* [gentoo-commits] proj/sci:master commit in: sci-biology/pairagon/
@ 2015-03-05 19:59 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-03-05 19:59 UTC (permalink / raw
To: gentoo-commits
commit: bcb9a5d452923bb22ec34d016db972ccb31b080f
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 5 19:58:57 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 5 19:58:57 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=bcb9a5d4
new package
Package-Manager: portage-2.2.15
sci-biology/pairagon/ChangeLog | 9 +++++++
sci-biology/pairagon/metadata.xml | 9 +++++++
sci-biology/pairagon/pairagon-1.1.ebuild | 42 ++++++++++++++++++++++++++++++++
3 files changed, 60 insertions(+)
diff --git a/sci-biology/pairagon/ChangeLog b/sci-biology/pairagon/ChangeLog
new file mode 100644
index 0000000..b7c1ceb
--- /dev/null
+++ b/sci-biology/pairagon/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/pairagon
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*pairagon-1.1 (05 Mar 2015)
+
+ 05 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+ +pairagon-1.1.ebuild:
+ new package
diff --git a/sci-biology/pairagon/metadata.xml b/sci-biology/pairagon/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/pairagon/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>
diff --git a/sci-biology/pairagon/pairagon-1.1.ebuild b/sci-biology/pairagon/pairagon-1.1.ebuild
new file mode 100644
index 0000000..bceba33
--- /dev/null
+++ b/sci-biology/pairagon/pairagon-1.1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="HMM-based cDNA to genome aligner"
+HOMEPAGE="http://mblab.wustl.edu/software.html"
+SRC_URI="http://mblab.wustl.edu/software/download/pairagon_.tar"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="dev-lang/perl"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/pairagon
+
+src_prepare(){
+ sed -e 's:src/get-glib-flags.sh:#src/get-glib-flags.sh:; s:-Wall -Werror::' -i Makefile
+}
+
+src_compile(){
+ emake pairagon-linux
+}
+
+src_install(){
+ # emake DESTDIR="${D}"/usr install
+ dobin bin/*
+ dodoc README
+ insinto /usr/share/pairagon
+ doins parameters/*
+ eval `perl '-V:installvendorlib'`
+ vendor_lib_install_dir="${installvendorlib}"
+ dodir ${vendor_lib_install_dir}/pairagon
+ insinto ${vendor_lib_install_dir}/pairagon
+ doins lib/perl5/Alignment.pm
+ echo "PERL5LIB="${vendor_lib_install_dir}"/pairagon" > ${S}"/99pairagon"
+ doenvd ${S}"/99pairagon" || die
+}
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/pairagon/
@ 2015-03-19 10:37 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-03-19 10:37 UTC (permalink / raw
To: gentoo-commits
commit: bba46880fc2e9fd6af8a92949d4a664e856f4dbb
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 19 10:36:38 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 19 10:36:38 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=bba46880
removing KEYWORDS until the perl files are installed to some other place. At the moment I get: 'perl-module.eclass: Suspicious environment values found. PERL5LIB="/usr/lib64/perl5/vendor_perl/5.18.2/pairagon"'
Package-Manager: portage-2.2.15
sci-biology/pairagon/ChangeLog | 5 +++++
sci-biology/pairagon/pairagon-1.1.ebuild | 2 +-
2 files changed, 6 insertions(+), 1 deletion(-)
diff --git a/sci-biology/pairagon/ChangeLog b/sci-biology/pairagon/ChangeLog
index b7c1ceb..1cc6bcb 100644
--- a/sci-biology/pairagon/ChangeLog
+++ b/sci-biology/pairagon/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> pairagon-1.1.ebuild:
+ removing KEYWORDS until the perl files are installed to some other place. At
+ the moment I get: 'perl-module.eclass: Suspicious environment values found.
+ PERL5LIB="/usr/lib64/perl5/vendor_perl/5.18.2/pairagon"'
+
*pairagon-1.1 (05 Mar 2015)
05 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
diff --git a/sci-biology/pairagon/pairagon-1.1.ebuild b/sci-biology/pairagon/pairagon-1.1.ebuild
index bceba33..b532f63 100644
--- a/sci-biology/pairagon/pairagon-1.1.ebuild
+++ b/sci-biology/pairagon/pairagon-1.1.ebuild
@@ -10,7 +10,7 @@ SRC_URI="http://mblab.wustl.edu/software/download/pairagon_.tar"
LICENSE="BSD-2"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
IUSE=""
DEPEND="dev-lang/perl"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pairagon/
@ 2015-04-17 23:56 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2015-04-17 23:56 UTC (permalink / raw
To: gentoo-commits
commit: 3d121e03a40d2858ee3715abc8553960c2877c3f
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 17 23:33:35 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 17 23:33:35 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3d121e03
sci-biology/pairagon: fixed installation of perl-related files
Package-Manager: portage-2.2.18
sci-biology/pairagon/ChangeLog | 3 +++
sci-biology/pairagon/pairagon-1.1.ebuild | 13 ++++++-------
2 files changed, 9 insertions(+), 7 deletions(-)
diff --git a/sci-biology/pairagon/ChangeLog b/sci-biology/pairagon/ChangeLog
index 1cc6bcb..2f0d713 100644
--- a/sci-biology/pairagon/ChangeLog
+++ b/sci-biology/pairagon/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> pairagon-1.1.ebuild:
+ sci-biology/pairagon: fixed installation of perl-related files
+
19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> pairagon-1.1.ebuild:
removing KEYWORDS until the perl files are installed to some other place. At
the moment I get: 'perl-module.eclass: Suspicious environment values found.
diff --git a/sci-biology/pairagon/pairagon-1.1.ebuild b/sci-biology/pairagon/pairagon-1.1.ebuild
index b532f63..6d78d0a 100644
--- a/sci-biology/pairagon/pairagon-1.1.ebuild
+++ b/sci-biology/pairagon/pairagon-1.1.ebuild
@@ -4,13 +4,16 @@
EAPI=5
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
+
DESCRIPTION="HMM-based cDNA to genome aligner"
HOMEPAGE="http://mblab.wustl.edu/software.html"
SRC_URI="http://mblab.wustl.edu/software/download/pairagon_.tar"
LICENSE="BSD-2"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
IUSE=""
DEPEND="dev-lang/perl"
@@ -30,13 +33,9 @@ src_install(){
# emake DESTDIR="${D}"/usr install
dobin bin/*
dodoc README
+ perl_set_version
insinto /usr/share/pairagon
doins parameters/*
- eval `perl '-V:installvendorlib'`
- vendor_lib_install_dir="${installvendorlib}"
- dodir ${vendor_lib_install_dir}/pairagon
- insinto ${vendor_lib_install_dir}/pairagon
+ insinto ${VENDOR_LIB}
doins lib/perl5/Alignment.pm
- echo "PERL5LIB="${vendor_lib_install_dir}"/pairagon" > ${S}"/99pairagon"
- doenvd ${S}"/99pairagon" || die
}
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/pairagon/
@ 2016-07-01 13:00 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-07-01 13:00 UTC (permalink / raw
To: gentoo-commits
commit: fd1b1f6eb93bbde7c06b9d12779290bd60af9c61
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 1 12:59:55 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 1 12:59:55 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=fd1b1f6e
sci-biology/pairagon: fix PERL5INC
Package-Manager: portage-2.2.28
sci-biology/pairagon/pairagon-1.1.ebuild | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/sci-biology/pairagon/pairagon-1.1.ebuild b/sci-biology/pairagon/pairagon-1.1.ebuild
index 136aedb..815332c 100644
--- a/sci-biology/pairagon/pairagon-1.1.ebuild
+++ b/sci-biology/pairagon/pairagon-1.1.ebuild
@@ -23,6 +23,7 @@ S="${WORKDIR}"/pairagon
src_prepare(){
sed -e 's:src/get-glib-flags.sh:#src/get-glib-flags.sh:; s:-Wall -Werror::' -i Makefile
+ sed -e 's/^use Alignment/use pairagon::Alignment/' -i bin/alignmentConvert.pl || die
}
src_compile(){
@@ -36,6 +37,6 @@ src_install(){
perl_set_version
insinto /usr/share/pairagon
doins parameters/*
- insinto ${VENDOR_LIB}
+ insinto ${VENDOR_LIB}/${PN}
doins lib/perl5/Alignment.pm
}
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/pairagon/
@ 2016-07-01 13:11 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2016-07-01 13:11 UTC (permalink / raw
To: gentoo-commits
commit: 95cb8f2e55c57dbc3c2c0d47ac9c98148e728823
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 1 13:11:27 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 1 13:11:27 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=95cb8f2e
sci-biology/pairagon: try to avoid 'emake DESTDIR=/usr install'
Package-Manager: portage-2.2.28
sci-biology/pairagon/pairagon-1.1.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-biology/pairagon/pairagon-1.1.ebuild b/sci-biology/pairagon/pairagon-1.1.ebuild
index 815332c..84e4fe8 100644
--- a/sci-biology/pairagon/pairagon-1.1.ebuild
+++ b/sci-biology/pairagon/pairagon-1.1.ebuild
@@ -31,8 +31,7 @@ src_compile(){
}
src_install(){
- # emake DESTDIR="${D}"/usr install
- dobin bin/*
+ dobin bin/pairagon bin/pairameter_estimate bin/Pairagon.pl bin/alignmentConvert.pl
dodoc README
perl_set_version
insinto /usr/share/pairagon
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/pairagon/
@ 2017-09-07 20:49 David Seifert
0 siblings, 0 replies; 6+ messages in thread
From: David Seifert @ 2017-09-07 20:49 UTC (permalink / raw
To: gentoo-commits
commit: 4bc9cc3e0c3601751f67183b64405caf98191ec8
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Sep 7 20:39:02 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Sep 7 20:39:02 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4bc9cc3e
sci-biology/pairagon: Fix double-prefix
Closes: https://bugs.gentoo.org/show_bug.cgi?id=587702
Package-Manager: Portage-2.3.8, Repoman-2.3.3
sci-biology/pairagon/pairagon-1.1.ebuild | 37 +++++++++++++++++---------------
1 file changed, 20 insertions(+), 17 deletions(-)
diff --git a/sci-biology/pairagon/pairagon-1.1.ebuild b/sci-biology/pairagon/pairagon-1.1.ebuild
index c23129f74..843198232 100644
--- a/sci-biology/pairagon/pairagon-1.1.ebuild
+++ b/sci-biology/pairagon/pairagon-1.1.ebuild
@@ -1,10 +1,9 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=6
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
+inherit perl-functions toolchain-funcs
DESCRIPTION="HMM-based cDNA to genome aligner"
HOMEPAGE="http://mblab.wustl.edu/software.html"
@@ -15,26 +14,30 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-DEPEND="dev-lang/perl"
+DEPEND="dev-lang/perl:="
RDEPEND="${DEPEND}"
-S="${WORKDIR}"/pairagon
+S=${WORKDIR}/${PN}
-src_prepare(){
- sed -e 's:src/get-glib-flags.sh:#src/get-glib-flags.sh:; s:-Wall -Werror::' -i Makefile
- sed -e 's/^use Alignment/use pairagon::Alignment/' -i bin/alignmentConvert.pl || die
+src_prepare() {
+ default
+
+ sed -e 's:src/get-glib-flags.sh:#src/get-glib-flags.sh:; s:-Wall -Werror::' \
+ -i Makefile || die
+ sed -e 's/^use Alignment/use pairagon::Alignment/' \
+ -i bin/alignmentConvert.pl || die
}
-src_compile(){
+src_compile() {
emake pairagon-linux
}
-src_install(){
- dobin bin/pairagon bin/pairameter_estimate bin/Pairagon.pl bin/alignmentConvert.pl
- dodoc README
- perl_set_version
+src_install() {
+ dobin bin/{pairagon,pairameter_estimate,Pairagon.pl,alignmentConvert.pl}
+ einstalldocs
+
insinto /usr/share/pairagon
- doins parameters/*
- insinto ${VENDOR_LIB}/${PN}
- doins lib/perl5/Alignment.pm
+ doins -r parameters/.
+
+ perl_domodule -C ${PN} lib/perl5/Alignment.pm
}
^ permalink raw reply related [flat|nested] 6+ messages in thread
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