[gentoo-commits] proj/sci:master commit in: sci-biology/ugene/
commit: 98ba084c90a88f4365be1740746df0585fb50823
Author: Martin Mokrejs gmail com>
AuthorDate: Tue Nov 30 14:00:53 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Nov 30 14:00:53 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=98ba084c
sci-biology/ugene: version bump
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/ugene/{ugene-37.0-r1.ebuild => ugene-40.1.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/ugene/ugene-37.0-r1.ebuild
b/sci-biology/ugene/ugene-40.1.ebuild
similarity index 100%
rename from sci-biology/ugene/ugene-37.0-r1.ebuild
rename to sci-biology/ugene/ugene-40.1.ebuild
[gentoo-commits] proj/sci:master commit in: sci-biology/minimap2/
commit: 227e281f30db2fd020beda0f962166b4783c5d95
Author: Martin Mokrejs gmail com>
AuthorDate: Tue Nov 30 12:41:07 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Nov 30 12:41:07 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=227e281f
sci-biology/minimap2: install more files, document incompleteness
I added notes on supported CPU instructions and additional python
bindings. Note the static library is linked into the minimap2 binary
by default but I think it may be handy to install the library and header
file too.
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/minimap2/minimap2-2.23.ebuild | 36 +--
1 file changed, 34 insertions(+), 2 deletions(-)
diff --git a/sci-biology/minimap2/minimap2-2.23.ebuild
b/sci-biology/minimap2/minimap2-2.23.ebuild
index 9f335e99c..ed458b91d 100644
--- a/sci-biology/minimap2/minimap2-2.23.ebuild
+++ b/sci-biology/minimap2/minimap2-2.23.ebuild
@@ -5,7 +5,7 @@ EAPI=7
inherit toolchain-funcs
-DESCRIPTION="splice-aware sequence aligner"
+DESCRIPTION="splice-aware sequence aligner with SSE2 and SSE4.1"
HOMEPAGE="https://github.com/lh3/minimap2;
SRC_URI="https://github.com/lh3/${PN}/releases/download/v${PV}/${P}.tar.bz2;
@@ -13,7 +13,9 @@ LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-DEPEND=""
+IUSE="+static"
+
+DEPEND="sys-libs/zlib"
RDEPEND="${DEPEND}"
BDEPEND=""
@@ -22,6 +24,36 @@ src_prepare(){
eapply_user
}
+# Minimap2 requires SSE2 instructions on x86 CPUs or NEON on ARM CPUs. It is
+# possible to add non-SIMD support, but it would make minimap2 slower by
+# several times.
+#
+# If you see compilation errors, try `make sse2only=1`
+# to disable SSE4 code, which will make minimap2 slightly slower.
+#
+# Minimap2 also works with ARM CPUs supporting the NEON instruction sets. To
+# compile for 32 bit ARM architectures (such as ARMv7), use `make arm_neon=1`.
To
+# compile for for 64 bit ARM architectures (such as ARMv8), use `make
arm_neon=1
+# aarch64=1`.
+#
+# Minimap2 can use [SIMD Everywhere (SIMDe)][simde] library for porting
+# implementation to the different SIMD instruction sets. To compile using
SIMDe,
+# use `make -f Makefile.simde`. To compile for ARM CPUs, use `Makefile.simde`
+# with the ARM related command lines given above.
+
+# This repository also provides Python bindings to a subset of C APIs. File
+# [python/README.rst](python/README.rst) gives the full documentation;
+# [python/minimap2.py](python/minimap2.py) shows an example. This Python
+# extension, mappy, is also [available from PyPI][mappypypi] via `pip install
+# mappy` or [from BioConda][mappyconda] via `conda install -c bioconda mappy`.
+
src_install(){
dobin "${PN}"
+ insinto /usr/include
+ doins minimap.h mmpriv.h
+ dolib.a libminimap2.a
+ insinto /usr/share/"${PN}"/examples
+ doins example.c
+ doman minimap2.1
+ dodoc README.md NEWS.md FAQ.md
}
[gentoo-commits] proj/sci:master commit in: sci-biology/minimap2/
commit: 6def45a03309ee5cee96b1b4988ab8c874d4f6df
Author: Martin Mokrejs gmail com>
AuthorDate: Tue Nov 30 11:54:26 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Nov 30 11:54:26 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6def45a0
sci-biology/minimap2: version bump
Respect CFLAGS although the Makefile compiles different routines
for SSE4.1 processors. The options appear later on the commandline
so should override eventual CFLAGS -mtune and -march values.
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
.../minimap2/{minimap2-2.17.ebuild => minimap2-2.23.ebuild}| 7 +++
1 file changed, 7 insertions(+)
diff --git a/sci-biology/minimap2/minimap2-2.17.ebuild
b/sci-biology/minimap2/minimap2-2.23.ebuild
similarity index 76%
rename from sci-biology/minimap2/minimap2-2.17.ebuild
rename to sci-biology/minimap2/minimap2-2.23.ebuild
index e4f51e1d9..9f335e99c 100644
--- a/sci-biology/minimap2/minimap2-2.17.ebuild
+++ b/sci-biology/minimap2/minimap2-2.23.ebuild
@@ -3,6 +3,8 @@
EAPI=7
+inherit toolchain-funcs
+
DESCRIPTION="splice-aware sequence aligner"
HOMEPAGE="https://github.com/lh3/minimap2;
SRC_URI="https://github.com/lh3/${PN}/releases/download/v${PV}/${P}.tar.bz2;
@@ -15,6 +17,11 @@ DEPEND=""
RDEPEND="${DEPEND}"
BDEPEND=""
+src_prepare(){
+ sed -e 's/-O2 //' -e 's/^CFLAGS=/CFLAGS+=/' -i Makefile || die
+ eapply_user
+}
+
src_install(){
dobin "${PN}"
}
[gentoo-commits] proj/sci:master commit in: sci-biology/LINKS/
commit: 5db6563203432be7454b285bba50fc79daaac21d
Author: Martin Mokrejs gmail com>
AuthorDate: Mon Nov 29 11:41:16 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Nov 29 11:41:16 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5db65632
sci-biology/LINKS: remove keywords
This package is supposed to be executed from within compiled
source tree. See comments in the ebuild what needs to be fixed.
https://github.com/bcgsc/LINKS/pull/59
https://github.com/bcgsc/LINKS/issues/31
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/LINKS/LINKS-1.8.7.ebuild | 31 ---
1 file changed, 28 insertions(+), 3 deletions(-)
diff --git a/sci-biology/LINKS/LINKS-1.8.7.ebuild
b/sci-biology/LINKS/LINKS-1.8.7.ebuild
index 5009e9922..898898b94 100644
--- a/sci-biology/LINKS/LINKS-1.8.7.ebuild
+++ b/sci-biology/LINKS/LINKS-1.8.7.ebuild
@@ -9,17 +9,42 @@
SRC_URI="https://github.com/bcgsc/LINKS/archive/refs/tags/v${PV}.tar.gz -> ${P}.
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
RESTRICT="test"
RDEPEND="
>=dev-lang/perl-1.6
dev-lang/swig
- sci-biology/btl_bloomfilter
+ dev-util/cppcheck
"
+# sci-biology/btl_bloomfilter
+
+src_compile(){
+ cd btllib | die "Cannot chdir to bundled btllib/"
+ ./compile-wrappers || die "Failed to compile bundled btllib"
+ # baah, this also does some kind of install
+ # SUCCESS: sdsl was installed successfully!
+ # The sdsl include files are located in
$foo'/LINKS/btllib/external/sdsl-lite/installdir/include'.
+ # The library files are located in
$foo'/LINKS/btllib/external/sdsl-lite/installdir/lib'.
+ #
+ # Sample programs can be found in the examples-directory.
+ # A program 'example.cpp' can be compiled with the command:
+ # g++ -std=c++11 -DNDEBUG -O3 [-msse4.2] \
+ #-I$foo/LINKS/btllib/external/sdsl-lite/installdir/include
-L$foo/LINKS/btllib/external/sdsl-lite/installdir/lib \
+ #example.cpp -lsdsl -ldivsufsort -ldivsufsort64
+ #
+ # Tests in the test-directory
+ # A cheat sheet in the extras/cheatsheet-directory.
+ # Have fun!
+ # [2/3] Installing files.
+ # Installing extras/python/_btllib.so to $foo/LINKS/btllib/python
+ # Installing $foo/LINKS/btllib/extras/python/btllib.py to
$foo/LINKS/btllib/python
+}
src_install(){
- dobin bin/LINKS *.pl releases/links_v1.8.5/tools/*.pl
+ sed -e 's#$(bin)/../src/##' -i bin/LINKS-make || die
+ sed -e 's#perl $(bin)/##' -i bin/LINKS-make || die
+ dobin bin/LINKS bin/LINKS-make src/LINKS_CPP bin/*.pl tools/*.pl
dodoc README.md
}
[gentoo-commits] proj/sci:master commit in: sci-biology/tigmint/
commit: 7b40dd3b9eb83ed33a243cbc61baca5d6c5b3ac1
Author: Martin Mokrejs gmail com>
AuthorDate: Thu Oct 21 08:59:06 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Oct 21 08:59:06 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7b40dd3b
sci-biology/tigmint: add undocumented DEPENDency on zsh
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/tigmint/tigmint-1.2.4-r1.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
index 6900ea7aa..84b582151 100644
--- a/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
+++ b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild
@@ -24,6 +24,7 @@ RDEPEND="
sci-biology/pybedtools[${PYTHON_USEDEP}]
sci-biology/pysam[${PYTHON_USEDEP}]
app-arch/pigz
+ app-shells/zsh
sci-biology/samtools
sci-biology/minimap2
sci-biology/seqtk
[gentoo-commits] proj/sci:master commit in: sci-biology/tigmint/
commit: 6c45174a480dae72e147dbf764bda33b72404a56
Author: Martin Mokrejs gmail com>
AuthorDate: Tue Oct 19 15:06:25 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Oct 19 15:06:25 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6c45174a
sci-biology/tigmint: drop KEYWORDS until python install path is fixed
The 'from read_fasta import read_fasta' is supposed to work but Makefile
places the file into $prefix.
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/tigmint/tigmint-1.2.4.ebuild | 27 ++-
1 file changed, 26 insertions(+), 1 deletion(-)
diff --git a/sci-biology/tigmint/tigmint-1.2.4.ebuild
b/sci-biology/tigmint/tigmint-1.2.4.ebuild
index 89d73318d..1b181ea44 100644
--- a/sci-biology/tigmint/tigmint-1.2.4.ebuild
+++ b/sci-biology/tigmint/tigmint-1.2.4.ebuild
@@ -13,7 +13,7 @@
SRC_URI="https://github.com/bcgsc/tigmint/releases/download/v${PV}/${P}.tar.gz;
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
RESTRICT="test"
@@ -28,3 +28,28 @@ RDEPEND="
"
distutils_enable_tests pytest
+
+# install the executable into /usr/bin
+# BUG: the read_fasta.py should be installed into python modules
+# so it can be imported into python
+src_prepare(){
+ sed -i Makefile -e 's#prefix=/usr/local#prefix=/usr#'
+ default
+}
+
+src_configure(){
+ python_setup
+ default
+}
+
+# do not run src_compile step as it runs git, makefile2graph, gsed, tred
+
+src_install(){
+ default
+ distutils-r1_src_install
+}
+
+src_test(){
+ default
+ python_foreach_impl python_test
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/tigmint/
commit: 60b98c5ebef8040cd4d47494fc8e6ee5aa3e26b0
Author: Martin Mokrejs gmail com>
AuthorDate: Tue Oct 19 14:24:00 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Tue Oct 19 14:24:00 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=60b98c5e
sci-biology/tigmint: add missing dependencies not listed by upstream
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/tigmint/tigmint-1.2.4.ebuild | 4
1 file changed, 4 insertions(+)
diff --git a/sci-biology/tigmint/tigmint-1.2.4.ebuild
b/sci-biology/tigmint/tigmint-1.2.4.ebuild
index 627aba19b..89d73318d 100644
--- a/sci-biology/tigmint/tigmint-1.2.4.ebuild
+++ b/sci-biology/tigmint/tigmint-1.2.4.ebuild
@@ -21,6 +21,10 @@ RDEPEND="
dev-python/intervaltree[${PYTHON_USEDEP}]
sci-biology/pybedtools[${PYTHON_USEDEP}]
sci-biology/pysam[${PYTHON_USEDEP}]
+ app-arch/pigz
+ sci-biology/samtools
+ sci-biology/minimap2
+ sci-biology/seqtk
"
distutils_enable_tests pytest
[gentoo-commits] proj/sci:master commit in: sci-biology/longstitch/
commit: 4f86aedbcbd2669eb91f62364c7661a384629e11
Author: Martin Mokrejs gmail com>
AuthorDate: Mon Oct 18 11:25:09 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Oct 18 11:25:09 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4f86aedb
sci-biology/longstitch: new package
A simple Makefile to run all the dependencies at once.
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/longstitch/longstitch-1.0.1.ebuild | 28 ++
sci-biology/longstitch/metadata.xml| 12 +++
2 files changed, 40 insertions(+)
diff --git a/sci-biology/longstitch/longstitch-1.0.1.ebuild
b/sci-biology/longstitch/longstitch-1.0.1.ebuild
new file mode 100644
index 0..787c3219b
--- /dev/null
+++ b/sci-biology/longstitch/longstitch-1.0.1.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Scaffold genome assemblies by Chromium/PacBio/Nanopore reads"
+HOMEPAGE="https://github.com/bcgsc/LongStitch;
+SRC_URI="https://github.com/bcgsc/LongStitch/archive/refs/tags/v${PV}.tar.gz
-> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RESTRICT="test"
+
+RDEPEND="
+ sci-biology/abyss
+ sci-biology/tigmint
+ sci-biology/LINKS
+ sci-biology/samtools
+"
+
+S="${WORKDIR}"/LongStitch-"${PV}"
+
+src_install(){
+ dobin longstitch
+ dodoc README.md LongStitch_overview.pdf
+}
diff --git a/sci-biology/longstitch/metadata.xml
b/sci-biology/longstitch/metadata.xml
new file mode 100644
index 0..138cb7705
--- /dev/null
+++ b/sci-biology/longstitch/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/tigmint/
commit: 63dcb460ddbccacd2c2b7deb9a66bdd5705eb7ec
Author: Martin Mokrejs gmail com>
AuthorDate: Sun Oct 17 16:21:54 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Oct 17 16:21:54 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=63dcb460
sci-biology/tigmint: any python3 is supported
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/tigmint/tigmint-1.2.4.ebuild | 5 +
1 file changed, 1 insertion(+), 4 deletions(-)
diff --git a/sci-biology/tigmint/tigmint-1.2.4.ebuild
b/sci-biology/tigmint/tigmint-1.2.4.ebuild
index 12a32bc2b..627aba19b 100644
--- a/sci-biology/tigmint/tigmint-1.2.4.ebuild
+++ b/sci-biology/tigmint/tigmint-1.2.4.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python3_{7,8} )
+PYTHON_COMPAT=( python3_{7,8,9} )
inherit distutils-r1
@@ -15,9 +15,6 @@ LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-# TODO: fix this
-# FileNotFoundError: [Errno 2] No such file or directory
-# happens even with --install
RESTRICT="test"
RDEPEND="
[gentoo-commits] proj/sci:master commit in: sci-biology/LINKS/
commit: 377d1d836ceacf807b6c0eec677a841eb8d45c2c
Author: Martin Mokrejs gmail com>
AuthorDate: Sun Oct 17 15:56:52 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Oct 17 15:56:52 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=377d1d83
sci-biology/LINKS: install the tools/*.pl files from archive
... until https://github.com/bcgsc/LINKS/issues/31 is fixed.
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/LINKS/LINKS-1.8.7.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/LINKS/LINKS-1.8.7.ebuild
b/sci-biology/LINKS/LINKS-1.8.7.ebuild
index e9cf2fbd8..5009e9922 100644
--- a/sci-biology/LINKS/LINKS-1.8.7.ebuild
+++ b/sci-biology/LINKS/LINKS-1.8.7.ebuild
@@ -20,6 +20,6 @@ RDEPEND="
"
src_install(){
- dobin bin/LINKS *.pl tools/*.pl
+ dobin bin/LINKS *.pl releases/links_v1.8.5/tools/*.pl
dodoc README.md
}
[gentoo-commits] proj/sci:master commit in: sci-biology/LINKS/
commit: f4a311c42b306a1a49fa91c28203f388d324d326
Author: Martin Mokrejs gmail com>
AuthorDate: Sun Oct 17 15:42:43 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Oct 17 15:42:43 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f4a311c4
sci-biology/LINKS: new package
The LINKS perl script probably needs some sed hackery to eventually
start using system-wide btl_bloomfilter file BloomFilter.i and also
perl's CORE/EXTERN.h.
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/LINKS/LINKS-1.8.7.ebuild | 25 +
sci-biology/LINKS/metadata.xml | 12
2 files changed, 37 insertions(+)
diff --git a/sci-biology/LINKS/LINKS-1.8.7.ebuild
b/sci-biology/LINKS/LINKS-1.8.7.ebuild
new file mode 100644
index 0..e9cf2fbd8
--- /dev/null
+++ b/sci-biology/LINKS/LINKS-1.8.7.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Scaffold genome assemblies by Chromium/PacBio/Nanopore reads"
+HOMEPAGE="https://github.com/bcgsc/LINKS;
+SRC_URI="https://github.com/bcgsc/LINKS/archive/refs/tags/v${PV}.tar.gz ->
${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RESTRICT="test"
+
+RDEPEND="
+ >=dev-lang/perl-1.6
+ dev-lang/swig
+ sci-biology/btl_bloomfilter
+"
+
+src_install(){
+ dobin bin/LINKS *.pl tools/*.pl
+ dodoc README.md
+}
diff --git a/sci-biology/LINKS/metadata.xml b/sci-biology/LINKS/metadata.xml
new file mode 100644
index 0..138cb7705
--- /dev/null
+++ b/sci-biology/LINKS/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ mmokr...@fold.natur.cuni.cz
+ Martin Mokrejs
+
+
+ sci-biol...@gentoo.org
+ Gentoo Biology Project
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/btl_bloomfilter/
commit: 3bb99c288aca047f32378919fcea06743f809020
Author: Martin Mokrejs gmail com>
AuthorDate: Sun Oct 17 15:39:24 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Oct 17 15:39:24 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3bb99c28
sci-biology/btl_bloomfilter: new package
The perl/swig BloomFilter.i file maybe should be probably installed
elsewhere? It is to be used by sci-biology/LINKS from
https://github.com/bcgsc/LINKS
Maybe also the pythonic files could be registered into python?
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
.../btl_bloomfilter/btl_bloomfilter-1.2.1.ebuild | 31 ++
sci-biology/btl_bloomfilter/metadata.xml | 12 +
2 files changed, 43 insertions(+)
diff --git a/sci-biology/btl_bloomfilter/btl_bloomfilter-1.2.1.ebuild
b/sci-biology/btl_bloomfilter/btl_bloomfilter-1.2.1.ebuild
new file mode 100644
index 0..359a0941d
--- /dev/null
+++ b/sci-biology/btl_bloomfilter/btl_bloomfilter-1.2.1.ebuild
@@ -0,0 +1,31 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="BTL C/C common bloom filters"
+HOMEPAGE="https://github.com/bcgsc/btl_bloomfilter;
+SRC_URI="https://github.com/bcgsc/btl_bloomfilter/archive/refs/tags/${PV}.tar.gz
-> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND=""
+
+src_prepare(){
+ sh ./autogen.sh || die
+ default
+}
+
+src_test(){
+ make check || die
+}
+
+src_install(){
+ default
+ insinto /usr/share/"${PN}"
+ doins -r swig pythonInterface Examples
+}
diff --git a/sci-biology/btl_bloomfilter/metadata.xml
b/sci-biology/btl_bloomfilter/metadata.xml
new file mode 100644
index 0..138cb7705
--- /dev/null
+++ b/sci-biology/btl_bloomfilter/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ mmokr...@fold.natur.cuni.cz
+ Martin Mokrejs
+
+
+ sci-biol...@gentoo.org
+ Gentoo Biology Project
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/arcs/
commit: 4aaaee31a3160848f6d3e665695c366a5a02cb11
Author: Martin Mokrejs gmail com>
AuthorDate: Sun Oct 17 13:14:52 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Oct 17 13:14:52 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4aaaee31
sci-biology/arcs: new package
Scaffolding genome sequence assemblies using linked (from 10x
Genomics chromium) or long read sequencing data (from Pacific
Biosystems, Oxford Nanopore).
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/arcs/arcs-1.2.2.ebuild | 35 +++
sci-biology/arcs/metadata.xml | 12
2 files changed, 47 insertions(+)
diff --git a/sci-biology/arcs/arcs-1.2.2.ebuild
b/sci-biology/arcs/arcs-1.2.2.ebuild
new file mode 100644
index 0..44a77c335
--- /dev/null
+++ b/sci-biology/arcs/arcs-1.2.2.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Scaffold genome sequence assemblies by Chromium/PacBio/Naopore
reads"
+HOMEPAGE="https://github.com/bcgsc/arcs;
+SRC_URI="https://github.com/bcgsc/arcs/releases/download/v${PV}/${P}.tar.gz;
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+IUSE="minimal"
+
+# TODO: fix this
+# FileNotFoundError: [Errno 2] No such file or directory
+# happens even with --install
+RESTRICT="test"
+
+RDEPEND="
+ dev-libs/boost
+ dev-cpp/sparsehash
+ !minimal? (
+ sci-biology/abyss
+ sci-biology/tigmint
+ )
+"
+# !minimal? ( sci-biology/LINKS )
+
+src_install(){
+ default
+ insinto /usr/share/"${PN}"
+ doins -r Examples
+}
diff --git a/sci-biology/arcs/metadata.xml b/sci-biology/arcs/metadata.xml
new file mode 100644
index 0..138cb7705
--- /dev/null
+++ b/sci-biology/arcs/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/tigmint/
commit: 12a8a79abb8942a51cd8e15db9668bd0683221d3
Author: Martin Mokrejs gmail com>
AuthorDate: Sun Oct 17 12:08:06 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Oct 17 12:08:06 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=12a8a79a
sci-biology/tigmint: version bump, update SRC_URI
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/tigmint/{tigmint-1.2.1.ebuild => tigmint-1.2.4.ebuild} | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/tigmint/tigmint-1.2.1.ebuild
b/sci-biology/tigmint/tigmint-1.2.4.ebuild
similarity index 89%
rename from sci-biology/tigmint/tigmint-1.2.1.ebuild
rename to sci-biology/tigmint/tigmint-1.2.4.ebuild
index e2a9c626a..12a32bc2b 100644
--- a/sci-biology/tigmint/tigmint-1.2.1.ebuild
+++ b/sci-biology/tigmint/tigmint-1.2.4.ebuild
@@ -9,7 +9,7 @@ inherit distutils-r1
DESCRIPTION="Correct misassemblies using linked reads from 10x Genomics
Chromium"
HOMEPAGE="https://github.com/bcgsc/tigmint https://bcgsc.github.io/tigmint/;
-SRC_URI="https://github.com/bcgsc/tigmint/archive/${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/bcgsc/tigmint/releases/download/v${PV}/${P}.tar.gz;
LICENSE="GPL-3"
SLOT="0"
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/
commit: 6c252245a4ab18f5d211723f9078682dfa06bd00
Author: Martin Mokrejs gmail com>
AuthorDate: Thu Apr 22 07:23:16 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Apr 22 07:23:16 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6c252245
sci-biology/abyss: add 2.3.1 release but keep patches
The PathConsensus crash fixes were not included by upstream,
keep them.
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/abyss/abyss-2.3.1.ebuild | 58
1 file changed, 58 insertions(+)
diff --git a/sci-biology/abyss/abyss-2.3.1.ebuild
b/sci-biology/abyss/abyss-2.3.1.ebuild
new file mode 100644
index 0..d9134813b
--- /dev/null
+++ b/sci-biology/abyss/abyss-2.3.1.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit autotools toolchain-funcs
+
+DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end
sequence assembler"
+HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/;
+SRC_URI="https://github.com/bcgsc/abyss/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="+mpi openmp misc-haskell"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-cpp/sparsehash
+ dev-libs/boost:=
+ misc-haskell? (
+ dev-libs/gmp:0=
+ dev-libs/libffi:0=
+ )
+ mpi? ( sys-cluster/openmpi )"
+DEPEND="${RDEPEND}
+ misc-haskell? (
+ dev-lang/ghc
+ )"
+
+PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch
+ "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch
+ )
+
+# todo: --enable-maxk=N configure option
+# todo: fix automagic mpi toggling
+
+pkg_pretend() {
+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+ [[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+src_prepare() {
+ default
+ sed -i -e "s/-Werror//" configure.ac || die #365195
+ sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die
+ eautoreconf
+}
+
+src_configure() {
+ # disable building haskell tool Misc/samtobreak
+ # unless request by user: bug #534412
+ use misc-haskell || export ac_cv_prog_ac_ct_GHC=
+
+ econf $(use_enable openmp) --enable-maxk=256
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/, sci-biology/abyss/files/
commit: f22bb3be4e8f283831edc5f4c38a839442355644
Author: Martin Mokrejs gmail com>
AuthorDate: Wed Apr 14 13:07:12 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Apr 14 13:07:12 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f22bb3be
sci-biology/abyss: fix PathConsensus crashes
Fixes: https://github.com/bcgsc/abyss/issues/267
Fix crashes of PathConsensus during long-scaffolding
step per @sjackman suggestions.
Add back 2.2.5 version which does not have yet the
RResolver which addition broke the paired de Bruijn
graph assembly approach and since that only the
Bloom filter-based approach works in 2.3.0.
Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Martin Mokrejs gmail.com>
.../abyss/{abyss-2.3.0.ebuild => abyss-2.2.5-r1.ebuild} | 4
.../abyss/{abyss-2.3.0.ebuild => abyss-2.3.0-r1.ebuild} | 4
sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch | 11 +++
.../abyss/files/abyss-2.2.5-PathConsensus-assert.patch| 11 +++
4 files changed, 30 insertions(+)
diff --git a/sci-biology/abyss/abyss-2.3.0.ebuild
b/sci-biology/abyss/abyss-2.2.5-r1.ebuild
similarity index 91%
copy from sci-biology/abyss/abyss-2.3.0.ebuild
copy to sci-biology/abyss/abyss-2.2.5-r1.ebuild
index 95438d3b4..d9134813b 100644
--- a/sci-biology/abyss/abyss-2.3.0.ebuild
+++ b/sci-biology/abyss/abyss-2.2.5-r1.ebuild
@@ -27,6 +27,10 @@ DEPEND="${RDEPEND}
dev-lang/ghc
)"
+PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch
+ "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch
+ )
+
# todo: --enable-maxk=N configure option
# todo: fix automagic mpi toggling
diff --git a/sci-biology/abyss/abyss-2.3.0.ebuild
b/sci-biology/abyss/abyss-2.3.0-r1.ebuild
similarity index 91%
rename from sci-biology/abyss/abyss-2.3.0.ebuild
rename to sci-biology/abyss/abyss-2.3.0-r1.ebuild
index 95438d3b4..d9134813b 100644
--- a/sci-biology/abyss/abyss-2.3.0.ebuild
+++ b/sci-biology/abyss/abyss-2.3.0-r1.ebuild
@@ -27,6 +27,10 @@ DEPEND="${RDEPEND}
dev-lang/ghc
)"
+PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch
+ "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch
+ )
+
# todo: --enable-maxk=N configure option
# todo: fix automagic mpi toggling
diff --git a/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch
b/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch
new file mode 100644
index 0..95181f082
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch
@@ -0,0 +1,11 @@
+--- abyss-2.2.5/Common/ContigProperties.h.ori 2020-09-18 20:42:12.0
+0200
abyss-2.2.5/Common/ContigProperties.h 2021-04-14 12:31:23.682158000
+0200
+@@ -171,7 +171,7 @@
+ template
+ ContigProperties& operator+=(ContigProperties& a, const T& b)
+ {
+- assert((int)a.length + (int)b.distance > 0);
++ assert((int)a.length + (int)b.distance >= 0);
+ a.length += b.distance;
+ return a;
+ }
diff --git a/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch
b/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch
new file mode 100644
index 0..754e25acc
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch
@@ -0,0 +1,11 @@
+--- abyss-2.2.5/MergePaths/PathConsensus.cpp 2020-09-18 20:42:12.0
+0200
abyss-2.2.5/MergePaths/PathConsensus.cpp 2021-04-12 22:26:28.780547000
+0200
+@@ -379,7 +379,7 @@
+ unsigned overlap, Sequence& seq,
+ const Sequence& s, const ContigNode& node, const Path& path)
+ {
+- assert(s.length() > overlap);
++ assert(s.length() >= overlap);
+ Sequence ao;
+ Sequence bo(s, 0, overlap);
+ Sequence o;
[gentoo-commits] proj/sci:master commit in: sci-biology/abyss/
commit: 85d646372a278f85c05c5c7c717b9e94fa967ddc
Author: Martin Mokrejs gmail com>
AuthorDate: Thu Apr 1 20:11:06 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Apr 1 20:11:06 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=85d64637
sci-biology/abyss: version bump
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/abyss/{abyss-2.2.5.ebuild => abyss-2.3.0.ebuild} | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/abyss/abyss-2.2.5.ebuild
b/sci-biology/abyss/abyss-2.3.0.ebuild
similarity index 97%
rename from sci-biology/abyss/abyss-2.2.5.ebuild
rename to sci-biology/abyss/abyss-2.3.0.ebuild
index 10c2fbff6..95438d3b4 100644
--- a/sci-biology/abyss/abyss-2.2.5.ebuild
+++ b/sci-biology/abyss/abyss-2.3.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
[gentoo-commits] proj/sci:master commit in: sci-biology/canu/
commit: a59c6f6546b9556a99d35f05abc3d96557f8bac2
Author: Martin Mokrejs gmail com>
AuthorDate: Wed Mar 17 19:26:26 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Mar 17 19:26:26 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a59c6f65
sci-biology/canu: add missing dependency
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/canu/canu-2.1.1.ebuild | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/canu/canu-2.1.1.ebuild
b/sci-biology/canu/canu-2.1.1.ebuild
index 201058fad..10e4f485a 100644
--- a/sci-biology/canu/canu-2.1.1.ebuild
+++ b/sci-biology/canu/canu-2.1.1.ebuild
@@ -22,6 +22,7 @@ RDEPEND="${PYTHON_DEPS}
dev-lang/perl
virtual/perl-File-Path
sci-visualization/gnuplot
+ sci-biology/minimap2
"
# =sci-biology/mhap-2.1.3 if we unbundle it
DEPEND="${RDEPEND}
[gentoo-commits] proj/sci:master commit in: sci-biology/minimap2/
commit: 601c9013c6e86a87af3ca3b3185c285bccdf90ce
Author: Martin Mokrejs gmail com>
AuthorDate: Wed Mar 17 18:19:11 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Mar 17 18:19:11 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=601c9013
sci-biology/minimap2: new package
Arguably we could do something about CPUFLAGS but as the
package compiles its for for all SSE2 up to SSE4.1 combinations
maybe we only should ensure -mtune and -march options
were filtered by the ebuild.
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/minimap2/metadata.xml | 15 +++
sci-biology/minimap2/minimap2-2.17.ebuild | 20
2 files changed, 35 insertions(+)
diff --git a/sci-biology/minimap2/metadata.xml
b/sci-biology/minimap2/metadata.xml
new file mode 100644
index 0..c9e82c96a
--- /dev/null
+++ b/sci-biology/minimap2/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
+
+
+ minimap2
+
+
diff --git a/sci-biology/minimap2/minimap2-2.17.ebuild
b/sci-biology/minimap2/minimap2-2.17.ebuild
new file mode 100644
index 0..e40058243
--- /dev/null
+++ b/sci-biology/minimap2/minimap2-2.17.ebuild
@@ -0,0 +1,20 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="splice-aware sequence aligner"
+HOMEPAGE="https://github.com/lh3/minimap2;
+SRC_URI="https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-2.17.tar.bz2
-> ${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND=""
+
+src_install(){
+ dobin "${PN}"
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
commit: 257e4e9f1776f2fe2e5e5a348a2f15f7baeec1ad
Author: Martin Mokrejs gmail com>
AuthorDate: Fri Mar 5 13:34:24 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Mar 5 13:34:24 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=257e4e9f
sci-biology/SPAdes: dropping KEYWORDS
src_install() phase does not install the files
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/SPAdes/SPAdes-3.15.1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild
b/sci-biology/SPAdes/SPAdes-3.15.1.ebuild
index 3e8943607..853524984 100644
--- a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.15.1.ebuild
@@ -12,7 +12,7 @@ SRC_URI="
https://cab.spbu.ru/files/release${PV}/truspades_manual.html ->
${P}_truspades_manual.html"
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
DEPEND="
sys-libs/zlib
[gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
commit: 11e7e6552d00645d27360186f403c23dfc807099
Author: Martin Mokrejs gmail com>
AuthorDate: Fri Mar 5 09:21:36 2021 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Mar 5 09:21:36 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=11e7e655
sci-biology/SPAdes: version bump to 3.15.1
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/SPAdes/{SPAdes-3.15.0.ebuild => SPAdes-3.15.1.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.15.0.ebuild
b/sci-biology/SPAdes/SPAdes-3.15.1.ebuild
similarity index 100%
rename from sci-biology/SPAdes/SPAdes-3.15.0.ebuild
rename to sci-biology/SPAdes/SPAdes-3.15.1.ebuild
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
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="$(usex sra 1 0)"
}
src_install() {
@@ -58,3 +61,7 @@ src_install() {
doins -r example
fi
}
+
+src_test(){
+ emake test
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/bedops/
commit: 2a28ea64417794f6c09e39345fec05445ff8ae44
Author: Martin Mokrejs gmail com>
AuthorDate: Fri Dec 18 10:53:44 2020 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Dec 18 10:54:07 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2a28ea64
sci-biology/bedops: fix install procedure
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/bedops/bedops-2.4.26.ebuild | 8 +++-
1 file changed, 7 insertions(+), 1 deletion(-)
diff --git a/sci-biology/bedops/bedops-2.4.26.ebuild
b/sci-biology/bedops/bedops-2.4.26.ebuild
index d281fbede..4ae167a08 100644
--- a/sci-biology/bedops/bedops-2.4.26.ebuild
+++ b/sci-biology/bedops/bedops-2.4.26.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -23,3 +23,9 @@ src_prepare(){
local PATCHES=("${FILESDIR}"/${P}-respect-cxxflags.patch)
epatch ${PATCHES[@]}
}
+
+src_install(){
+ emake install
+ dobin bin/*
+ dodoc README.md
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: f1b4f4489e2e9181bca1dde19fffb24a9155bef7
Author: Martin Mokrejs gmail com>
AuthorDate: Sat Dec 12 15:23:20 2020 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat Dec 12 15:23:38 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f1b4f448
sci-biology/pybedtools: document more dependencies
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 7 +++
1 file changed, 7 insertions(+)
diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
index 9edb8f366..a91de8cca 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
@@ -19,11 +19,18 @@ RESTRICT="test"
# Tests reported to fail on Gentoo:
# https://github.com/daler/pybedtools/issues/329
+# see requirements.txt
RDEPEND="
sci-biology/bedtools
sci-biology/pysam
+ dev-python/numpy
+ dev-python/pandas
!minimal? ( sci-libs/htslib )
doc? ( dev-python/sphinx )"
+# optional-requirements.txt also lists:
+# ucsc-bigwigtobedgraph
+# ucsc-bedgraphtobigwig
+# ucsc-wigtobigwig
DEPEND="${RDEPEND}
dev-python/cython[${PYTHON_USEDEP}]"
[gentoo-commits] proj/sci:master commit in: sci-biology/rtg-tools/
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/"${PN}"
+ doins build/rtg-tools.jar
+ doins lib/gzipfix.jar
+ dodoc installer/resources/tools/RTGOperationsManual.pdf
+ doins -r installer/resources/tools/RTGOperationsManual
+ dodoc installer/resources/tools/scripts/README.txt
+ dodoc installer/ReleaseNotes.txt
+ # TODO
+ # extract more files from the generated rtg-tools-3.11-39691f9f-base.zip
+ # file or better the installer/resources/ source directory
+ #
+ # install installer/resources/common/scripts/rtg-bash-completion
+}
+
+src_test(){
+ ant runalltests || die
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/RSeQC/
commit: af893929af04f870cdb56c83d35153eb8d8d1cdc
Author: Martin Mokrejs gmail com>
AuthorDate: Sun Oct 18 08:32:35 2020 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sun Oct 18 08:34:07 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=af893929
sci-biology/RSeQC: version bump
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/RSeQC/{RSeQC-2.6.1.ebuild => RSeQC-4.0.0.ebuild} | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
b/sci-biology/RSeQC/RSeQC-4.0.0.ebuild
similarity index 90%
rename from sci-biology/RSeQC/RSeQC-2.6.1.ebuild
rename to sci-biology/RSeQC/RSeQC-4.0.0.ebuild
index d3bbd9104..871aa946b 100644
--- a/sci-biology/RSeQC/RSeQC-2.6.1.ebuild
+++ b/sci-biology/RSeQC/RSeQC-4.0.0.ebuild
@@ -9,7 +9,7 @@ inherit distutils-r1
DESCRIPTION="Utilities for RNA-seq data quality control"
HOMEPAGE="https://rseqc.sourceforge.net;
-SRC_URI="https://sourceforge.net/projects/rseqc/files/RSeQC-2.6.1.tar.gz
+SRC_URI="https://sourceforge.net/projects/rseqc/files/RSeQC-${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/
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
-> ${P}.zip"
LICENSE="GPL-3+"
SLOT="0"
[gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
commit: f3a538b68e80b3fc42af81717f48a5cbfb283f45
Author: Martin Mokrejs gmail com>
AuthorDate: Fri May 15 19:30:28 2020 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri May 15 19:30:47 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f3a538b6
sci-biology/SPAdes: version bump to 3.14.1
This is a bug-fix release, which includes:
- Fix for read filtering tool;
- Soft and hard-filtered transcripts are now copied to the output
folder in rnaSPAdes;
- Minor fix in biosyntheticSPAdes pipeline;
- Minor fix in metaplasmidSPAdes contig output;
- Several usability fixes in `spades.py';
- Other minor bug-fixes.
Package-Manager: Portage-2.3.99, Repoman-2.3.22
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/SPAdes/{SPAdes-3.14.0.ebuild => SPAdes-3.14.1.ebuild} | 6 +-
1 file changed, 1 insertion(+), 5 deletions(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.14.0.ebuild
b/sci-biology/SPAdes/SPAdes-3.14.1.ebuild
similarity index 87%
rename from sci-biology/SPAdes/SPAdes-3.14.0.ebuild
rename to sci-biology/SPAdes/SPAdes-3.14.1.ebuild
index d3c1e0a57..773ccf658 100644
--- a/sci-biology/SPAdes/SPAdes-3.14.0.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.14.1.ebuild
@@ -13,11 +13,7 @@ SRC_URI="
https://github.com/ablab/spades/releases/download/v${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 ->
${P}_truspades_manual.html"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS=""
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: 3a0d3cb989aa14f980ad867cb8b7d7db5284789f
Author: Martin Mokrejs gmail com>
AuthorDate: Wed May 6 18:27:40 2020 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed May 6 18:28:05 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a0d3cb9
sci-biology/pybedtools: hopefully install generated HTML files
Package-Manager: Portage-2.3.95, Repoman-2.3.22
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 6 ++
1 file changed, 6 insertions(+)
diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
index 9d4dc23c0..440e644b7 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
@@ -29,3 +29,9 @@ src_compile(){
default
use doc && cd docs && emake html
}
+
+src_install(){
+ default
+ insinto /usr/share/doc/"${PN}"
+ doins -r docs/build/html
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
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[${PYTHON_USEDEP}]"
src_compile(){
python setup.py cythonize
default
+ use doc && cd docs && emake html
}
[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/
commit: ae5eb7ca6ede7e8579ade25afb8eb005c62ee35a
Author: Martin Mokrejs gmail com>
AuthorDate: Wed May 6 17:44:42 2020 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed May 6 17:44:49 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ae5eb7ca
sci-biology/pybedtools: update homepage, explicitly run cythonize
Package-Manager: Portage-2.3.95, Repoman-2.3.22
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 13 ++---
1 file changed, 10 insertions(+), 3 deletions(-)
diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
index d817a594f..cd444a09e 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 python3_{5,6,7,8} )
inherit distutils-r1
DESCRIPTION="Use BED and GFF files from python using BEDtools"
-HOMEPAGE="http://pythonhosted.org/pybedtools/;
+HOMEPAGE="https://daler.github.io/pybedtools;
SRC_URI="https://github.com/daler/pybedtools/archive/v${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/
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/
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/
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/
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/
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="${DEPEND}"
[gentoo-commits] proj/sci:master commit in: sci-biology/pysam/, sci-biology/pysamstats/
commit: b1ad15e7a10105fb9f0905ea5aac0835a62b46f3
Author: Martin Mokrejs gmail com>
AuthorDate: Fri Jan 10 16:32:20 2020 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jan 10 16:52:47 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b1ad15e7
sci-biology/pysamstats: version bump
sci-biology/pysam: version bump
I am not sure if the path pysam-0.12-fix-buildsystem.patch is still
needed or not. Nevertheless, the modules do not import properly into
python so the ebuild needs more work.
Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/pysam/metadata.xml | 12 ++
sci-biology/pysam/pysam-0.15.3.ebuild | 46 ++
...stats-0.24.2.ebuild => pysamstats-1.1.2.ebuild} | 9 +++--
3 files changed, 64 insertions(+), 3 deletions(-)
diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml
new file mode 100644
index 0..6182254bd
--- /dev/null
+++ b/sci-biology/pysam/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+sci-biol...@gentoo.org
+Gentoo Biology Project
+
+
+pysam
+pysam-developers/pysam
+
+
diff --git a/sci-biology/pysam/pysam-0.15.3.ebuild
b/sci-biology/pysam/pysam-0.15.3.ebuild
new file mode 100644
index 0..4224df0be
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.15.3.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_6 )
+
+inherit distutils-r1
+
+DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping
format"
+HOMEPAGE="
+ https://github.com/pysam-developers/pysam
+ https://pypi.org/project/pysam/;
+SRC_URI="mirror://pypi/${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="${DEPEND}"
[gentoo-commits] proj/sci:master commit in: sci-biology/tigmint/
commit: 61199804d047b3bb60a69643a79263d4d9f9ff6c
Author: Martin Mokrejs gmail com>
AuthorDate: Fri Jan 10 16:13:53 2020 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jan 10 16:13:58 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=61199804
sci-biology/tigmint: fix package name
Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/tigmint/tigmint-1.1.0.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/tigmint/tigmint-1.1.0.ebuild
b/sci-biology/tigmint/tigmint-1.1.0.ebuild
index 66a1f3460..7e2d6d143 100644
--- a/sci-biology/tigmint/tigmint-1.1.0.ebuild
+++ b/sci-biology/tigmint/tigmint-1.1.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -21,7 +21,7 @@ RDEPEND="${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/
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/
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="${DEPEND}"
[gentoo-commits] proj/sci:master commit in: sci-biology/NGSEPcore/, sci-biology/NGSEPcore/files/
commit: 0495ef801513cebc129bbcd392d955e86dea2fc9
Author: Martin Mokrejs gmail com>
AuthorDate: Fri Jan 10 15:55:18 2020 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jan 10 15:57:51 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0495ef80
sci-biology/NGSEPcore: cleanup the ebuild
Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs gmail.com>
sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild | 23 --
.../files/NGSEPcore_drop_utf8_chars.patch | 81 ++
.../files/NGSEPcore_fix_compilation.patch | 0
3 files changed, 97 insertions(+), 7 deletions(-)
diff --git a/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild
b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild
index 3f844bf16..24445eb0d 100644
--- a/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild
+++ b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -6,7 +6,8 @@ EAPI=7
inherit java-pkg-2 java-ant-2
DESCRIPTION="NGSEP (CNV and indel discovery)"
-HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home;
+HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home
+ https://github.com/NGSEP/NGSEPcore;
SRC_URI="https://sourceforge.net/projects/ngsep/files/SourceCode/NGSEPcore_${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/
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/
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/
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/
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/
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 $CONFIG_OPTS \
+ --with-lzma --with-gnutls --with-nettle --with-hdf5 --with-gmp
--with-fftw
+}
+
+pkg_postinst(){
+ einfo "The io_lib, snappy dependencies are not strictly needed"
+ einfo "but were forced for optimal libmaus2 performance."
+ einfo "igzip is only used if gzip level is set to 11."
+}
[gentoo-commits] proj/sci:master commit in: sci-libs/libmaus2/
commit: 6a52a6c327152d555ec8699271d8d4445a27f285
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Dec 30 15:14:45 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Dec 30 15:14:45 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6a52a6c3
sci-libs/libmaus2: update the ebuild for gitlab.com site
Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-libs/libmaus2/libmaus2-2.0.587.ebuild | 8 ++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
b/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
index 1c61df056..593fe083f 100644
--- a/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
+++ b/sci-libs/libmaus2/libmaus2-2.0.587.ebuild
@@ -5,9 +5,10 @@ EAPI=7
inherit autotools
+release_data="20190122104826"
DESCRIPTION="Library for biobambam2"
HOMEPAGE="https://github.com/gt1/libmaus;
-SRC_URI="https://gitlab.com/german.tischler/libmaus2/-/archive/master/${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/
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 ->
${P}.tar.gz"
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
commit: 37d6c90ece12854ac4ae220e0d95bc88ec3af1b9
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Dec 23 15:38:01 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Dec 23 15:38:01 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=37d6c90e
sci-biology/bowtie: version bump
Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/bowtie/bowtie-2.3.5.1.ebuild | 60 ++
.../bowtie/files/bowtie-2.3.5-fix-fifo.patch | 15 --
.../files/bowtie-2.3.5-fix-interleaved.patch | 15 --
3 files changed, 60 insertions(+), 30 deletions(-)
diff --git a/sci-biology/bowtie/bowtie-2.3.5.1.ebuild
b/sci-biology/bowtie/bowtie-2.3.5.1.ebuild
new file mode 100644
index 0..c2fef8667
--- /dev/null
+++ b/sci-biology/bowtie/bowtie-2.3.5.1.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
+HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/;
+SRC_URI="mirror://sourceforge/project/${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/
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/
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/
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/
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 -> ${P}.tar.gz"
-LICENSE="abyss"
+LICENSE="GPL-3"
SLOT="0"
IUSE="+mpi openmp misc-haskell"
KEYWORDS="~amd64 ~x86"
[gentoo-commits] proj/sci:master commit in: sci-biology/BRAKER/
commit: c7a40f0c2955843da5c85d0abbeed58351547ce1
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Thu Jul 18 17:12:10 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Jul 18 17:12:10 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c7a40f0c
sci-biology/BRAKER: version bump
New HOMEPAGE, SRC_URI, layout of .tar.gz tarball
Package-Manager: Portage-2.3.69, Repoman-2.3.16
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
.../BRAKER/{BRAKER-2.1.0.ebuild => BRAKER-2.1.2.ebuild} | 15 +++
1 file changed, 7 insertions(+), 8 deletions(-)
diff --git a/sci-biology/BRAKER/BRAKER-2.1.0.ebuild
b/sci-biology/BRAKER/BRAKER-2.1.2.ebuild
similarity index 79%
rename from sci-biology/BRAKER/BRAKER-2.1.0.ebuild
rename to sci-biology/BRAKER/BRAKER-2.1.2.ebuild
index 13d63d4b8..908e57e51 100644
--- a/sci-biology/BRAKER/BRAKER-2.1.0.ebuild
+++ b/sci-biology/BRAKER/BRAKER-2.1.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -8,9 +8,10 @@ inherit perl-module
DESCRIPTION="Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS"
# http://bioinf.uni-greifswald.de/bioinf/publications/pag2015.pdf
-HOMEPAGE="http://bioinf.uni-greifswald.de/bioinf/braker
+HOMEPAGE="https://github.com/Gaius-Augustus/BRAKER
+ http://bioinf.uni-greifswald.de/bioinf/braker
http://bioinf.uni-greifswald.de/augustus/downloads;
-SRC_URI="http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER_v"${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/
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/
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/
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/
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/
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/
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/
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="${RDEPEND}
[gentoo-commits] proj/sci:master commit in: sci-biology/chiron/
commit: e5ce549c694e952e624f1c4b2b751db1618294ec
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Sat Apr 13 20:36:02 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat Apr 13 20:36:02 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e5ce549c
sci-biology/chiron: Fix RDEPEND issue
RDEPEND uses the = operator with no revision:
'=sci-libs/tensorflow-1.0.1';
if any revision is acceptable, use '~' instead;
if only -r0 then please append '-r0' to the dep
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/chiron/chiron-.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/chiron/chiron-.ebuild
b/sci-biology/chiron/chiron-.ebuild
index cd99cb976..4294326ee 100644
--- a/sci-biology/chiron/chiron-.ebuild
+++ b/sci-biology/chiron/chiron-.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
PYTHON_COMPAT=( python2_7 pypy )
@@ -17,6 +17,6 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND="=sci-libs/tensorflow-1.0.1"
+DEPEND="~sci-libs/tensorflow-1.0.1"
RDEPEND="${DEPEND}
dev-python/h5py"
[gentoo-commits] proj/sci:master commit in: sci-mathematics/dolfin/
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++/
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/
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 "${DISTDIR}"/velvetk.pl
-}
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
commit: a6b601e64f7b9313fc7d7c2fec43d0f4d4d7ec1f
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Sat Mar 30 06:42:42 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat Mar 30 06:42:42 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a6b601e6
sci-biology/ncbi-tools++: document possible issue with builds
I have the following defined due to ncbi-tools++-18.0.0 installed
on my system:
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/32:
/usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0:
/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/32:
/usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0:
/usr/lib/llvm/7/lib32:
/usr/lib/llvm/7/lib64:
/usr/lib64/itcl4.1.1:
/usr/lib64/itk4.1.0:
/lib64:
/usr/lib64:
/usr/local/lib64:
/lib32:
/usr/lib32:
/usr/lib64/rust-1.29.2:
/usr/lib64/R/lib:
/usr/lib64/fltk:
/usr/lib64/ncbi-tools++:
/usr/lib64/staden:
grep: /etc: No such file or directory
grep: /etc/env.d: No such file or directory
/etc/env.d/99ncbi-tools++:LDPATH=/usr/lib64/ncbi-tools++
...
That in turn makes linker pick "${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="${PYTHON_REQUIRED_USE}"
# sys-libs/db should be compiled with USE=cxx
+# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test]
then?
DEPEND="
!sci-biology/sra_sdk
app-arch/cpio
berkdb? ( sys-libs/db:4.3[cxx] )
- boost? ( dev-libs/boost )
+ boost? ( dev-libs/boost[tools] )
curl? ( net-misc/curl )
sqlite? ( >=dev-db/sqlite-3.6.6:3 )
mysql? ( virtual/mysql )
[gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/
commit: 220946d413cfcfa399e3609f2b215eabdc8df3a8
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Sat Mar 30 00:13:51 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat Mar 30 00:13:51 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=220946d4
sci-biology/ncbi-tools++: version bump
It does not link if older version is installed because linker
picks up older version of libraries and obviously does not find
newly added functions.
Upstream says:
Please try either supplying an LD_RUN_PATH environment setting
or a -Wl,-rpath-link,... flag pointing at your build tree's lib
directory. Also, please bear in mind that adding the old
installation's library directory to the central search path largely
defeats the purpose of making it a separate directory.
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
.../ncbi-tools++/ncbi-tools++-22.0.0.ebuild| 380 +
1 file changed, 380 insertions(+)
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
new file mode 100644
index 0..585042f9f
--- /dev/null
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -0,0 +1,380 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit eutils flag-o-matic multilib python-single-r1 toolchain-funcs
+
+MY_TAG="Mar_28_2019"
+MY_Y="${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/
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
-> ${PN}-Zhang_et_al_2006.pdf"
LICENSE="GPL-3"
[gentoo-commits] proj/sci:master commit in: sci-biology/KaKs_Calculator/
commit: 9434b7843e92befab076411b1b39764ff4a35738
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Fri Mar 29 23:58:06 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Mar 29 23:58:06 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9434b784
sci-biology/KaKs_Calculator: fix download URL
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
index 5edd1323a..e6620b359 100644
--- a/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
+++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-2.0.ebuild
@@ -11,7 +11,7 @@ HOMEPAGE="https://code.google.com/p/kaks-calculator
https://www.sciencedirect.com/science/article/pii/S1672022910600083;
SRC_URI="
https://netcologne.dl.sourceforge.net/project/kakscalculator2/${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
-> ${PN}-Zhang_et_al_2006.pdf"
LICENSE="GPL-3"
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/, sci-biology/bowtie/files/
commit: 346ebf0f53a5e272706bcb6ad909ad72a62bb4c7
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Fri Mar 29 23:28:32 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Mar 29 23:28:32 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=346ebf0f
sci-biology/bowtie: add another upstream patch
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/bowtie/bowtie-2.3.5-r1.ebuild | 3 ++-
sci-biology/bowtie/files/bowtie-2.3.5-fix-fifo.patch | 15 +++
.../bowtie/files/bowtie-2.3.5-fix-interleaved.patch | 2 ++
3 files changed, 19 insertions(+), 1 deletion(-)
diff --git a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
index f79dcb9cb..2a6fc04eb 100644
--- a/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
+++ b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
@@ -27,7 +27,8 @@ S="${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/
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 "${S}"/configure || die
- # The below is wrong as it causes:
- # Enter path [
/var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/work/RepeatMasker ]:
- # -- Building monolithic RM database...sh:
/var/tmp/portage/sci-biology/repeatmasker-4.0.1-r1/image///usr/share/repeatmasker/Libraries/RepeatMasker.lib:
[gentoo-commits] proj/sci:master commit in: sci-biology/repeatmasker-libraries/
commit: 192396a3084735738acce2fbb93475b5da28078e
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Fri Mar 29 13:30:44 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Mar 29 13:30:44 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=192396a3
sci-biology/repeatmasker-libraries: dohtml has been banned for EAPI 7
This slipped through repoman checks.
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
.../repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild | 2 +-
.../repeatmasker-libraries/repeatmasker-libraries-20160829.ebuild | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git
a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild
b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild
index 160d8c62d..4b1222536 100644
--- a/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild
+++ b/sci-biology/repeatmasker-libraries/repeatmasker-libraries-20150807.ebuild
@@ -33,5 +33,5 @@ src_install() {
insinto /usr/share/repeatmasker/Libraries
doins "${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/
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/
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/
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 $f || die;
+ done
+}
+
+src_compile() {
+ emake clean && default
+
+ # compile stuff not compiled by default
+ # https://github.com/Gaius-Augustus/Augustus/issues/52
+ cd auxprogs/aln2wig || die
+ emake
+}
+
+src_ins
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet/
commit: 6ff12313344e3b1b686430875f4b866c67ab8d4f
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Thu Mar 28 22:06:49 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Mar 28 22:06:49 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6ff12313
sci-biology/tablet: fix indentation
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/tablet/tablet-.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/tablet/tablet-.ebuild
b/sci-biology/tablet/tablet-.ebuild
index 5cebde785..e9ae6890d 100644
--- a/sci-biology/tablet/tablet-.ebuild
+++ b/sci-biology/tablet/tablet-.ebuild
@@ -51,7 +51,7 @@ src_install() {
java-pkg_dojar lib/samtools-linux64.jar
fi
if [ "${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/
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+/
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/
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/
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="${WORKDIR}"/maker/src
pkg_
[gentoo-commits] proj/sci:master commit in: sci-biology/NGSTools/
commit: 6d35d6134317057345c6c80f77d35fa937083219
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Thu Mar 28 21:41:36 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Thu Mar 28 21:41:36 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6d35d613
sci-biology/NGSTools: renamed into NGSEPcore and NGSEPplugin
sci-biology/NGSTools/NGSTools-2.0.5.ebuild | 20
sci-biology/NGSTools/metadata.xml | 15 ---
2 files changed, 35 deletions(-)
diff --git a/sci-biology/NGSTools/NGSTools-2.0.5.ebuild
b/sci-biology/NGSTools/NGSTools-2.0.5.ebuild
deleted file mode 100644
index 862983fec..0
--- a/sci-biology/NGSTools/NGSTools-2.0.5.ebuild
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit java-pkg-2 java-ant-2 eutils
-
-S="${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="${DEPEND}"
diff --git a/sci-biology/NGSTools/metadata.xml
b/sci-biology/NGSTools/metadata.xml
deleted file mode 100644
index 642261079..0
--- a/sci-biology/NGSTools/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-
- mmokr...@fold.natur.cuni.cz
- Martin Mokrejs
-
-
- sci-biol...@gentoo.org
- Gentoo Biology Project
-
-
- ngsep
-
-
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/files/, sci-biology/bowtie/
commit: 2b44f30b60c65d2485250cb71e7dabe10a2694a6
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Wed Mar 27 22:45:47 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Mar 27 22:45:47 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2b44f30b
sci-biology/bowtie: patch --interleaved, add KEYWORDS
Do not unset contents of CFLAGS and CXXFLAGS.
Thanks to ch4rr0 at
https://github.com/BenLangmead/bowtie2/issues/239
Add deemed patch from
https://github.com/BenLangmead/bowtie2/issues/240
Added KEYWORDS.
Closes: https://bugs.gentoo.org/649824
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
.../bowtie/{bowtie-2.3.5.ebuild => bowtie-2.3.5-r1.ebuild} | 5 ++---
sci-biology/bowtie/files/bowtie-2.3.5-fix-interleaved.patch | 13 +
2 files changed, 15 insertions(+), 3 deletions(-)
diff --git a/sci-biology/bowtie/bowtie-2.3.5.ebuild
b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
similarity index 94%
rename from sci-biology/bowtie/bowtie-2.3.5.ebuild
rename to sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
index dd4d8be66..f79dcb9cb 100644
--- a/sci-biology/bowtie/bowtie-2.3.5.ebuild
+++ b/sci-biology/bowtie/bowtie-2.3.5-r1.ebuild
@@ -12,7 +12,7 @@
SRC_URI="https://github.com/BenLangmead/${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/
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}_${PV}"
+
+src_prepare(){
+ rm -f lib/NGSEPcore_3.3.1.jar lib/SortSam.jar lib/jcommon-1.0.17.jar
lib/xchart-2.4.2.jar || die
+ default
+}
+
+src_install(){
+ java-pkg_dojar *.jar
+}
diff --git a/sci-biology/NGSEPplugin/metadata.xml
b/sci-biology/NGSEPplugin/metadata.xml
new file mode 100644
index 0..642261079
--- /dev/null
+++ b/sci-biology/NGSEPplugin/metadata.xml
@@ -0,0 +1,15 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ mmokr...@fold.natur.cuni.cz
+ Martin Mokrejs
+
+
+ sci-biol...@gentoo.org
+ Gentoo Biology Project
+
+
+ ngsep
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/NGSEPcore/
commit: 26f7eab8fcc5e6148f85e81a876d1362c28c8e4f
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Wed Mar 27 16:23:05 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Wed Mar 27 16:23:05 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=26f7eab8
sci-biology/NGSEPcore: some improvements with the package
Still unfinished work.
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild | 37
sci-biology/NGSEPcore/metadata.xml | 15 +++
2 files changed, 52 insertions(+)
diff --git a/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild
b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild
new file mode 100644
index 0..3f844bf16
--- /dev/null
+++ b/sci-biology/NGSEPcore/NGSEPcore-3.3.1.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="NGSEP (CNV and indel discovery)"
+HOMEPAGE="https://sourceforge.net/p/ngsep/wiki/Home;
+SRC_URI="https://sourceforge.net/projects/ngsep/files/SourceCode/NGSEPcore_${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}"/${P}_user_manual.pdf
+}
diff --git a/sci-biology/NGSEPcore/metadata.xml
b/sci-biology/NGSEPcore/metadata.xml
new file mode 100644
index 0..642261079
--- /dev/null
+++ b/sci-biology/NGSEPcore/metadata.xml
@@ -0,0 +1,15 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ mmokr...@fold.natur.cuni.cz
+ Martin Mokrejs
+
+
+ sci-biol...@gentoo.org
+ Gentoo Biology Project
+
+
+ ngsep
+
+
[gentoo-commits] proj/sci:master commit in: sci-biology/bamql/
commit: f96c7ec91d0add7dfef7af06a4d81bc97cf0b7d9
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Mar 25 23:56:31 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Mar 25 23:56:31 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f96c7ec9
sci-biology/bamql: switch to `$(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 \
+ $(use_enable static-libs static)
}
[gentoo-commits] proj/sci:master commit in: sci-biology/bamql/, sci-biology/bamql/files/
commit: 732c892485ba23fb419d064b28cba2b0dd982f90
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Mar 25 23:52:45 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Mar 25 23:52:45 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=732c8924
sci-biology/bamql: remove dependency on llvm static libs
Thanks for the patch and guidance to François Bissey:
https://github.com/gentoo/sci/issues/907
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/bamql/bamql-1.6.1.ebuild | 12 ++-
sci-biology/bamql/bamql-.ebuild| 12 ++-
.../bamql-1.6.1_drop_enable_static_llvm.patch | 23 ++
3 files changed, 37 insertions(+), 10 deletions(-)
diff --git a/sci-biology/bamql/bamql-1.6.1.ebuild
b/sci-biology/bamql/bamql-1.6.1.ebuild
index 146793318..dacad6029 100644
--- a/sci-biology/bamql/bamql-1.6.1.ebuild
+++ b/sci-biology/bamql/bamql-1.6.1.ebuild
@@ -22,14 +22,16 @@ DEPEND="
dev-libs/libpcre"
RDEPEND="${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+/
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/
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/${PN}" > 99Tablet
[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/
commit: a12a2d7f3f65eb66e44d3fc907f4b24e85ef201a
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Mar 25 11:50:28 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Mar 25 11:50:28 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a12a2d7f
dev-java/htsjdk: drop old 2.1.0 version
dev-java/htsjdk/htsjdk-2.1.0.ebuild | 47 -
1 file changed, 47 deletions(-)
diff --git a/dev-java/htsjdk/htsjdk-2.1.0.ebuild
b/dev-java/htsjdk/htsjdk-2.1.0.ebuild
deleted file mode 100644
index c94f79781..0
--- a/dev-java/htsjdk/htsjdk-2.1.0.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc source"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats"
-HOMEPAGE="https://samtools.github.io/htsjdk/;
-SRC_URI="https://github.com/samtools/htsjdk/archive/${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 "${S}"/javadoc
-}
[gentoo-commits] proj/sci:master commit in: sci-biology/gffread/files/, sci-biology/gffread/
commit: e55065dc88a894edab65609ffdd4e275cdcd4bd0
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Mar 25 11:49:49 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Mar 25 11:49:49 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e55065dc
sci-biology/gffread: bump to 0.11.0, drop old patch, use sed hackery
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/gffread/files/Makefile.patch | 39 --
...gffread-0.9.12.ebuild => gffread-0.11.0.ebuild} | 25 +++---
2 files changed, 20 insertions(+), 44 deletions(-)
diff --git a/sci-biology/gffread/files/Makefile.patch
b/sci-biology/gffread/files/Makefile.patch
deleted file mode 100644
index 35e6b088e..0
--- a/sci-biology/gffread/files/Makefile.patch
+++ /dev/null
@@ -1,39 +0,0 @@
gffread-0.9.12/Makefile2018-06-26 09:52:26.024747027 +0200
-+++ gffread-0.9.12/Makefile2018-06-26 09:52:41.845177021 +0200
-@@ -1,4 +1,4 @@
--GCLDIR := ../gclib
-+GCLDIR := ../gclib-0.10.2
- SEARCHDIRS := -I. -I${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-"${PV}" gclib || die
+}
+
+src_compile(){
+ emake release
+}
+
+src_install(){
+ dobin gffread
+}
[gentoo-commits] proj/sci:master commit in: sci-biology/bowtie/
commit: 922b05adcf80432d8e8212128b90b456b8ad3fc5
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Mar 25 11:20:55 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Mar 25 11:20:55 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=922b05ad
sci-biology/bowtie: update SRC_URI and hash for 2.3.5
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/bowtie/{bowtie-2.3.4.3.ebuild => bowtie-2.3.5.ebuild} | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/bowtie/bowtie-2.3.4.3.ebuild
b/sci-biology/bowtie/bowtie-2.3.5.ebuild
similarity index 93%
rename from sci-biology/bowtie/bowtie-2.3.4.3.ebuild
rename to sci-biology/bowtie/bowtie-2.3.5.ebuild
index eea3059cf..dd4d8be66 100644
--- a/sci-biology/bowtie/bowtie-2.3.4.3.ebuild
+++ b/sci-biology/bowtie/bowtie-2.3.5.ebuild
@@ -8,6 +8,7 @@ inherit toolchain-funcs
DESCRIPTION="Popular short read aligner for Next-generation sequencing data"
HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/;
SRC_URI="mirror://sourceforge/project/${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/
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
${CDEPEND}"
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/
commit: 6520aa795d79c63f0566d8b1059acb95899f8f81
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Mar 25 09:40:18 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Mar 25 09:40:18 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6520aa79
sci-biology/tablet-bin: update license
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild | 14 +-
1 file changed, 1 insertion(+), 13 deletions(-)
diff --git a/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
index 51f2d7921..fb89b4208 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
@@ -14,19 +14,7 @@ SRC_URI="
amd64? (
https://ics.hutton.ac.uk/resources/tablet/installers/tablet_linux_x64_$(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/
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/
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 -> ${P}.sh )
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet-bin/
commit: 9f62533afcb9014961a43534237d3a31a7aa4d00
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Mar 25 09:03:15 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Mar 25 09:03:15 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9f62533a
sci-biology/tablet-bin: version bump, ebuild cleanup
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
...tablet-bin-1.16.09.06.ebuild => tablet-bin-1.17.08.17.ebuild} | 9 +
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
b/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
similarity index 93%
rename from sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
rename to sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
index 401515e00..6934743b1 100644
--- a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild
+++ b/sci-biology/tablet-bin/tablet-bin-1.17.08.17.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -10,8 +10,8 @@ inherit java-pkg-2 python-r1
DESCRIPTION="Viewer of next generation sequence assemblies and alignments"
HOMEPAGE="http://ics.hutton.ac.uk/tablet/;
SRC_URI="
- x86? (
http://bioinf.hutton.ac.uk/tablet/installers/tablet_linux_x86_$(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="${DEPEND}
+ >=virtual/jre-1.8:*"
# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar
# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not
sci-biology/samtools either
# replacing picard.jar with a symlink to picard.jar from sci-biology.picard
does not help either
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet/
commit: d54980d211f803108c958cd6b255827a0f9bd2a5
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Mar 25 09:25:31 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Mar 25 09:25:31 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d54980d2
sci-biology/tablet: drop old version
sci-biology/tablet/tablet-1.15.09.01.ebuild | 51 -
1 file changed, 51 deletions(-)
diff --git a/sci-biology/tablet/tablet-1.15.09.01.ebuild
b/sci-biology/tablet/tablet-1.15.09.01.ebuild
deleted file mode 100644
index c0b67d139..0
--- a/sci-biology/tablet/tablet-1.15.09.01.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit java-pkg-2 java-ant-2 python-r1
-
-# [ "$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/${PN}/" > 99Tablet
- doenvd 99Tablet
-}
[gentoo-commits] proj/sci:master commit in: sci-biology/tablet/
commit: b7d442c1ad60516bf1f2e25bdb4f7287ac29a0cd
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Mon Mar 25 09:30:16 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Mar 25 09:30:16 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b7d442c1
sci-biology/tablet: update ebuild
New homepage, switch from svn to github, new license, switch
from picard to htsjdk
There is no ./classes/ so `ant build` does not work for me.
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
...-1.16.09.06.ebuild => tablet-1.17.08.17.ebuild} | 25 ++--
sci-biology/tablet/tablet-.ebuild | 27 +++---
2 files changed, 25 insertions(+), 27 deletions(-)
diff --git a/sci-biology/tablet/tablet-1.16.09.06.ebuild
b/sci-biology/tablet/tablet-1.17.08.17.ebuild
similarity index 63%
rename from sci-biology/tablet/tablet-1.16.09.06.ebuild
rename to sci-biology/tablet/tablet-1.17.08.17.ebuild
index e72339d61..08a272961 100644
--- a/sci-biology/tablet/tablet-1.16.09.06.ebuild
+++ b/sci-biology/tablet/tablet-1.17.08.17.ebuild
@@ -1,26 +1,25 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
PYTHON_COMPAT=( python2_7 )
inherit java-pkg-2 java-ant-2 python-r1
-# [ "$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/
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/
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
