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

2021-03-06 Thread Andrew Ammerlaan 
commit: 3135d13c5e61485a195eeade8c0486176dd83264
Author: Andrew Ammerlaan  riseup  net>
AuthorDate: Sat Mar  6 11:04:43 2021 +
Commit: Andrew Ammerlaan  riseup  net>
CommitDate: Sat Mar  6 11:04:43 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3135d13c

sci-biology/freebayes: version bump 1.3.5, EAPI bump

fix build, use the meson build file

Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan  riseup.net>

 sci-biology/freebayes/freebayes-1.3.5.ebuild |  25 ++
 sci-biology/freebayes/freebayes-.ebuild  | 110 ---
 2 files changed, 25 insertions(+), 110 deletions(-)

diff --git a/sci-biology/freebayes/freebayes-1.3.5.ebuild 
b/sci-biology/freebayes/freebayes-1.3.5.ebuild
new file mode 100644
index 0..836508195
--- /dev/null
+++ b/sci-biology/freebayes/freebayes-1.3.5.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit meson
+
+DESCRIPTION="Bayesian gen. variant detector to find short polymorphisms"
+HOMEPAGE="https://github.com/ekg/freebayes;
+SRC_URI="https://github.com/freebayes/freebayes/releases/download/v${PV}/${P}-src.tar.gz;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+# tests not included in release tarball?
+RESTRICT="test"
+
+DEPEND=""
+RDEPEND="${DEPEND}
+   sci-libs/htslib
+   sci-biology/bamtools
+   sci-biology/samtools:*"
+
+S="${WORKDIR}/${PN}"

diff --git a/sci-biology/freebayes/freebayes-.ebuild 
b/sci-biology/freebayes/freebayes-.ebuild
deleted file mode 100644
index 34b92b2ef..0
--- a/sci-biology/freebayes/freebayes-.ebuild
+++ /dev/null
@@ -1,110 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils git-r3 toolchain-funcs
-
-DESCRIPTION="Bayesian gen. variant detector to find short polymorphisms"
-HOMEPAGE="https://github.com/ekg/freebayes;
-EGIT_REPO_URI="https://github.com/ekg/freebayes.git;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-CDEPEND="dev-util/cmake"
-DEPEND=""
-RDEPEND="${DEPEND}
-   sci-libs/htslib
-   sci-biology/bamtools
-   sci-biology/samtools:*"
-
-# $ git clone --recursive https://github.com/ekg/freebayes.git
-# Cloning into 'freebayes'...
-# remote: Counting objects: 4942, done.
-# remote: Total 4942 (delta 0), reused 0 (delta 0), pack-reused 4942
-# Receiving objects: 100% (4942/4942), 5.93 MiB | 1.13 MiB/s, done.
-# Resolving deltas: 100% (3274/3274), done.
-# Submodule 'SeqLib' (https://github.com/walaj/SeqLib.git) registered for path 
'SeqLib'
-# Submodule 'bamtools' (https://github.com/ekg/bamtools.git) registered for 
path 'bamtools'
-# Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) 
registered for path 'intervaltree'
-# Submodule 'bash-tap' (https://github.com/illusori/bash-tap.git) registered 
for path 'test/bash-tap'
-# Submodule 'test/test-simple-bash' 
(https://github.com/ingydotnet/test-simple-bash.git) registered for path 
'test/test-simple-bash'
-# Submodule 'vcflib' (https://github.com/vcflib/vcflib.git) registered for 
path 'vcflib'
-# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib'...
-# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/bamtools'...
-# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/intervaltree'...
-# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/test/bash-tap'...
-# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/test/test-simple-bash'...
-# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib'...
-# Submodule path 'SeqLib': checked out 
'cce1e410ef6d2ac64972f5cacd8a0f9b86cecdd8'
-# Submodule 'bwa' (https://github.com/jwalabroad/bwa) registered for path 
'SeqLib/bwa'
-# Submodule 'fermi-lite' (https://github.com/jwalabroad/fermi-lite) registered 
for path 'SeqLib/fermi-lite'
-# Submodule 'htslib' (https://github.com/samtools/htslib) registered for path 
'SeqLib/htslib'
-# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib/bwa'...
-# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib/fermi-lite'...
-# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib/htslib'...
-# Submodule path 'SeqLib/bwa': checked out 
'fbd4dbc03904eccd71cdca8cac7aa48da749c19c'
-# Submodule path 'SeqLib/fermi-lite': checked out 
'5bc90f8d70e2b66184eccbd223a3be714c914365'
-# Submodule path 'SeqLib/htslib': checked out 
'0f298ce22c5c825c506129bf242348a31630c382'
-# Submodule path 'bamtools': checked out 
'e77a43f5097ea7eee432ee765049c6b246d49baa'
-# Submodule path 'intervaltree': checked out 
'dbb4c513d1ad3baac516fc1484c995daf9b42838'
-# Submodule path 'test/bash-tap': checked out 
'c38fbfa401600cc81ccda66bfc0da3ea56288d03'
-# Submodule path

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

2018-01-20 Thread Martin Mokrejs 
commit: 3a5f9397ff4676cca0e05d3a89022af10ed8a044
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sat Jan 20 21:25:21 2018 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sat Jan 20 21:25:21 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a5f9397

sci-biology/freebayes: switch git:// to https://

Package-Manager: Portage-2.3.19, Repoman-2.3.6

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

diff --git a/sci-biology/freebayes/freebayes-.ebuild 
b/sci-biology/freebayes/freebayes-.ebuild
index db4bb6d0e..34b92b2ef 100644
--- a/sci-biology/freebayes/freebayes-.ebuild
+++ b/sci-biology/freebayes/freebayes-.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -21,7 +21,7 @@ RDEPEND="${DEPEND}
sci-biology/bamtools
sci-biology/samtools:*"
 
-# $ git clone --recursive git://github.com/ekg/freebayes.git
+# $ git clone --recursive https://github.com/ekg/freebayes.git
 # Cloning into 'freebayes'...
 # remote: Counting objects: 4942, done.
 # remote: Total 4942 (delta 0), reused 0 (delta 0), pack-reused 4942

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

2017-04-06 Thread Martin Mokrejs 
commit: aa9b6b16359dd555a865114f42119883ed03fd81
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Apr  6 23:23:28 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Apr  6 23:23:28 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=aa9b6b16

sci-biology/freebayes: use https instead of git protocol

Package-Manager: Portage-2.3.5, Repoman-2.3.1

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

diff --git a/sci-biology/freebayes/freebayes-.ebuild 
b/sci-biology/freebayes/freebayes-.ebuild
index 0018eae64..db4bb6d0e 100644
--- a/sci-biology/freebayes/freebayes-.ebuild
+++ b/sci-biology/freebayes/freebayes-.ebuild
@@ -7,7 +7,7 @@ inherit eutils git-r3 toolchain-funcs
 
 DESCRIPTION="Bayesian gen. variant detector to find short polymorphisms"
 HOMEPAGE="https://github.com/ekg/freebayes;
-EGIT_REPO_URI="git://github.com/ekg/freebayes.git"
+EGIT_REPO_URI="https://github.com/ekg/freebayes.git;
 
 LICENSE="MIT"
 SLOT="0"

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

2017-02-16 Thread Martin Mokrejs 
commit: 82ed45d332749dd1ace55c76840fe10e772d9150
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Feb 16 12:32:02 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Feb 16 12:32:02 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=82ed45d3

sci-biology/freebayes: use CDEPEND

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/freebayes/freebayes-.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/freebayes/freebayes-.ebuild 
b/sci-biology/freebayes/freebayes-.ebuild
index a5e640591..47ca72c0a 100644
--- a/sci-biology/freebayes/freebayes-.ebuild
+++ b/sci-biology/freebayes/freebayes-.ebuild
@@ -15,7 +15,8 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
-DEPEND="dev-util/cmake"
+CDEPEND="dev-util/cmake"
+DEPEND=""
 RDEPEND="${DEPEND}
sci-libs/htslib
sci-biology/bamtools

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

2017-02-16 Thread Martin Mokrejs 
commit: 456c869b7e5ae4d6efd1c2293b1181e59a5e6a67
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Feb 16 10:56:54 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Feb 16 10:56:54 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=456c869b

sci-biology/freebayes: respect CC/CXX/CFLAGS/CXXFLAGS

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/freebayes/freebayes-.ebuild | 21 +++--
 1 file changed, 19 insertions(+), 2 deletions(-)

diff --git a/sci-biology/freebayes/freebayes-.ebuild 
b/sci-biology/freebayes/freebayes-.ebuild
index 1b1eb89ed..a5e640591 100644
--- a/sci-biology/freebayes/freebayes-.ebuild
+++ b/sci-biology/freebayes/freebayes-.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=6
 
-inherit eutils git-r3
+inherit eutils git-r3 toolchain-funcs
 
 DESCRIPTION="Bayesian gen. variant detector to find short polymorphisms"
 HOMEPAGE="https://github.com/ekg/freebayes;
@@ -15,7 +15,7 @@ SLOT="0"
 KEYWORDS=""
 IUSE=""
 
-DEPEND=""
+DEPEND="dev-util/cmake"
 RDEPEND="${DEPEND}
sci-libs/htslib
sci-biology/bamtools
@@ -84,6 +84,23 @@ RDEPEND="${DEPEND}
 
 # g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../ttmath -I../bamtools/src/ 
-I../vcflib/src/ -I../vcflib/tabixpp/ -I../vcflib/smithwaterman/ 
-I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/tabixpp/htslib 
-I../SeqLib -I../SeqLib/htslib -c freebayes.cpp
 
+src_prepare(){
+   find . -name Makefile | while read f; do \
+   sed -e "s/-O3 -D_FILE_OFFSET_BITS=64/${CFLAGS}/" -i $f || die
+   sed -e "s/^CFLAGS:= -O3/CFLAGS ?= ${CFLAGS}/" -i $f || die
+   sed -e "s/^CXX = g++/CXX = $(tc-getCXX)/;s/^CXX=g++/CXX = 
$(tc-getCXX)/" -i $f || die
+   sed -e "s/g++ /$(tc-getCXX) /" -i $f || die
+   sed -e "s/-O3/${CXXFLAGS}/" -i $f || die
+   sed -e "s/^CC[  ]*=[]gcc/CC = $(tc-getCC)/" -i $f || die
+   sed -e "s/-g -Wall -O2/${CFLAGS}/;s/-g -Wall 
-Wno-unused-function -O2/${CFLAGS}/" -i $f || die
+   sed -e "s/-O3 /${CFLAGS}/;s/ -O3/${CFLAGS}/" -i $f || die
+   done
+   sed -e "s/^C=gcc/C = $(tc-getCC)/" -i Makefile || die
+   sed -e "s/gcc/$(tc-getCC)/" -i SeqLib/bwa/Makefile 
SeqLib/fermi-lite/Makefile || die
+   sed -e "s/g++/$(tc-getCXX)/" -i SeqLib/src/Makefile.am || die
+   default
+}
+
 src_compile(){
emake -j1 # vcflib/smithwaterman/ sometimes does not compile
 }

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

2017-02-16 Thread Martin Mokrejs 
commit: 5f3f4d9525b701b6643ecbdfa3835051201c6e25
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Feb 16 09:53:34 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Feb 16 09:53:34 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5f3f4d95

sci-biology/freebayes: force compilation in a single thread as parallel build 
fails

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/freebayes/freebayes-.ebuild | 6 +-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/sci-biology/freebayes/freebayes-.ebuild 
b/sci-biology/freebayes/freebayes-.ebuild
index b4eee4419..1b1eb89ed 100644
--- a/sci-biology/freebayes/freebayes-.ebuild
+++ b/sci-biology/freebayes/freebayes-.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -84,6 +84,10 @@ RDEPEND="${DEPEND}
 
 # g++ -O3 -D_FILE_OFFSET_BITS=64 -g -I../ttmath -I../bamtools/src/ 
-I../vcflib/src/ -I../vcflib/tabixpp/ -I../vcflib/smithwaterman/ 
-I../vcflib/multichoose/ -I../vcflib/filevercmp/ -I../vcflib/tabixpp/htslib 
-I../SeqLib -I../SeqLib/htslib -c freebayes.cpp
 
+src_compile(){
+   emake -j1 # vcflib/smithwaterman/ sometimes does not compile
+}
+
 src_install(){
dobin bin/freebayes bin/bamleftalign
 }

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

2016-12-08 Thread Martin Mokrejs 
commit: 34cc1e0894a7db5f6f6ce80372e3ca44e6eeaa6e
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Dec  8 23:06:32 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Dec  8 23:06:32 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=34cc1e08

sci-biology/freebayes: fix package herd name

Package-Manager: portage-2.3.3

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

diff --git a/sci-biology/freebayes/freebayes-.ebuild 
b/sci-biology/freebayes/freebayes-.ebuild
index 3a2b70b..b4eee44 100644
--- a/sci-biology/freebayes/freebayes-.ebuild
+++ b/sci-biology/freebayes/freebayes-.ebuild
@@ -17,9 +17,9 @@ IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}
-   sci-biology/htslib
+   sci-libs/htslib
sci-biology/bamtools
-   sci-biology/samtools"
+   sci-biology/samtools:*"
 
 # $ git clone --recursive git://github.com/ekg/freebayes.git
 # Cloning into 'freebayes'...

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

2016-12-02 Thread Martin Mokrejs 
commit: cb254becffa1b3891a42871345dfdf2977b134fa
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Fri Dec  2 21:45:13 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Dec  2 21:45:13 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=cb254bec

sci-biology/freebayes: note the many bundled deps we need to unbundle

Package-Manager: portage-2.3.2

 sci-biology/freebayes/freebayes-.ebuild | 64 +
 1 file changed, 64 insertions(+)

diff --git a/sci-biology/freebayes/freebayes-.ebuild 
b/sci-biology/freebayes/freebayes-.ebuild
index 02bfc0b..3a2b70b 100644
--- a/sci-biology/freebayes/freebayes-.ebuild
+++ b/sci-biology/freebayes/freebayes-.ebuild
@@ -17,9 +17,73 @@ IUSE=""
 
 DEPEND=""
 RDEPEND="${DEPEND}
+   sci-biology/htslib
sci-biology/bamtools
sci-biology/samtools"
 
+# $ git clone --recursive git://github.com/ekg/freebayes.git
+# Cloning into 'freebayes'...
+# remote: Counting objects: 4942, done.
+# remote: Total 4942 (delta 0), reused 0 (delta 0), pack-reused 4942
+# Receiving objects: 100% (4942/4942), 5.93 MiB | 1.13 MiB/s, done.
+# Resolving deltas: 100% (3274/3274), done.
+# Submodule 'SeqLib' (https://github.com/walaj/SeqLib.git) registered for path 
'SeqLib'
+# Submodule 'bamtools' (https://github.com/ekg/bamtools.git) registered for 
path 'bamtools'
+# Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) 
registered for path 'intervaltree'
+# Submodule 'bash-tap' (https://github.com/illusori/bash-tap.git) registered 
for path 'test/bash-tap'
+# Submodule 'test/test-simple-bash' 
(https://github.com/ingydotnet/test-simple-bash.git) registered for path 
'test/test-simple-bash'
+# Submodule 'vcflib' (https://github.com/vcflib/vcflib.git) registered for 
path 'vcflib'
+# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib'...
+# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/bamtools'...
+# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/intervaltree'...
+# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/test/bash-tap'...
+# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/test/test-simple-bash'...
+# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib'...
+# Submodule path 'SeqLib': checked out 
'cce1e410ef6d2ac64972f5cacd8a0f9b86cecdd8'
+# Submodule 'bwa' (https://github.com/jwalabroad/bwa) registered for path 
'SeqLib/bwa'
+# Submodule 'fermi-lite' (https://github.com/jwalabroad/fermi-lite) registered 
for path 'SeqLib/fermi-lite'
+# Submodule 'htslib' (https://github.com/samtools/htslib) registered for path 
'SeqLib/htslib'
+# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib/bwa'...
+# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib/fermi-lite'...
+# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/SeqLib/htslib'...
+# Submodule path 'SeqLib/bwa': checked out 
'fbd4dbc03904eccd71cdca8cac7aa48da749c19c'
+# Submodule path 'SeqLib/fermi-lite': checked out 
'5bc90f8d70e2b66184eccbd223a3be714c914365'
+# Submodule path 'SeqLib/htslib': checked out 
'0f298ce22c5c825c506129bf242348a31630c382'
+# Submodule path 'bamtools': checked out 
'e77a43f5097ea7eee432ee765049c6b246d49baa'
+# Submodule path 'intervaltree': checked out 
'dbb4c513d1ad3baac516fc1484c995daf9b42838'
+# Submodule path 'test/bash-tap': checked out 
'c38fbfa401600cc81ccda66bfc0da3ea56288d03'
+# Submodule path 'test/test-simple-bash': checked out 
'124673ff204b01c8e96b7fc9f9b32ee35d898acc'
+# Submodule path 'vcflib': checked out 
'5e3ce04f758c6df16bc4d242b18a24d725d2e6e5'
+# Submodule 'fastahack' (https://github.com/ekg/fastahack.git) registered for 
path 'vcflib/fastahack'
+# Submodule 'filevercmp' (https://github.com/ekg/filevercmp.git) registered 
for path 'vcflib/filevercmp'
+# Submodule 'fsom' (https://github.com/ekg/fsom.git) registered for path 
'vcflib/fsom'
+# Submodule 'googletest' (https://github.com/google/googletest.git) registered 
for path 'vcflib/googletest'
+# Submodule 'intervaltree' (https://github.com/ekg/intervaltree.git) 
registered for path 'vcflib/intervaltree'
+# Submodule 'multichoose' (https://github.com/ekg/multichoose.git) registered 
for path 'vcflib/multichoose'
+# Submodule 'smithwaterman' (https://github.com/ekg/smithwaterman.git) 
registered for path 'vcflib/smithwaterman'
+# Submodule 'tabixpp' (https://github.com/ekg/tabixpp.git) registered for path 
'vcflib/tabixpp'
+# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/fastahack'...
+# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/filevercmp'...
+# Cloning into 
'/home/mmokrejs/proj/sci/sci-biology/freebayes/a/freebayes/vcflib/fsom'...
+# Cloning into

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

2016-07-27 Thread Martin Mokrejs 
commit: 119a938243db6ec4fc221bc31435ad8c3b11a44c
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Wed Jul 27 11:03:37 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Wed Jul 27 11:03:37 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=119a9382

sci-biology/freebayes: adjust to current devel tree

Package-Manager: portage-2.2.28

 sci-biology/freebayes/freebayes-.ebuild | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/sci-biology/freebayes/freebayes-.ebuild 
b/sci-biology/freebayes/freebayes-.ebuild
index a21a4da..02bfc0b 100644
--- a/sci-biology/freebayes/freebayes-.ebuild
+++ b/sci-biology/freebayes/freebayes-.ebuild
@@ -6,7 +6,7 @@ EAPI=6
 
 inherit eutils git-r3
 
-DESCRIPTION="Bayesian gen. variant detector to find small polymorphisms"
+DESCRIPTION="Bayesian gen. variant detector to find short polymorphisms"
 HOMEPAGE="https://github.com/ekg/freebayes;
 EGIT_REPO_URI="git://github.com/ekg/freebayes.git"
 
@@ -22,5 +22,4 @@ RDEPEND="${DEPEND}
 
 src_install(){
dobin bin/freebayes bin/bamleftalign
-   dobin vcflib/bin/*
 }

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

2016-02-14 Thread Justin Lecher 
commit: 2a3502b66122751757dd86d441bd520d57e900cf
Author: Justin Lecher  gentoo  org>
AuthorDate: Sun Feb 14 17:30:14 2016 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Sun Feb 14 17:30:14 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2a3502b6

sci-biology/freebayes: Bump to EAPI=6

* Use git-r3.eclass

Package-Manager: portage-2.2.27
Signed-off-by: Justin Lecher  gentoo.org>

 sci-biology/freebayes/freebayes-.ebuild | 27 ++-
 1 file changed, 6 insertions(+), 21 deletions(-)

diff --git a/sci-biology/freebayes/freebayes-.ebuild 
b/sci-biology/freebayes/freebayes-.ebuild
index c344fd0..a21a4da 100644
--- a/sci-biology/freebayes/freebayes-.ebuild
+++ b/sci-biology/freebayes/freebayes-.ebuild
@@ -1,33 +1,18 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
-inherit eutils
+inherit eutils git-r3
 
-[ "$PV" == "" ] && inherit git-2
-
-DESCRIPTION="Bayesian gen. variant detector to find small polymorphisms: SNPs, 
indels, MNPs and complex events"
+DESCRIPTION="Bayesian gen. variant detector to find small polymorphisms"
 HOMEPAGE="https://github.com/ekg/freebayes;
-
-if [ "$PV" == "" ]; then
-   EGIT_REPO_URI="git://github.com/ekg/freebayes.git"
-   EGIT_OPTIONS="--recursive --recurse-submodules"
-   KEYWORDS=""
-else
-   EGIT_REPO_URI="git://github.com/ekg/freebayes.git"
-   EGIT_OPTIONS="--recursive --recurse-submodules"
-   EGIT_BRANCH="v0.9.21"
-   KEYWORDS=""
-fi
-
-# To build freebayes you must use git to also download its submodules.
-#   Do so by downloading freebayes again using this command (note --recursive 
flag):
-#   git clone --recursive git://github.com/ekg/freebayes.git
+EGIT_REPO_URI="git://github.com/ekg/freebayes.git"
 
 LICENSE="MIT"
 SLOT="0"
+KEYWORDS=""
 IUSE=""
 
 DEPEND=""

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

2015-06-05 Thread Justin Lecher 
commit: f214d7f47d30cf809d9c63801b80b215ab98d46f
Author: Justin Lecher jlec AT gentoo DOT org
AuthorDate: Fri Jun  5 11:04:40 2015 +
Commit: Justin Lecher jlec AT gentoo DOT org
CommitDate: Fri Jun  5 11:04:40 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f214d7f4

sci-biology/freebayes: Add github to remote-id in metadata.xml

Package-Manager: portage-2.2.20

 sci-biology/freebayes/ChangeLog| 3 +++
 sci-biology/freebayes/metadata.xml | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/sci-biology/freebayes/ChangeLog b/sci-biology/freebayes/ChangeLog
index 8921fb7..be68896 100644
--- a/sci-biology/freebayes/ChangeLog
+++ b/sci-biology/freebayes/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 Jun 2015; Justin Lecher j...@gentoo.org metadata.xml:
+  sci-biology/freebayes: Add github to remote-id in metadata.xml
+
   13 Mar 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz
   freebayes-.ebuild:
   install also the vcftools binaries although it should be a separate package

diff --git a/sci-biology/freebayes/metadata.xml 
b/sci-biology/freebayes/metadata.xml
index 2bc8930..88b3811 100644
--- a/sci-biology/freebayes/metadata.xml
+++ b/sci-biology/freebayes/metadata.xml
@@ -6,4 +6,7 @@
 emailmmokr...@fold.natur.cuni.cz/email
 nameMartin Mokrejs/name
   /maintainer
+  upstream
+remote-id type=githubekg/freebayes/remote-id
+  /upstream
 /pkgmetadata

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

2015-03-13 Thread Martin Mokrejs 
commit: 4e4ed2d2a3189ee59a93d417d840a25527ca33bc
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Fri Mar 13 12:33:03 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Fri Mar 13 12:33:03 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4e4ed2d2

install also the vcftools binaries although it should be a separate package

Package-Manager: portage-2.2.15

 sci-biology/freebayes/ChangeLog | 4 
 sci-biology/freebayes/freebayes-.ebuild | 3 ++-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/sci-biology/freebayes/ChangeLog b/sci-biology/freebayes/ChangeLog
index e30f7d3..8921fb7 100644
--- a/sci-biology/freebayes/ChangeLog
+++ b/sci-biology/freebayes/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  13 Mar 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz
+  freebayes-.ebuild:
+  install also the vcftools binaries although it should be a separate package
+
   11 Mar 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz
   freebayes-.ebuild:
   added src_install()

diff --git a/sci-biology/freebayes/freebayes-.ebuild 
b/sci-biology/freebayes/freebayes-.ebuild
index 2f9aac4..88f6212 100644
--- a/sci-biology/freebayes/freebayes-.ebuild
+++ b/sci-biology/freebayes/freebayes-.ebuild
@@ -36,5 +36,6 @@ RDEPEND=${DEPEND}
sci-biology/samtools
 
 src_install(){
-   dobin  bin/freebayes bin/bamleftalign
+   dobin bin/freebayes bin/bamleftalign
+   dobin vcflib/bin/*
 }

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

2015-03-11 Thread Martin Mokrejs 
commit: e7341cf8c7b18b1d2288a690636b912fe7dd8870
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Wed Mar 11 20:25:51 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Wed Mar 11 20:25:51 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e7341cf8

ebuild cleanup; the git clone --recursive flag does not work

Package-Manager: portage-2.2.15

 sci-biology/freebayes/ChangeLog |  6 +-
 sci-biology/freebayes/freebayes-.ebuild | 18 --
 2 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/sci-biology/freebayes/ChangeLog b/sci-biology/freebayes/ChangeLog
index 9374edf..8915dfe 100644
--- a/sci-biology/freebayes/ChangeLog
+++ b/sci-biology/freebayes/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/freebayes
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  11 Mar 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz
+  freebayes-.ebuild:
+  ebuild cleanup; the git clone --recursive flag does not work
+
   16 Sep 2014; Christoph Junghans ott...@gentoo.org freebayes-.ebuild:
   fixed DESCRIPTION
 

diff --git a/sci-biology/freebayes/freebayes-.ebuild 
b/sci-biology/freebayes/freebayes-.ebuild
index 3d40b37..f43e1d2 100644
--- a/sci-biology/freebayes/freebayes-.ebuild
+++ b/sci-biology/freebayes/freebayes-.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -10,18 +10,24 @@ inherit eutils
 
 DESCRIPTION=Bayesian gen. variant detector to find small polymorphisms: SNPs, 
indels, MNPs and complex events
 HOMEPAGE=https://github.com/ekg/freebayes;
-EGIT_REPO_URI=git://github.com/ekg/freebayes.git
 
-# need top checkout vcflib/ as well
-#
+if [ $PV ==  ]; then
+   EGIT_REPO_URI=git://github.com/ekg/freebayes.git
+   EGIT_OPTIONS=--recursive --recurse-submodules
+   KEYWORDS=
+else
+   EGIT_REPO_URI=git://github.com/ekg/freebayes.git
+   EGIT_OPTIONS=--recursive --recurse-submodules
+   EGIT_BRANCH=v0.9.21
+   KEYWORDS=
+fi
+
 # To build freebayes you must use git to also download its submodules.
 #   Do so by downloading freebayes again using this command (note --recursive 
flag):
 #   git clone --recursive git://github.com/ekg/freebayes.git
-#
 
 LICENSE=MIT
 SLOT=0
-KEYWORDS=
 IUSE=
 
 DEPEND=

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

2015-03-11 Thread Martin Mokrejs 
commit: c539619b5a6eed42d40d34c185d035ef5b3350c4
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Wed Mar 11 20:39:04 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Wed Mar 11 20:39:04 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c539619b

added src_install()

Package-Manager: portage-2.2.15

 sci-biology/freebayes/ChangeLog | 4 
 sci-biology/freebayes/freebayes-.ebuild | 4 
 2 files changed, 8 insertions(+)

diff --git a/sci-biology/freebayes/ChangeLog b/sci-biology/freebayes/ChangeLog
index 8915dfe..e30f7d3 100644
--- a/sci-biology/freebayes/ChangeLog
+++ b/sci-biology/freebayes/ChangeLog
@@ -4,6 +4,10 @@
 
   11 Mar 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz
   freebayes-.ebuild:
+  added src_install()
+
+  11 Mar 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz
+  freebayes-.ebuild:
   ebuild cleanup; the git clone --recursive flag does not work
 
   16 Sep 2014; Christoph Junghans ott...@gentoo.org freebayes-.ebuild:

diff --git a/sci-biology/freebayes/freebayes-.ebuild 
b/sci-biology/freebayes/freebayes-.ebuild
index f43e1d2..2f9aac4 100644
--- a/sci-biology/freebayes/freebayes-.ebuild
+++ b/sci-biology/freebayes/freebayes-.ebuild
@@ -34,3 +34,7 @@ DEPEND=
 RDEPEND=${DEPEND}
sci-biology/bamtools
sci-biology/samtools
+
+src_install(){
+   dobin  bin/freebayes bin/bamleftalign
+}

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

2014-09-16 Thread Christoph Junghans 
commit: 37ad6d45a24e84fb0dd6ac03f7325390c251d156
Author: Christoph Junghans ottxor AT gentoo DOT org
AuthorDate: Tue Sep 16 17:27:37 2014 +
Commit: Christoph Junghans ottxor AT gentoo DOT org
CommitDate: Tue Sep 16 17:27:37 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=37ad6d45

fixed DESCRIPTION

Package-Manager: portage-2.2.8-r1

---
 sci-biology/freebayes/ChangeLog | 4 +++-
 sci-biology/freebayes/freebayes-.ebuild | 2 +-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/sci-biology/freebayes/ChangeLog b/sci-biology/freebayes/ChangeLog
index 17424da..9374edf 100644
--- a/sci-biology/freebayes/ChangeLog
+++ b/sci-biology/freebayes/ChangeLog
@@ -2,9 +2,11 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  16 Sep 2014; Christoph Junghans ott...@gentoo.org freebayes-.ebuild:
+  fixed DESCRIPTION
+
 *freebayes- (24 Mar 2014)
 
   24 Mar 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz
   +freebayes-.ebuild, +metadata.xml:
   a new package skeleton; need to retrive from git in a recursive way
-

diff --git a/sci-biology/freebayes/freebayes-.ebuild 
b/sci-biology/freebayes/freebayes-.ebuild
index 0876efb..3d40b37 100644
--- a/sci-biology/freebayes/freebayes-.ebuild
+++ b/sci-biology/freebayes/freebayes-.ebuild
@@ -8,7 +8,7 @@ inherit eutils
 
 [ $PV ==  ]  inherit git-2
 
-DESCRIPTION=Bayesian genetic variant detector designed to find small 
polymorphisms: SNPs, indels, MNPs and complex events
+DESCRIPTION=Bayesian gen. variant detector to find small polymorphisms: SNPs, 
indels, MNPs and complex events
 HOMEPAGE=https://github.com/ekg/freebayes;
 EGIT_REPO_URI=git://github.com/ekg/freebayes.git

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

2014-03-23 Thread Martin Mokrejs 
commit: 5c73aaa78d02e3b384be3b52120625ed8b507e19
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Mon Mar 24 01:41:35 2014 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Mon Mar 24 01:41:35 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5c73aaa7

sci-biology/freebayes: a new package skeleton; need to retrive from git in a 
recursive way

---
 sci-biology/freebayes/ChangeLog | 10 ++
 sci-biology/freebayes/freebayes-.ebuild | 30 +
 sci-biology/freebayes/metadata.xml  |  9 +
 3 files changed, 49 insertions(+)

diff --git a/sci-biology/freebayes/ChangeLog b/sci-biology/freebayes/ChangeLog
new file mode 100644
index 000..17424da
--- /dev/null
+++ b/sci-biology/freebayes/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/freebayes
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*freebayes- (24 Mar 2014)
+
+  24 Mar 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz
+  +freebayes-.ebuild, +metadata.xml:
+  a new package skeleton; need to retrive from git in a recursive way
+

diff --git a/sci-biology/freebayes/freebayes-.ebuild 
b/sci-biology/freebayes/freebayes-.ebuild
new file mode 100644
index 000..0876efb
--- /dev/null
+++ b/sci-biology/freebayes/freebayes-.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit eutils
+
+[ $PV ==  ]  inherit git-2
+
+DESCRIPTION=Bayesian genetic variant detector designed to find small 
polymorphisms: SNPs, indels, MNPs and complex events
+HOMEPAGE=https://github.com/ekg/freebayes;
+EGIT_REPO_URI=git://github.com/ekg/freebayes.git
+
+# need top checkout vcflib/ as well
+#
+# To build freebayes you must use git to also download its submodules.
+#   Do so by downloading freebayes again using this command (note --recursive 
flag):
+#   git clone --recursive git://github.com/ekg/freebayes.git
+#
+
+LICENSE=MIT
+SLOT=0
+KEYWORDS=
+IUSE=
+
+DEPEND=
+RDEPEND=${DEPEND}
+   sci-biology/bamtools
+   sci-biology/samtools

diff --git a/sci-biology/freebayes/metadata.xml 
b/sci-biology/freebayes/metadata.xml
new file mode 100644
index 000..2bc8930
--- /dev/null
+++ b/sci-biology/freebayes/metadata.xml
@@ -0,0 +1,9 @@
+?xml version=1.0 encoding=UTF-8?
+!DOCTYPE pkgmetadata SYSTEM http://www.gentoo.org/dtd/metadata.dtd;
+pkgmetadata
+  herdsci-biology/herd
+  maintainer
+emailmmokr...@fold.natur.cuni.cz/email
+nameMartin Mokrejs/name
+  /maintainer
+/pkgmetadata