[gentoo-commits] proj/sci:master commit in: sci-biology/pairagon/, profiles/
commit: d5d8cc85ba517280e18f4b6b79d61983e35f1daf
Author: Andrew Ammerlaan riseup net>
AuthorDate: Tue Jan 19 10:24:24 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Tue Jan 19 10:24:32 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d5d8cc85
sci-biology/pairagon: fix fetching
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
profiles/package.mask| 1 -
sci-biology/pairagon/pairagon-1.1.ebuild | 14 +-
2 files changed, 9 insertions(+), 6 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 39be2454d..2a4e0a317 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -92,4 +92,3 @@ sci-biology/MuSeqBox
sci-biology/OBO-Edit
sci-biology/ONTO-PERL
sci-biology/ORFcor
-sci-biology/pairagon
diff --git a/sci-biology/pairagon/pairagon-1.1.ebuild
b/sci-biology/pairagon/pairagon-1.1.ebuild
index 843198232..3e97758a6 100644
--- a/sci-biology/pairagon/pairagon-1.1.ebuild
+++ b/sci-biology/pairagon/pairagon-1.1.ebuild
@@ -1,18 +1,22 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
inherit perl-functions 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;
+HOMEPAGE="https://mblab.wustl.edu/software.html;
+#SRC_URI="http://mblab.wustl.edu/software/download/pairagon_.tar;
+# ERROR: cannot verify mblab.wustl.edu's certificate, issued by ‘CN=InCommon
RSA Server CA,OU=InCommon,O=Internet2,L=Ann Arbor,ST=MI,C=US’:
+# Unable to locally verify the issuer's authority.
+# To connect to mblab.wustl.edu insecurely, use `--no-check-certificate'.
+RESTRICT="fetch"
+SRC_URI="pairagon_.tar"
LICENSE="BSD-2"
SLOT="0"
KEYWORDS="~amd64"
-IUSE=""
DEPEND="dev-lang/perl:="
RDEPEND="${DEPEND}"
[gentoo-commits] proj/sci:master commit in: sci-biology/pairagon/
commit: 4bc9cc3e0c3601751f67183b64405caf98191ec8
Author: David Seifert gentoo org>
AuthorDate: Thu Sep 7 20:39:02 2017 +
Commit: David Seifert gentoo org>
CommitDate: Thu Sep 7 20:39:02 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4bc9cc3e
sci-biology/pairagon: Fix double-prefix
Closes: https://bugs.gentoo.org/show_bug.cgi?id=587702
Package-Manager: Portage-2.3.8, Repoman-2.3.3
sci-biology/pairagon/pairagon-1.1.ebuild | 37 +---
1 file changed, 20 insertions(+), 17 deletions(-)
diff --git a/sci-biology/pairagon/pairagon-1.1.ebuild
b/sci-biology/pairagon/pairagon-1.1.ebuild
index c23129f74..843198232 100644
--- a/sci-biology/pairagon/pairagon-1.1.ebuild
+++ b/sci-biology/pairagon/pairagon-1.1.ebuild
@@ -1,10 +1,9 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=6
-PERL_EXPORT_PHASE_FUNCTIONS=no
-inherit perl-module eutils toolchain-funcs
+inherit perl-functions toolchain-funcs
DESCRIPTION="HMM-based cDNA to genome aligner"
HOMEPAGE="http://mblab.wustl.edu/software.html;
@@ -15,26 +14,30 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-DEPEND="dev-lang/perl"
+DEPEND="dev-lang/perl:="
RDEPEND="${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 ${PN} lib/perl5/Alignment.pm
}
[gentoo-commits] proj/sci:master commit in: sci-biology/pairagon/
commit: 95cb8f2e55c57dbc3c2c0d47ac9c98148e728823
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jul 1 13:11:27 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jul 1 13:11:27 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=95cb8f2e
sci-biology/pairagon: try to avoid 'emake DESTDIR=/usr install'
Package-Manager: portage-2.2.28
sci-biology/pairagon/pairagon-1.1.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-biology/pairagon/pairagon-1.1.ebuild
b/sci-biology/pairagon/pairagon-1.1.ebuild
index 815332c..84e4fe8 100644
--- a/sci-biology/pairagon/pairagon-1.1.ebuild
+++ b/sci-biology/pairagon/pairagon-1.1.ebuild
@@ -31,8 +31,7 @@ src_compile(){
}
src_install(){
- # emake DESTDIR="${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
[gentoo-commits] proj/sci:master commit in: sci-biology/pairagon/
commit: fd1b1f6eb93bbde7c06b9d12779290bd60af9c61
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Fri Jul 1 12:59:55 2016 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Fri Jul 1 12:59:55 2016 +
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
}
[gentoo-commits] proj/sci:master commit in: sci-biology/pairagon/
commit: 3d121e03a40d2858ee3715abc8553960c2877c3f
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Fri Apr 17 23:33:35 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Fri Apr 17 23:33:35 2015 +
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 mmokr...@fold.natur.cuni.cz
pairagon-1.1.ebuild:
+ sci-biology/pairagon: fixed installation of perl-related files
+
19 Mar 2015; Martin Mokrejs mmokr...@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
}
[gentoo-commits] proj/sci:master commit in: sci-biology/pairagon/
commit: bba46880fc2e9fd6af8a92949d4a664e856f4dbb Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz AuthorDate: Thu Mar 19 10:36:38 2015 + Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz CommitDate: Thu Mar 19 10:36:38 2015 + 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 mmokr...@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 mmokr...@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
[gentoo-commits] proj/sci:master commit in: sci-biology/pairagon/
commit: bcb9a5d452923bb22ec34d016db972ccb31b080f
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Thu Mar 5 19:58:57 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Thu Mar 5 19:58:57 2015 +
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 000..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 mmokr...@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 000..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
+ herdsci-biology/herd
+ maintainer
+emailmmokr...@fold.natur.cuni.cz/email
+nameMartin 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 000..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
+}
