* [gentoo-commits] proj/sci:master commit in: sci-biology/barrnap/
@ 2014-04-15 8:54 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2014-04-15 8:54 UTC (permalink / raw
To: gentoo-commits
commit: 34c1dd0d45a5787936bd8ee86afbdf8f21138f55
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Apr 15 08:51:30 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Apr 15 08:51:30 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=34c1dd0d
sci-biology/barrnap: new package, package contains bundled binaries, untested
Package-Manager: portage-2.2.7
---
sci-biology/barrnap/ChangeLog | 9 +++++++++
sci-biology/barrnap/barrnap-0.3.ebuild | 22 ++++++++++++++++++++++
sci-biology/barrnap/metadata.xml | 9 +++++++++
3 files changed, 40 insertions(+)
diff --git a/sci-biology/barrnap/ChangeLog b/sci-biology/barrnap/ChangeLog
new file mode 100644
index 0000000..df39571
--- /dev/null
+++ b/sci-biology/barrnap/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/barrnap
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*barrnap-0.3 (15 Apr 2014)
+
+ 15 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +barrnap-0.3.ebuild,
+ +metadata.xml:
+ sci-biology/barrnap: new package, package contains bundled binaries, untested
diff --git a/sci-biology/barrnap/barrnap-0.3.ebuild b/sci-biology/barrnap/barrnap-0.3.ebuild
new file mode 100644
index 0000000..f5af3ab
--- /dev/null
+++ b/sci-biology/barrnap/barrnap-0.3.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit perl-module
+
+DESCRIPTION="Predict Bacterial and Archaeal rRNA genes and output in GFF3 format"
+HOMEPAGE="http://www.vicbioinformatics.com/software.barrnap.shtml"
+SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+# contains bundled binaries of hmmer-3.1 (dev version)
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ sci-biology/nesoni"
diff --git a/sci-biology/barrnap/metadata.xml b/sci-biology/barrnap/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/barrnap/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] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/barrnap/
@ 2014-06-26 13:49 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2014-06-26 13:49 UTC (permalink / raw
To: gentoo-commits
commit: 21729f2ab37071b29b5419db9b6916f65135687d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jun 26 13:49:09 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jun 26 13:49:09 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=21729f2a
sci-biology/barrnap: working ebuild although installing a pre-compiled binary and until somebody hacks teh main perl code it need to be installed into /usr/share/{PN} and modifies PATH accordingly
Package-Manager: portage-2.2.7
---
sci-biology/barrnap/ChangeLog | 15 +++++++++++++++
sci-biology/barrnap/barrnap-0.3.ebuild | 18 ++++++++++++++++++
2 files changed, 33 insertions(+)
diff --git a/sci-biology/barrnap/ChangeLog b/sci-biology/barrnap/ChangeLog
index df39571..c90ac20 100644
--- a/sci-biology/barrnap/ChangeLog
+++ b/sci-biology/barrnap/ChangeLog
@@ -2,6 +2,21 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 26 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> barrnap-0.3.ebuild:
+ sci-biology/barrnap: working ebuild although installing a pre-compiled binary
+ and until somebody hacks teh main perl code it need to be installed into
+ /usr/share/ and modifies
+ /home/mmokrejs/bin:/usr/local/bin:/usr/bin:/bin:/opt/bin:/usr/x86_64-pc-linux-
+ gnu/gcc-bin/4.8.2:/opt/vmware/bin:/opt/ucsc-genome-browser/bin:/opt/Apollo:/op
+ t/Tablet:$PATH:/usr/share/cgview_comparison_tool/scripts:/opt/meme/bin:/opt/45
+ 4/bin:/usr/local/pedant/PEDANT2/soft/PEDANT2/PERL:/home/mokrejs/proj/pedant-
+ tools/perl:/home/mokrejs/proj/mysql-tools::/usr/local/staden-linux-1-6-0
+ /linux-bin/:/home/mmokrejs/software/i386_linux24/usr/local/bin:/home/mmokrejs/
+ bin/SPDBV:/home/mmokrejs/bin/PDBViewer_230303:/home/mmokrejs/bin/AstexViewer2/
+ bin:/usr/local/modeller9v4/bin:/usr/local/chimera/bin:/opt/454/bin:/usr/local/
+ pedant/PEDANT2/soft/PEDANT2/PERL:/home/mokrejs/proj/pedant-
+ tools/perl:/home/mokrejs/proj/mysql-tools: accordingly
+
*barrnap-0.3 (15 Apr 2014)
15 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +barrnap-0.3.ebuild,
diff --git a/sci-biology/barrnap/barrnap-0.3.ebuild b/sci-biology/barrnap/barrnap-0.3.ebuild
index f5af3ab..68901a7 100644
--- a/sci-biology/barrnap/barrnap-0.3.ebuild
+++ b/sci-biology/barrnap/barrnap-0.3.ebuild
@@ -19,4 +19,22 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
+ >=dev-lang/perl-5.6
sci-biology/nesoni"
+
+src_install(){
+ # the below recreates the whole layout
+ insinto /usr/share/"${PN}"
+ doins barrnap
+ chmod a+rx "${D}"/usr/share/"${PN}"/barrnap
+ insinto /usr/share/"${PN}"/binaries
+ doins binaries/nhmmer.linux
+ chmod a+rx "${D}"/usr/share/"${PN}"/binaries/nhmmer.linux
+ insinto /usr/share/"${PN}"/db
+ doins db/*
+ insinto /usr/share/examples
+ doins examples/*
+
+ echo PATH=/usr/share/"${PN}":$PATH > "${S}"/99barrnap
+ doenvd "${S}"/99barrnap
+}
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/barrnap/
@ 2015-01-07 21:47 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2015-01-07 21:47 UTC (permalink / raw
To: gentoo-commits
commit: 94630596f71351dc8f23722d5fd965fabda645a2
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 7 21:46:16 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 7 21:46:16 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=94630596
generalized dependency on perl
Package-Manager: portage-2.2.7
---
sci-biology/barrnap/ChangeLog | 5 ++++-
sci-biology/barrnap/barrnap-0.3.ebuild | 5 +++--
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/sci-biology/barrnap/ChangeLog b/sci-biology/barrnap/ChangeLog
index c90ac20..50bd6cd 100644
--- a/sci-biology/barrnap/ChangeLog
+++ b/sci-biology/barrnap/ChangeLog
@@ -1,7 +1,10 @@
# ChangeLog for sci-biology/barrnap
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> barrnap-0.3.ebuild:
+ generalized dependency on perl
+
26 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> barrnap-0.3.ebuild:
sci-biology/barrnap: working ebuild although installing a pre-compiled binary
and until somebody hacks teh main perl code it need to be installed into
diff --git a/sci-biology/barrnap/barrnap-0.3.ebuild b/sci-biology/barrnap/barrnap-0.3.ebuild
index 68901a7..43d1a13 100644
--- a/sci-biology/barrnap/barrnap-0.3.ebuild
+++ b/sci-biology/barrnap/barrnap-0.3.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: $
@@ -16,10 +16,11 @@ KEYWORDS=""
IUSE=""
# contains bundled binaries of hmmer-3.1 (dev version)
+# needs >=perl-5.6
DEPEND=""
RDEPEND="${DEPEND}
- >=dev-lang/perl-5.6
+ dev-lang/perl
sci-biology/nesoni"
src_install(){
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/barrnap/
@ 2015-04-27 10:58 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2015-04-27 10:58 UTC (permalink / raw
To: gentoo-commits
commit: f3ff593d2e85576411873642f086c9e574431083
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 27 10:57:24 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 27 10:57:24 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f3ff593d
sci-biology/barrnap: version bump; adjust the ebuild to new install layout
Package-Manager: portage-2.2.18
sci-biology/barrnap/ChangeLog | 6 ++++++
sci-biology/barrnap/barrnap-0.3.ebuild | 2 +-
.../{barrnap-0.3.ebuild => barrnap-0.4.ebuild} | 20 +++++++++++---------
3 files changed, 18 insertions(+), 10 deletions(-)
diff --git a/sci-biology/barrnap/ChangeLog b/sci-biology/barrnap/ChangeLog
index 50bd6cd..05d6b32 100644
--- a/sci-biology/barrnap/ChangeLog
+++ b/sci-biology/barrnap/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*barrnap-0.4 (27 Apr 2015)
+
+ 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +barrnap-0.4.ebuild,
+ barrnap-0.3.ebuild:
+ sci-biology/barrnap: version bump; adjust the ebuild to new install layout
+
07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> barrnap-0.3.ebuild:
generalized dependency on perl
diff --git a/sci-biology/barrnap/barrnap-0.3.ebuild b/sci-biology/barrnap/barrnap-0.3.ebuild
index 43d1a13..06d01c3 100644
--- a/sci-biology/barrnap/barrnap-0.3.ebuild
+++ b/sci-biology/barrnap/barrnap-0.3.ebuild
@@ -12,7 +12,7 @@ SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz"
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
IUSE=""
# contains bundled binaries of hmmer-3.1 (dev version)
diff --git a/sci-biology/barrnap/barrnap-0.3.ebuild b/sci-biology/barrnap/barrnap-0.4.ebuild
similarity index 64%
copy from sci-biology/barrnap/barrnap-0.3.ebuild
copy to sci-biology/barrnap/barrnap-0.4.ebuild
index 43d1a13..8855b27 100644
--- a/sci-biology/barrnap/barrnap-0.3.ebuild
+++ b/sci-biology/barrnap/barrnap-0.4.ebuild
@@ -12,7 +12,7 @@ SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz"
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
IUSE=""
# contains bundled binaries of hmmer-3.1 (dev version)
@@ -25,17 +25,19 @@ RDEPEND="${DEPEND}
src_install(){
# the below recreates the whole layout
- insinto /usr/share/"${PN}"
- doins barrnap
- chmod a+rx "${D}"/usr/share/"${PN}"/barrnap
- insinto /usr/share/"${PN}"/binaries
- doins binaries/nhmmer.linux
- chmod a+rx "${D}"/usr/share/"${PN}"/binaries/nhmmer.linux
+ insinto /usr/share/"${PN}"/bin
+ doins bin/barrnap
+ chmod a+rx "${D}"/usr/share/"${PN}"/bin/barrnap || die
+ insinto /usr/share/"${PN}"/binaries/linux
+ doins binaries/linux/nhmmer
+ chmod a+rx "${D}"/usr/share/"${PN}"/binaries/linux/nhmmer || die
insinto /usr/share/"${PN}"/db
doins db/*
- insinto /usr/share/examples
+ insinto /usr/share/"${PN}"/examples
doins examples/*
- echo PATH=/usr/share/"${PN}":$PATH > "${S}"/99barrnap
+ echo PATH=/usr/share/"${PN}"/bin:$PATH > "${S}"/99barrnap
doenvd "${S}"/99barrnap
+
+ dodoc README.md
}
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/barrnap/
@ 2017-04-20 17:32 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2017-04-20 17:32 UTC (permalink / raw
To: gentoo-commits
commit: 14c57c8236e3017dded7c652c4989e56e4b662dc
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 20 17:32:35 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 20 17:32:35 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=14c57c82
sci-biology/barrnap: get satisfied by any SLOT
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/barrnap/barrnap-0.3.ebuild | 4 ++--
sci-biology/barrnap/barrnap-0.4.ebuild | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/sci-biology/barrnap/barrnap-0.3.ebuild b/sci-biology/barrnap/barrnap-0.3.ebuild
index 03fc0b02a..021092d43 100644
--- a/sci-biology/barrnap/barrnap-0.3.ebuild
+++ b/sci-biology/barrnap/barrnap-0.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -19,7 +19,7 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
- dev-lang/perl
+ dev-lang/perl:=
sci-biology/nesoni"
src_install(){
diff --git a/sci-biology/barrnap/barrnap-0.4.ebuild b/sci-biology/barrnap/barrnap-0.4.ebuild
index 0be6cd39d..e4839f3f4 100644
--- a/sci-biology/barrnap/barrnap-0.4.ebuild
+++ b/sci-biology/barrnap/barrnap-0.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -19,7 +19,7 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
- dev-lang/perl
+ dev-lang/perl:=
sci-biology/nesoni"
src_install(){
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/barrnap/
@ 2017-04-24 23:07 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2017-04-24 23:07 UTC (permalink / raw
To: gentoo-commits
commit: ec86c3fe13488da9117b3195983a6dd8d1977b23
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 24 23:06:52 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 24 23:06:52 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ec86c3fe
sci-biology/barrnap: respect EPREFIX
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/barrnap/barrnap-0.3.ebuild | 4 ++--
sci-biology/barrnap/barrnap-0.4.ebuild | 4 ++--
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/sci-biology/barrnap/barrnap-0.3.ebuild b/sci-biology/barrnap/barrnap-0.3.ebuild
index 021092d43..be281351f 100644
--- a/sci-biology/barrnap/barrnap-0.3.ebuild
+++ b/sci-biology/barrnap/barrnap-0.3.ebuild
@@ -26,10 +26,10 @@ src_install(){
# the below recreates the whole layout
insinto /usr/share/"${PN}"
doins barrnap
- chmod a+rx "${D}"/usr/share/"${PN}"/barrnap
+ chmod a+rx "${ED}"/usr/share/"${PN}"/barrnap
insinto /usr/share/"${PN}"/binaries
doins binaries/nhmmer.linux
- chmod a+rx "${D}"/usr/share/"${PN}"/binaries/nhmmer.linux
+ chmod a+rx "${ED}"/usr/share/"${PN}"/binaries/nhmmer.linux
insinto /usr/share/"${PN}"/db
doins db/*
insinto /usr/share/examples
diff --git a/sci-biology/barrnap/barrnap-0.4.ebuild b/sci-biology/barrnap/barrnap-0.4.ebuild
index e4839f3f4..f4559fddc 100644
--- a/sci-biology/barrnap/barrnap-0.4.ebuild
+++ b/sci-biology/barrnap/barrnap-0.4.ebuild
@@ -26,10 +26,10 @@ src_install(){
# the below recreates the whole layout
insinto /usr/share/"${PN}"/bin
doins bin/barrnap
- chmod a+rx "${D}"/usr/share/"${PN}"/bin/barrnap || die
+ chmod a+rx "${ED}"/usr/share/"${PN}"/bin/barrnap || die
insinto /usr/share/"${PN}"/binaries/linux
doins binaries/linux/nhmmer
- chmod a+rx "${D}"/usr/share/"${PN}"/binaries/linux/nhmmer || die
+ chmod a+rx "${ED}"/usr/share/"${PN}"/binaries/linux/nhmmer || die
insinto /usr/share/"${PN}"/db
doins db/*
insinto /usr/share/"${PN}"/examples
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/barrnap/
@ 2020-09-27 7:57 Horea Christian
0 siblings, 0 replies; 9+ messages in thread
From: Horea Christian @ 2020-09-27 7:57 UTC (permalink / raw
To: gentoo-commits
commit: 048c61f03abe33efb441bb6aa06514e10e7629de
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 07:56:32 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 07:56:32 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=048c61f0
sci-biology/barrnap: version bump 0.9
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/barrnap/barrnap-0.3.ebuild | 40 ----------------------
.../{barrnap-0.4.ebuild => barrnap-0.9.ebuild} | 8 ++---
2 files changed, 4 insertions(+), 44 deletions(-)
diff --git a/sci-biology/barrnap/barrnap-0.3.ebuild b/sci-biology/barrnap/barrnap-0.3.ebuild
deleted file mode 100644
index be281351f..000000000
--- a/sci-biology/barrnap/barrnap-0.3.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit perl-module
-
-DESCRIPTION="Predict Bacterial and Archaeal rRNA genes and output in GFF3 format"
-HOMEPAGE="http://www.vicbioinformatics.com/software.barrnap.shtml"
-SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-# contains bundled binaries of hmmer-3.1 (dev version)
-# needs >=perl-5.6
-
-DEPEND=""
-RDEPEND="${DEPEND}
- dev-lang/perl:=
- sci-biology/nesoni"
-
-src_install(){
- # the below recreates the whole layout
- insinto /usr/share/"${PN}"
- doins barrnap
- chmod a+rx "${ED}"/usr/share/"${PN}"/barrnap
- insinto /usr/share/"${PN}"/binaries
- doins binaries/nhmmer.linux
- chmod a+rx "${ED}"/usr/share/"${PN}"/binaries/nhmmer.linux
- insinto /usr/share/"${PN}"/db
- doins db/*
- insinto /usr/share/examples
- doins examples/*
-
- echo PATH=/usr/share/"${PN}":$PATH > "${S}"/99barrnap
- doenvd "${S}"/99barrnap
-}
diff --git a/sci-biology/barrnap/barrnap-0.4.ebuild b/sci-biology/barrnap/barrnap-0.9.ebuild
similarity index 87%
rename from sci-biology/barrnap/barrnap-0.4.ebuild
rename to sci-biology/barrnap/barrnap-0.9.ebuild
index f4559fddc..e60736e57 100644
--- a/sci-biology/barrnap/barrnap-0.4.ebuild
+++ b/sci-biology/barrnap/barrnap-0.9.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=7
inherit perl-module
DESCRIPTION="Predict Bacterial and Archaeal rRNA genes and output in GFF3 format"
HOMEPAGE="http://www.vicbioinformatics.com/software.barrnap.shtml"
-SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz"
+SRC_URI="https://github.com/tseemann/barrnap/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
@@ -20,7 +20,7 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
dev-lang/perl:=
- sci-biology/nesoni"
+ "
src_install(){
# the below recreates the whole layout
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/barrnap/
@ 2021-01-20 8:40 Andrew Ammerlaan
0 siblings, 0 replies; 9+ messages in thread
From: Andrew Ammerlaan @ 2021-01-20 8:40 UTC (permalink / raw
To: gentoo-commits
commit: dc56cf6f3cd779473af822058190d91263a7971d
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Jan 20 08:39:28 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Jan 20 08:39:28 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=dc56cf6f
sci-biology/barrnap: update homepage
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/barrnap/barrnap-0.9.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/barrnap/barrnap-0.9.ebuild b/sci-biology/barrnap/barrnap-0.9.ebuild
index e60736e57..999f065c1 100644
--- a/sci-biology/barrnap/barrnap-0.9.ebuild
+++ b/sci-biology/barrnap/barrnap-0.9.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
@@ -6,7 +6,7 @@ EAPI=7
inherit perl-module
DESCRIPTION="Predict Bacterial and Archaeal rRNA genes and output in GFF3 format"
-HOMEPAGE="http://www.vicbioinformatics.com/software.barrnap.shtml"
+HOMEPAGE="https://vicbioinformatics.com/software.barrnap.shtml"
SRC_URI="https://github.com/tseemann/barrnap/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-3"
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/barrnap/
@ 2023-02-17 20:50 Horea Christian
0 siblings, 0 replies; 9+ messages in thread
From: Horea Christian @ 2023-02-17 20:50 UTC (permalink / raw
To: gentoo-commits
commit: f2301f1261c61aeee7f1a513897bc20e99ffb08c
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Feb 17 20:50:31 2023 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Feb 17 20:50:31 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f2301f12
sci-biology/barrnap: update HOMEPAGE
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/barrnap/barrnap-0.9.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/barrnap/barrnap-0.9.ebuild b/sci-biology/barrnap/barrnap-0.9.ebuild
index 999f065c1..6b7176e14 100644
--- a/sci-biology/barrnap/barrnap-0.9.ebuild
+++ b/sci-biology/barrnap/barrnap-0.9.ebuild
@@ -6,7 +6,7 @@ EAPI=7
inherit perl-module
DESCRIPTION="Predict Bacterial and Archaeal rRNA genes and output in GFF3 format"
-HOMEPAGE="https://vicbioinformatics.com/software.barrnap.shtml"
+HOMEPAGE="https://github.com/tseemann/barrnap"
SRC_URI="https://github.com/tseemann/barrnap/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-3"
^ permalink raw reply related [flat|nested] 9+ messages in thread
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