* [gentoo-commits] proj/sci:master commit in: sci-biology/cortex_var/
@ 2015-04-18 1:02 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2015-04-18 1:02 UTC (permalink / raw
To: gentoo-commits
commit: f140979d8539071c3643839bab3bd3736b42cfd5
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 18 01:01:20 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 18 01:01:20 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f140979d
sci-biology/cortex_var: new package with bundled htslib and gsl libraries
Package-Manager: portage-2.2.18
sci-biology/cortex_var/ChangeLog | 9 +++++
sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild | 47 +++++++++++++++++++++++
sci-biology/cortex_var/metadata.xml | 9 +++++
3 files changed, 65 insertions(+)
diff --git a/sci-biology/cortex_var/ChangeLog b/sci-biology/cortex_var/ChangeLog
new file mode 100644
index 0000000..7be9c85
--- /dev/null
+++ b/sci-biology/cortex_var/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/cortex_var
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*cortex_var-1.0.5.21 (18 Apr 2015)
+
+ 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +cortex_var-1.0.5.21.ebuild, +metadata.xml:
+ sci-biology/cortex_var: new package with bundled htslib and gsl libraries
diff --git a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
new file mode 100644
index 0000000..391b45f
--- /dev/null
+++ b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
+
+DESCRIPTION="Assemble and compare genotype variants (variant discovery without reference sequence)"
+HOMEPAGE="http://cortexassembler.sourceforge.net/index_cortex_var.html"
+SRC_URI="http://sourceforge.net/projects/cortexassembler/files/cortex_var/latest/CORTEX_release_v1.0.5.21.tgz
+ http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# http://www.well.ox.ac.uk/project-stampy
+
+DEPEND="sci-biology/vcftools
+ sci-libs/gsl
+ sci-libs/htslib
+ dev-lang/perl"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/CORTEX_release_v1.0.5.21
+
+src_prepare(){
+ sed -e "s/ -O3 / ${CFLAGS} /" Makefile || die
+}
+
+src_compile(){
+ rm -rf libs/htslib libs/gsl-1.15
+ make NUM_COLS=1 MAXK=31 cortex_var || die
+}
+
+src_install(){
+ bash install.sh || die
+ perl_set_version
+ insinto ${VENDOR_LIB}
+ doins scripts/analyse_variants/bioinf-perl/lib/* scripts/calling/*
+ echo "PATH=/usr/share/${PN}/scripts/analyse_variants/needleman_wunsch" > "${S}/99${PN}"
+ doenvd "${S}/99${PN}"
+ dodoc ${DISTDIR}/cortex_var_user_manual.pdf
+}
diff --git a/sci-biology/cortex_var/metadata.xml b/sci-biology/cortex_var/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/cortex_var/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/cortex_var/
@ 2015-04-18 1:03 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2015-04-18 1:03 UTC (permalink / raw
To: gentoo-commits
commit: 67abb4812d9f96a428aa5a956949a5c756736a96
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr 18 01:02:46 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr 18 01:02:46 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=67abb481
sci-biology/cortex_var: cleanup ebuild syntax
Package-Manager: portage-2.2.18
sci-biology/cortex_var/ChangeLog | 4 ++++
sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild | 4 ++--
2 files changed, 6 insertions(+), 2 deletions(-)
diff --git a/sci-biology/cortex_var/ChangeLog b/sci-biology/cortex_var/ChangeLog
index 7be9c85..645e306 100644
--- a/sci-biology/cortex_var/ChangeLog
+++ b/sci-biology/cortex_var/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ cortex_var-1.0.5.21.ebuild:
+ sci-biology/cortex_var: cleanup ebuild syntax
+
*cortex_var-1.0.5.21 (18 Apr 2015)
18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
index 391b45f..70118b8 100644
--- a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
+++ b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
@@ -32,7 +32,7 @@ src_prepare(){
}
src_compile(){
- rm -rf libs/htslib libs/gsl-1.15
+ rm -rf libs/htslib libs/gsl-1.15
make NUM_COLS=1 MAXK=31 cortex_var || die
}
@@ -43,5 +43,5 @@ src_install(){
doins scripts/analyse_variants/bioinf-perl/lib/* scripts/calling/*
echo "PATH=/usr/share/${PN}/scripts/analyse_variants/needleman_wunsch" > "${S}/99${PN}"
doenvd "${S}/99${PN}"
- dodoc ${DISTDIR}/cortex_var_user_manual.pdf
+ dodoc "${DISTDIR}"/cortex_var_user_manual.pdf
}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/cortex_var/
@ 2021-02-01 10:33 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2021-02-01 10:33 UTC (permalink / raw
To: gentoo-commits
commit: d71c56239475f71bc640d54a4e70f71335c9d637
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Feb 1 10:32:54 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Feb 1 10:32:54 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d71c5623
sci-biology/cortex_var: fix sed calls
but still does not compile, needs a patch
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
index 0e611a6c6..f5b86e25c 100644
--- a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
+++ b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
@@ -28,13 +28,15 @@ S="${WORKDIR}/CORTEX_release_v${PV}"
src_prepare(){
default
- sed -e "s/ -O3 / ${CFLAGS} /" Makefile || die
- sed -e "s#libs/gsl-1.15#${EPREFIX}/usr/include/gsl#" Makefile || die
+ sed -i -e "s/ -O3 / ${CFLAGS} /" Makefile || die
+ sed -i -e "s#libs/gsl-1.15#${EPREFIX}/usr/include/gsl#" Makefile || die
}
src_compile(){
rm -rf libs/htslib libs/gsl-1.15 || die
- emake NUM_COLS=1 MAXK=31 cortex_var || die
+ emake -C libs/string_buffer
+ emake STRING_BUF_PATH="${S}/libs/string_buffer" HTS_PATH="/usr/include/" -C libs/seq_file
+ emake NUM_COLS=1 MAXK=31 cortex_var
}
src_install(){
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/cortex_var/
@ 2021-03-18 18:54 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2021-03-18 18:54 UTC (permalink / raw
To: gentoo-commits
commit: c45961e65b1e5228dc796cf903fa6434d15b6738
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar 18 18:50:01 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar 18 18:50:01 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c45961e6
sci-biology/cortex_var: use perl_domodule
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
index f5b86e25c..d368f5db3 100644
--- a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
+++ b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
@@ -42,8 +42,7 @@ src_compile(){
src_install(){
bash install.sh || die
perl_set_version
- insinto ${VENDOR_LIB}
- doins scripts/analyse_variants/bioinf-perl/lib/* scripts/calling/*
+ perl_domodule scripts/analyse_variants/bioinf-perl/lib/* scripts/calling/*
echo \
"PATH=${EPREFIX}/usr/share/${PN}/scripts/analyse_variants/needleman_wunsch" \
> "${T}/99${PN}" || die
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/cortex_var/
@ 2022-01-25 13:34 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 13:34 UTC (permalink / raw
To: gentoo-commits
commit: 4faeb566066c8a06f19584614067ed826407c17f
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 13:33:55 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 13:33:55 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4faeb566
sci-biology/cortex_var: drop dead package
last update 2013
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild | 51 -----------------------
sci-biology/cortex_var/metadata.xml | 15 -------
2 files changed, 66 deletions(-)
diff --git a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
deleted file mode 100644
index d368f5db3..000000000
--- a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit perl-functions
-
-DESCRIPTION="Genotype variant discovery without reference sequence"
-HOMEPAGE="http://cortexassembler.sourceforge.net/index_cortex_var.html" # no https
-SRC_URI="
- https://sourceforge.net/projects/cortexassembler/files/cortex_var/latest/CORTEX_release_v${PV}.tgz
- http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-
-# http://www.well.ox.ac.uk/project-stampy
-
-DEPEND="
- sci-biology/vcftools
- sci-libs/gsl
- sci-libs/htslib:0=
- dev-lang/perl"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}/CORTEX_release_v${PV}"
-
-src_prepare(){
- default
- sed -i -e "s/ -O3 / ${CFLAGS} /" Makefile || die
- sed -i -e "s#libs/gsl-1.15#${EPREFIX}/usr/include/gsl#" Makefile || die
-}
-
-src_compile(){
- rm -rf libs/htslib libs/gsl-1.15 || die
- emake -C libs/string_buffer
- emake STRING_BUF_PATH="${S}/libs/string_buffer" HTS_PATH="/usr/include/" -C libs/seq_file
- emake NUM_COLS=1 MAXK=31 cortex_var
-}
-
-src_install(){
- bash install.sh || die
- perl_set_version
- perl_domodule scripts/analyse_variants/bioinf-perl/lib/* scripts/calling/*
- echo \
- "PATH=${EPREFIX}/usr/share/${PN}/scripts/analyse_variants/needleman_wunsch" \
- > "${T}/99${PN}" || die
- doenvd "${T}/99${PN}"
- dodoc "${DISTDIR}"/cortex_var_user_manual.pdf
-}
diff --git a/sci-biology/cortex_var/metadata.xml b/sci-biology/cortex_var/metadata.xml
deleted file mode 100644
index a2867d6fd..000000000
--- a/sci-biology/cortex_var/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">cortexassembler</remote-id>
- </upstream>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 5+ messages in thread
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