci-libs/hdf5
net-libs/gnutls
dev-libs/nettle"
 # --with-daligner
 # --with-irods
-S="${WORKDIR}"/libmaus2-2.0.499-release-20180606122508
+S="${WORKDIR}"/libmaus2-master-27828cd78121d5e4b19c263c5527e462360f5901
 
 src_configure(){
local CONFIG_OPTS
use cpu_flags_x86_ssse3 && CONFIG_OPTS+=( --enable-ssse3 )
( use cpu_flags_x86_sse4_1 || use cpu_flags_x86_sse4_2 ) && 
CONFIG_OPTS+=( --enable-sse4 )
-   econf --with-snappy --with-seqan --with-io_lib $CONFIG_OPTS \
+   econf --with-snappy --with-io_lib $CONFIG_OPTS \
--with-lzma --with-gnutls --with-nettle --with-hdf5 --with-gmp 
--with-fftw
 }
 
 pkg_postinst(){
-   einfo "The io_lib, snappy and seqan dependencies are not strictly 
needed"
+   einfo "The io_lib, snappy dependencies are not strictly needed"
einfo "but were forced for optimal libmaus2 performance."
einfo "igzip is only used if gzip level is set to 11."
 }

diff --git a/sci-libs/libmaus2/libmaus2-.ebuild 
b/sci-libs/libmaus2/libmaus2-.ebuild
index 01aa74a92..c371d5432 100644
--- a/sci-libs/libmaus2/libmaus2-.ebuild
+++ b/sci-libs/libmaus2/libmaus2-.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Authors
+# Copyright 2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -7,7 +7,7 @@ inherit autotools git-r3
 
 DESCRIPTION="Library for biobambam2"
 HOMEPAGE="https://github.com/gt1/libmaus;
-EGIT_REPO_URI="https://github.com/gt1/libmaus2.git;
+EGIT_REPO_URI="https://gitlab.com/german.tischler/libmaus2;
 
 LICENSE="BSD-2 GPL-2 GPL-3 MIT ZLIB" # BUG: incomplete list of licenses, see 
AUTHORS
 SLOT="0"
@@ -16,9 +16,8 @@ IUSE="cpu_flags_x86_ssse3 cpu_flags_x86_sse4_1 
cpu_flags_x86_sse4_2"
 
 DEPEND="
!sci-libs/libmaus
-   sci-libs/io_lib
+   >=sci-libs/io_lib-1.14.11
app-arch/snappy
-   sci-biology/seqan
sci-libs/fftw
sci-libs/hdf5
net-libs/gnutls
@@ -35,12 +34,12 @@ src_configure(){
local CONFIG_OPTS
use cpu_flags_x86_ssse3 && CONFIG_OPTS+=( --enable-ssse3 )
( use cpu_flags_x86_sse4_1 || use cpu_flags_x86_sse4_2 ) && 
CONFIG_OPTS+=( --enable-sse4 )
-   econf --with-snappy --with-seqan --with-io_lib $CONFIG_OPTS \
+   econf --with-snappy --with-io_lib $CONFIG_OPTS \
--with-lzma --with-gnutls --with-nettle --with-hdf5 --with-gmp 
--with-fftw
 }
 
 pkg_postinst(){
-   einfo "The io_lib, snappy and seqan dependencies are not strictly 
needed"
+   einfo "The io_lib, snappy dependencies are not strictly needed"
einfo "but were forced for optimal libmaus2 performance."
einfo "igzip is only used if gzip level is set to 11."
 }



[gentoo-commits] proj/sci:master commit in: sci-libs/io_lib/

2019-01-22 Thread Martin Mokrejs
commit: 0434ac4d8411a5efd26cfee76642e182efd0f2c6
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Tue Jan 22 14:10:29 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Jan 22 14:10:29 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0434ac4d

sci-libs/io_lib: add libdeflate to USE flags and require it

Package-Manager: Portage-2.3.56, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-libs/io_lib/io_lib-1.14.11.ebuild | 4 ++--
 sci-libs/io_lib/metadata.xml  | 5 -
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/sci-libs/io_lib/io_lib-1.14.11.ebuild 
b/sci-libs/io_lib/io_lib-1.14.11.ebuild
index 73263df65..0d8fcc5ca 100644
--- a/sci-libs/io_lib/io_lib-1.14.11.ebuild
+++ b/sci-libs/io_lib/io_lib-1.14.11.ebuild
@@ -14,7 +14,7 @@ 
SRC_URI="https://github.com/jkbonfield/io_lib/archive/${PN}-${MY_PV}.tar.gz -> $
 LICENSE="BSD"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="+bzip2 curl +lzma static-libs" # maybe introduce libdeflate USE flag?
+IUSE="+bzip2 curl +libdeflate lzma static-libs"
 
 S="${WORKDIR}"/"${PN}-${PN}-${MY_PV}"
 
@@ -36,7 +36,7 @@ BUILD_DIR="${S}"
 # versions 1.8.11 and 1.8.12 will work with the BioPerl Staden extensions.)
 #DEPEND="!sci-biology/bioperl"
 DEPEND="
-   app-arch/libdeflate
+   libdeflate? ( app-arch/libdeflate )
lzma? ( app-arch/xz-utils:= app-arch/lzma )
bzip2? ( app-arch/bzip2 )
curl? ( net-misc/curl )

diff --git a/sci-libs/io_lib/metadata.xml b/sci-libs/io_lib/metadata.xml
index f2d955844..9d56a9c0f 100644
--- a/sci-libs/io_lib/metadata.xml
+++ b/sci-libs/io_lib/metadata.xml
@@ -10,7 +10,10 @@ io_lib is a library of file reading and writing code to 
provide a
 general purpose trace file (and Experiment File) reading interface. The
 programmer simply calls the (eg) read_reading to create a "Read" C structure
 with the data loaded into memory.
-
+   
+   
+   Use libdeflate for faster decompression 
than zlib
+   

staden




[gentoo-commits] proj/sci:master commit in: app-arch/libdeflate/files/, app-arch/libdeflate/

2019-01-22 Thread Martin Mokrejs
commit: 8fc8b0f3f4e3c4aac5ecbf81c5a9d1d1e9769d1b
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Tue Jan 22 13:31:48 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Jan 22 13:31:48 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=8fc8b0f3

app-arch/libdeflate: make a patch to fix EPREFIX installations

Package-Manager: Portage-2.3.56, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 .../files/libdeflate-1.2-respect_EPREFIX.patch | 54 ++
 app-arch/libdeflate/libdeflate-1.2.ebuild  |  9 ++--
 2 files changed, 57 insertions(+), 6 deletions(-)

diff --git a/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch 
b/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch
new file mode 100644
index 0..a583d7d2e
--- /dev/null
+++ b/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch
@@ -0,0 +1,54 @@
+--- libdeflate-1.2/Makefile2019-01-15 06:37:48.0 +0100
 libdeflate-1.2/Makefile2019-01-22 14:06:13.427054892 +0100
+@@ -21,7 +21,7 @@
+ 1>&2 2>/dev/null; then echo $(1); fi)
+ 
+ override CFLAGS :=\
+-  $(CFLAGS) -O2 -fomit-frame-pointer -std=c99 -I. -Icommon\
++  -O2 $(CFLAGS) -fomit-frame-pointer -std=c99 -I. -Icommon\
+   -Wall -Wundef   \
+   $(call cc-option,-Wpedantic)\
+   $(call cc-option,-Wdeclaration-after-statement) \
+@@ -34,6 +34,9 @@
+ ##
+ 
+ PREFIX ?= /usr
++BINDIR ?= $(PREFIX)/bin
++INCDIR ?= $(PREFIX)/include
++LIBDIR ?= $(PREFIX)/lib
+ 
+ SOVERSION  := 0
+ STATIC_LIB_SUFFIX  := .a
+@@ -240,20 +243,20 @@
+ all:$(DEFAULT_TARGETS)
+ 
+ install:all
+-  install -Dm644 -t $(DESTDIR)$(PREFIX)/lib $(STATIC_LIB)
+-  install -Dm755 -t $(DESTDIR)$(PREFIX)/lib $(SHARED_LIB)
+-  ln -sf $(SHARED_LIB) $(DESTDIR)$(PREFIX)/lib/libdeflate.so
+-  install -Dm644 -t $(DESTDIR)$(PREFIX)/include libdeflate.h
+-  install -Dm755 gzip $(DESTDIR)$(PREFIX)/bin/libdeflate-gzip
+-  ln -f $(DESTDIR)$(PREFIX)/bin/libdeflate-gzip 
$(DESTDIR)$(PREFIX)/bin/libdeflate-gunzip
++  install -Dm644 -t $(DESTDIR)$(LIBDIR) $(STATIC_LIB)
++  install -Dm755 -t $(DESTDIR)$(LIBDIR) $(SHARED_LIB)
++  ln -sf $(SHARED_LIB) $(DESTDIR)$(LIBDIR)/libdeflate.so
++  install -Dm644 -t $(DESTDIR)$(INCDIR) libdeflate.h
++  install -Dm755 gzip $(DESTDIR)$(BINDIR)/libdeflate-gzip
++  ln -f $(DESTDIR)$(BINDIR)/libdeflate-gzip 
$(DESTDIR)$(BINDIR)/libdeflate-gunzip
+ 
+ uninstall:
+-  rm -f $(DESTDIR)$(PREFIX)/lib/$(STATIC_LIB) \
+-  $(DESTDIR)$(PREFIX)/lib/$(SHARED_LIB) \
+-  $(DESTDIR)$(PREFIX)/lib/libdeflate.so \
+-  $(DESTDIR)$(PREFIX)/include/libdeflate.h \
+-  $(DESTDIR)$(PREFIX)/bin/libdeflate-gzip \
+-  $(DESTDIR)$(PREFIX)/bin/libdeflate-gunzip
++  rm -f $(DESTDIR)$(LIBDIR)/$(STATIC_LIB) \
++  $(DESTDIR)$(LIBDIR)/$(SHARED_LIB) \
++  $(DESTDIR)$(LIBDIR)/libdeflate.so \
++  $(DESTDIR)$(INCDIR)/libdeflate.h \
++  $(DESTDIR)$(BINDIR)/libdeflate-gzip \
++  $(DESTDIR)$(BINDIR)/libdeflate-gunzip
+ 
+ test_programs:$(TEST_PROGRAMS)
+ 

diff --git a/app-arch/libdeflate/libdeflate-1.2.ebuild 
b/app-arch/libdeflate/libdeflate-1.2.ebuild
index a4baea15e..5548ea150 100644
--- a/app-arch/libdeflate/libdeflate-1.2.ebuild
+++ b/app-arch/libdeflate/libdeflate-1.2.ebuild
@@ -18,15 +18,12 @@ DEPEND=""
 RDEPEND="${DEPEND}"
 BDEPEND=""
 
-src_prepare(){
-   sed -e 's/ -O2 / /' -i Makefile || die
-   sed -e "s#${DESTDIR}${PREFIX}/lib#${ED}/usr/$(get_libdir)#" -i Makefile 
|| die
-   default
-}
+PATCHES=( "${FILESDIR}"/libdeflate-1.2-respect_EPREFIX.patch )
 
 src_install() {
-   default
if ! use static-libs; then
find "${ED}" -name '*.a' -delete || die
fi
+   emake install DESTDIR="${ED}" LIBDIR=/usr/"$(get_libdir)"
+   dodoc NEWS README.md
 }



[gentoo-commits] proj/sci:master commit in: app-arch/libdeflate/

2019-01-22 Thread Martin Mokrejs
commit: ed76a2870546469253f9e498eaccfc1e82f4ec91
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Tue Jan 22 12:54:18 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Jan 22 12:54:18 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ed76a287

app-arch/libdeflate: respect EPREFIX and use get_libdir

Package-Manager: Portage-2.3.56, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 app-arch/libdeflate/libdeflate-1.2.ebuild | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/app-arch/libdeflate/libdeflate-1.2.ebuild 
b/app-arch/libdeflate/libdeflate-1.2.ebuild
index dd65e7aef..a4baea15e 100644
--- a/app-arch/libdeflate/libdeflate-1.2.ebuild
+++ b/app-arch/libdeflate/libdeflate-1.2.ebuild
@@ -3,6 +3,8 @@
 
 EAPI=7
 
+inherit multilib
+
 DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
 HOMEPAGE="https://github.com/ebiggers/libdeflate;
 SRC_URI="https://github.com/ebiggers/libdeflate/archive/v1.2.tar.gz -> 
${P}.tar.gz"
@@ -18,6 +20,7 @@ BDEPEND=""
 
 src_prepare(){
sed -e 's/ -O2 / /' -i Makefile || die
+   sed -e "s#${DESTDIR}${PREFIX}/lib#${ED}/usr/$(get_libdir)#" -i Makefile 
|| die
default
 }
 



[gentoo-commits] proj/sci:master commit in: sci-libs/io_lib/

2019-01-22 Thread Martin Mokrejs
commit: bb7161d41c11db40813d5ad231aeaa60b6db3b86
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Tue Jan 22 12:17:12 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Jan 22 12:18:03 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=bb7161d4

sci-libs/io_lib: version bump

Add a new version with experimental CRAM support.

Force dependency on libdeflate although it could/should be maybe
protected by USE flag. However, it is recommended by upstream authors.

https://github.com/jkbonfield/io_lib/issues/11
https://github.com/jkbonfield/io_lib/issues/12
https://github.com/jkbonfield/io_lib/issues/13

Package-Manager: Portage-2.3.56, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-libs/io_lib/io_lib-1.14.11.ebuild | 71 +++
 sci-libs/io_lib/io_lib-1.14.7.ebuild  | 28 --
 2 files changed, 71 insertions(+), 28 deletions(-)

diff --git a/sci-libs/io_lib/io_lib-1.14.11.ebuild 
b/sci-libs/io_lib/io_lib-1.14.11.ebuild
new file mode 100644
index 0..73263df65
--- /dev/null
+++ b/sci-libs/io_lib/io_lib-1.14.11.ebuild
@@ -0,0 +1,71 @@
+# Copyright 2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit autotools-utils eutils versionator
+MY_PV=$(replace_all_version_separators '-')
+
+DESCRIPTION="General purpose trace and experiment file reading/writing 
interface"
+HOMEPAGE="https://github.com/jkbonfield/io_lib
+   http://staden.sourceforge.net/;
+SRC_URI="https://github.com/jkbonfield/io_lib/archive/${PN}-${MY_PV}.tar.gz -> 
${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="+bzip2 curl +lzma static-libs" # maybe introduce libdeflate USE flag?
+
+S="${WORKDIR}"/"${PN}-${PN}-${MY_PV}"
+
+# >>> Working in BUILD_DIR: 
"/scratch/var/tmp/portage/sci-libs/io_lib-1.14.11/work/io_lib-1.14.11_build"
+# /scratch/var/tmp/portage/sci-libs/io_lib-1.14.11/temp/environment: line 530: 
pushd: 
/scratch/var/tmp/portage/sci-libs/io_lib-1.14.11/work/io_lib-1.14.11_build: No 
such file or directory
+#  * ERROR: sci-libs/io_lib-1.14.11::science failed (install phase):
+#  *   (no error message)
+#  * 
+#  * Call stack:
+#  * ebuild.sh, line  124:  Called src_install
+#  *   environment, line 2506:  Called autotools-utils_src_install
+#  *   environment, line  530:  Called die
+#  * The specific snippet of code:
+#  *   pushd "${BUILD_DIR}" > /dev/null || die;
+# 
+BUILD_DIR="${S}"
+
+# Prototype changes in io_lib-1.9.0 create incompatibilities with BioPerl. 
(Only
+# versions 1.8.11 and 1.8.12 will work with the BioPerl Staden extensions.)
+#DEPEND="!sci-biology/bioperl"
+DEPEND="
+   app-arch/libdeflate
+   lzma? ( app-arch/xz-utils:= app-arch/lzma )
+   bzip2? ( app-arch/bzip2 )
+   curl? ( net-misc/curl )
+   sys-libs/zlib"
+RDEPEND="${DEPEND}"
+
+src_prepare(){
+   # https://github.com/jkbonfield/io_lib/issues/12
+   eautoreconf
+   default
+}
+
+src_configure(){
+   # https://github.com/jkbonfield/io_lib/issues/11
+   # https://github.com/jkbonfield/io_lib/issues/13
+   local myconf=()
+   ! use static-libs && myconf+=( "--enable-static=no" )
+   econf ${myconf[@]} $(use_with libdeflate)
+}
+
+src_compile(){
+   # BUG: "have to" provide my own src_compile() because ${P}_build dir is 
missing now
+   # alternatively BUILD_DIR="${S}" would probably help here too
+   emake
+}
+
+src_install() {
+   # cd "${S}" || die # this does not help to get around the ${P}_build 
missing
+   # what helped was to set BUILD_DIR="${S}" above
+   autotools-utils_src_install
+   dodoc docs/{Hash_File_Format,ZTR_format}
+}

diff --git a/sci-libs/io_lib/io_lib-1.14.7.ebuild 
b/sci-libs/io_lib/io_lib-1.14.7.ebuild
deleted file mode 100644
index d76cffe92..0
--- a/sci-libs/io_lib/io_lib-1.14.7.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools-utils
-
-DESCRIPTION="General purpose trace and experiment file reading/writing 
interface"
-HOMEPAGE="http://staden.sourceforge.net/;
-SRC_URI="mirror://sourceforge/staden/${P}.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="static-libs"
-
-# Prototype changes in io_lib-1.9.0 create incompatibilities with BioPerl. 
(Only
-# versions 1.8.11 and 1.8.12 will work with the BioPerl Staden extensions.)
-#DEPEND="!sci-biology/bioperl"
-DEPEND="
-   net-misc/curl
-   sys-libs/zlib"
-RDEPEND="${DEPEND}"
-
-src_install() {
-   autotools-utils_src_install
-   dodoc docs/{Hash_File_Format,ZTR_format}
-}



[gentoo-commits] proj/sci:master commit in: app-arch/libdeflate/

2019-01-22 Thread Martin Mokrejs
commit: f7b7df2da789550f34d886c37a6b679b073cd68d
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Tue Jan 22 11:56:27 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Jan 22 11:56:27 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f7b7df2d

app-arch/libdeflate: new package

Add highly CPU optimized implementation of deflate/zlib/gzip

The package is highly preferred due to its speed by:
sci-biology/io_lib-1.14.11
sci-libs/htslib-1.9
and maybe some more

 * Searching for libdeflate ...
 * Contents of app-arch/libdeflate-1.2:
/usr
/usr/bin
/usr/bin/libdeflate-gunzip
/usr/bin/libdeflate-gzip
/usr/include
/usr/include/libdeflate.h
/usr/lib
/usr/lib/libdeflate.so -> libdeflate.so.0
/usr/lib/libdeflate.so.0
/usr/share
/usr/share/doc
/usr/share/doc/libdeflate-1.2
/usr/share/doc/libdeflate-1.2/NEWS.bz2
/usr/share/doc/libdeflate-1.2/README.md.bz2

Seems the libdeflate-gunzip and libdeflate-gzip have statically
linked in /usr/lib/libdeflate.a (which is deleted but later
in src_install() unless USE=static-libs . Probably something to
inspected but more experienced devs.

I am not interested in maintaining this package in Gentoo
(I would be happy if somebody from other herds take this over).

Package-Manager: Portage-2.3.56, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 app-arch/libdeflate/libdeflate-1.2.ebuild | 29 +
 app-arch/libdeflate/metadata.xml  | 12 
 2 files changed, 41 insertions(+)

diff --git a/app-arch/libdeflate/libdeflate-1.2.ebuild 
b/app-arch/libdeflate/libdeflate-1.2.ebuild
new file mode 100644
index 0..dd65e7aef
--- /dev/null
+++ b/app-arch/libdeflate/libdeflate-1.2.ebuild
@@ -0,0 +1,29 @@
+# Copyright 2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression"
+HOMEPAGE="https://github.com/ebiggers/libdeflate;
+SRC_URI="https://github.com/ebiggers/libdeflate/archive/v1.2.tar.gz -> 
${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="static-libs"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND=""
+
+src_prepare(){
+   sed -e 's/ -O2 / /' -i Makefile || die
+   default
+}
+
+src_install() {
+   default
+   if ! use static-libs; then
+   find "${ED}" -name '*.a' -delete || die
+   fi
+}

diff --git a/app-arch/libdeflate/metadata.xml b/app-arch/libdeflate/metadata.xml
new file mode 100644
index 0..138cb7705
--- /dev/null
+++ b/app-arch/libdeflate/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+   
+   mmokr...@fold.natur.cuni.cz
+   Martin Mokrejs
+   
+   
+   sci-biol...@gentoo.org
+   Gentoo Biology Project
+   
+



[gentoo-commits] proj/sci:master commit in: sci-biology/blasr/

2019-01-17 Thread Martin Mokrejs
commit: f093654801e9bb7ad831c30a592f1da016ed9aca
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Thu Jan 17 12:38:17 2019 +
Commit:     Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Jan 17 12:38:17 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f0936548

sci-biology/blasr: partial improvements of the ebuild

Package-Manager: Portage-2.3.55, Repoman-2.3.12
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/blasr/blasr-.ebuild | 30 ++
 1 file changed, 22 insertions(+), 8 deletions(-)

diff --git a/sci-biology/blasr/blasr-.ebuild 
b/sci-biology/blasr/blasr-.ebuild
index 2b1716bdd..3fe868450 100644
--- a/sci-biology/blasr/blasr-.ebuild
+++ b/sci-biology/blasr/blasr-.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -16,17 +16,31 @@ SLOT="0"
 IUSE="hdf5"
 KEYWORDS=""
 
-DEPEND="hdf5? ( >=sci-libs/hdf5-1.8.12[cxx] )" # needs H5Cpp.h
+CDEPEND="
+   dev-util/meson
+   dev-util/ninja
+   dev-util/cmake
+   dev-util/pkgconfig"
+# needs libblasr
+DEPEND="
+   sci-biology/pbbam
+   dev-libs/boost:=[threads]
+   hdf5? ( >=sci-libs/hdf5-1.8.12[cxx] )" # needs H5Cpp.h
 RDEPEND=""
 
 S="${WORKDIR}/blasr-"
 
-src_configure(){
-   if use hdf5; then \
-   python ./configure.py --shared --sub --no-pbbam 
HDF5_INCLUDE="${EPREFIX}"/usr/include HDF5_LIB="${EPREFIX}"/usr/lib64 || die
-   else
-   python ./configure.py --shared --sub --no-pbbam || die
-   fi
+#src_configure(){
+#  if use hdf5; then \
+#  python ./configure.py --shared --sub --no-pbbam 
HDF5_INCLUDE="${EPREFIX}"/usr/include HDF5_LIB="${EPREFIX}"/usr/lib64 || die
+#  else
+#  python ./configure.py --shared --sub --no-pbbam || die
+#  fi
+#}
+
+src_compile(){
+   bash scripts/ci/build.sh || die
+   # BUG: meson.build:54:0: ERROR:  Dependency "pbbam" not found, tried 
pkgconfig and cmake
 }
 
 src_install() {



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