* [gentoo-commits] proj/sci:master commit in: sci-biology/augustus/
@ 2015-03-30 22:44 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2015-03-30 22:44 UTC (permalink / raw
To: gentoo-commits
commit: d80145ef93597dea34ba14fb06ee4975740c6c84
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 30 22:44:17 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 30 22:44:17 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d80145ef
sci-biology/augustus: version bump, new license (temporarily), new dependencies since 3.0 series
Package-Manager: portage-2.2.18
sci-biology/augustus/ChangeLog | 78 ++++++++++++++++++++++++++++++
sci-biology/augustus/augustus-3.0.3.ebuild | 59 ++++++++++++++++++++++
sci-biology/augustus/metadata.xml | 5 ++
3 files changed, 142 insertions(+)
diff --git a/sci-biology/augustus/ChangeLog b/sci-biology/augustus/ChangeLog
new file mode 100644
index 0000000..ee07f16
--- /dev/null
+++ b/sci-biology/augustus/ChangeLog
@@ -0,0 +1,78 @@
+# ChangeLog for sci-biology/augustus
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/ChangeLog,v 1.19 2013/03/11 14:37:00 jlec Exp $
+
+ 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
+ Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
+
+ 31 Jan 2013; Justin Lecher <jlec@gentoo.org> -augustus-2.3.1.ebuild,
+ -augustus-2.4.ebuild, -augustus-2.5.ebuild, metadata.xml:
+ Drop old, fixes multiple QA issues, #454822
+
+ 31 Jan 2013; Agostino Sarubbo <ago@gentoo.org> augustus-2.5.5.ebuild:
+ Stable for x86, wrt bug #454842
+
+ 31 Jan 2013; Agostino Sarubbo <ago@gentoo.org> augustus-2.5.5.ebuild:
+ Stable for amd64, wrt bug #454842
+
+*augustus-2.5.5 (23 Jun 2011)
+
+ 23 Jun 2011; Justin Lecher <jlec@gentoo.org> augustus-2.3.1.ebuild,
+ augustus-2.4.ebuild, augustus-2.5.ebuild, +augustus-2.5.5.ebuild,
+ +files/augustus-2.5.5-sane-build.patch:
+ Version Bump, respect LDFLAGS, #337655
+
+ 09 Mar 2011; Markos Chandras <hwoarang@gentoo.org> augustus-2.4.ebuild:
+ Stable on amd64 wrt bug #353573
+
+ 09 Mar 2011; Thomas Kahle <tomka@gentoo.org> augustus-2.4.ebuild:
+ x86 stable per bug 353573
+
+ 04 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> augustus-2.4.ebuild,
+ augustus-2.5.ebuild:
+ Respect LDFLAGS
+
+*augustus-2.5 (03 Feb 2011)
+
+ 03 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> augustus-2.4.ebuild,
+ +augustus-2.5.ebuild:
+ Version bump, update SRC_URI
+
+*augustus-2.4 (26 Sep 2010)
+
+ 26 Sep 2010; Andrey Kislyuk <weaver@gentoo.org> -augustus-2.1.ebuild,
+ -files/augustus-2.1-glibc-2.10.patch, +augustus-2.4.ebuild:
+ Version bump, drop old
+
+ 09 Feb 2010; Pacho Ramos <pacho@gentoo.org> augustus-2.3.1.ebuild:
+ amd64 stable, bug 298767
+
+ 29 Dec 2009; Christian Faulhammer <fauli@gentoo.org>
+ augustus-2.3.1.ebuild:
+ stable x86, bug 298767
+
+*augustus-2.3.1 (16 Nov 2009)
+
+ 16 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> +augustus-2.3.1.ebuild:
+ Version bump
+
+ 31 Oct 2009; Markus Meier <maekke@gentoo.org> augustus-2.1.ebuild:
+ amd64/x86 stable, bug #290924
+
+ 09 Aug 2009; Samuli Suominen <ssuominen@gentoo.org> augustus-2.1.ebuild,
+ +files/augustus-2.1-glibc-2.10.patch:
+ Fix building with GLIBC 2.10+ wrt #276719.
+
+*augustus-2.1 (19 Mar 2009)
+
+ 19 Mar 2009; Andrey Kislyuk <weaver@gentoo.org>
+ -files/augustus-2.0.3-cflags.patch, -files/augustus-2.0.3-gcc4.3.patch,
+ -augustus-2.0.3.ebuild, +augustus-2.1.ebuild:
+ Version bump
+
+*augustus-2.0.3 (04 Jan 2009)
+
+ 04 Jan 2009; weaver <weaver@gentoo.org>
+ +files/augustus-2.0.3-cflags.patch, +files/augustus-2.0.3-gcc4.3.patch,
+ +metadata.xml, +augustus-2.0.3.ebuild:
+ Initial commit, ebuild written by me
diff --git a/sci-biology/augustus/augustus-3.0.3.ebuild b/sci-biology/augustus/augustus-3.0.3.ebuild
new file mode 100644
index 0000000..da2db42
--- /dev/null
+++ b/sci-biology/augustus/augustus-3.0.3.ebuild
@@ -0,0 +1,59 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/augustus-2.5.5.ebuild,v 1.3 2013/01/31 18:42:11 ago Exp $
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Eukaryotic gene predictor"
+HOMEPAGE="http://augustus.gobics.de/"
+SRC_URI="http://bioinf.uni-greifswald.de/augustus/binaries/${P}.tar.gz"
+
+LICENSE="GPL-3"
+# temporary drop in licensing scheme, see http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/HISTORY.TXT
+# http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/LICENCE.TXT
+# LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="examples"
+
+DEPEND="
+ sci-libs/gsl
+ dev-libs/boost
+ sys-libs/zlib
+ sys-devel/flex"
+RDEPEND="${DEPEND}"
+
+src_prepare() {
+ # TODO: do we need anything from the 2.5.5 patch?
+ # epatch "${FILESDIR}"/${P}-sane-build.patch
+ tc-export CC CXX
+}
+
+src_compile() {
+ emake clean && emake
+}
+
+src_install() {
+ dobin bin/*
+# dobin src/{augustus,etraining,consensusFinder,curve2hints,fastBlockSearch,prepareAlign}
+
+ exeinto /usr/libexec/${PN}
+ doexe scripts/*.p*
+ insinto /usr/libexec/${PN}
+ doins scripts/*.conf
+
+ insinto /usr/share/${PN}
+ doins -r config
+
+ echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}"
+ doenvd "${S}/99${PN}"
+
+ dodoc -r README.TXT HISTORY.TXT docs/*.{pdf,txt}
+
+ if use examples; then
+ insinto /usr/share/${PN}/
+ doins -r docs/tutorial examples
+ fi
+}
diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml
new file mode 100644
index 0000000..f17a827
--- /dev/null
+++ b/sci-biology/augustus/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/augustus/
@ 2015-04-08 9:45 Justin Lecher
0 siblings, 0 replies; 13+ messages in thread
From: Justin Lecher @ 2015-04-08 9:45 UTC (permalink / raw
To: gentoo-commits
commit: 2c793fdd99a16242897e0ae5f838156723b87ca6
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Apr 8 09:44:32 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Apr 8 09:44:32 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2c793fdd
sci-biology/augustus: Drop suspect DEPEND
Package-Manager: portage-2.2.18
sci-biology/augustus/ChangeLog | 5 ++++-
sci-biology/augustus/augustus-3.0.3.ebuild | 4 ++--
2 files changed, 6 insertions(+), 3 deletions(-)
diff --git a/sci-biology/augustus/ChangeLog b/sci-biology/augustus/ChangeLog
index ee07f16..b0fde43 100644
--- a/sci-biology/augustus/ChangeLog
+++ b/sci-biology/augustus/ChangeLog
@@ -1,7 +1,10 @@
# ChangeLog for sci-biology/augustus
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/ChangeLog,v 1.19 2013/03/11 14:37:00 jlec Exp $
+ 08 Apr 2015; Justin Lecher <jlec@gentoo.org> augustus-3.0.3.ebuild:
+ sci-biology/augustus: Drop suspect DEPEND
+
11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml:
Drop Andrey as maintainer so that bugs get assigned to sci-biology directly
diff --git a/sci-biology/augustus/augustus-3.0.3.ebuild b/sci-biology/augustus/augustus-3.0.3.ebuild
index da2db42..a8bc269 100644
--- a/sci-biology/augustus/augustus-3.0.3.ebuild
+++ b/sci-biology/augustus/augustus-3.0.3.ebuild
@@ -21,9 +21,9 @@ IUSE="examples"
DEPEND="
sci-libs/gsl
dev-libs/boost
- sys-libs/zlib
+ sys-libs/zlib"
+RDEPEND="${DEPEND}
sys-devel/flex"
-RDEPEND="${DEPEND}"
src_prepare() {
# TODO: do we need anything from the 2.5.5 patch?
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/augustus/
@ 2015-04-16 6:34 Justin Lecher
0 siblings, 0 replies; 13+ messages in thread
From: Justin Lecher @ 2015-04-16 6:34 UTC (permalink / raw
To: gentoo-commits
commit: 73279dca5c2ff3b859c936ae0fac7c5b2903addf
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Apr 16 06:26:59 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Apr 16 06:26:59 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=73279dca
sci-biology/augustus: Switch RDEPEND - DEPEND
Package-Manager: portage-2.2.18
sci-biology/augustus/ChangeLog | 3 +++
sci-biology/augustus/augustus-3.0.3.ebuild | 4 ++--
2 files changed, 5 insertions(+), 2 deletions(-)
diff --git a/sci-biology/augustus/ChangeLog b/sci-biology/augustus/ChangeLog
index b0fde43..ae9f1c6 100644
--- a/sci-biology/augustus/ChangeLog
+++ b/sci-biology/augustus/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/ChangeLog,v 1.19 2013/03/11 14:37:00 jlec Exp $
+ 16 Apr 2015; Justin Lecher <jlec@gentoo.org> augustus-3.0.3.ebuild:
+ sci-biology/augustus: Switch RDEPEND - DEPEND
+
08 Apr 2015; Justin Lecher <jlec@gentoo.org> augustus-3.0.3.ebuild:
sci-biology/augustus: Drop suspect DEPEND
diff --git a/sci-biology/augustus/augustus-3.0.3.ebuild b/sci-biology/augustus/augustus-3.0.3.ebuild
index e4524e2..d0fe711 100644
--- a/sci-biology/augustus/augustus-3.0.3.ebuild
+++ b/sci-biology/augustus/augustus-3.0.3.ebuild
@@ -18,11 +18,11 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="examples"
-DEPEND="
+RDEPEND="
sci-libs/gsl
dev-libs/boost
sys-libs/zlib"
-RDEPEND="${DEPEND}
+DEPEND="${RDEPEND}
sys-devel/flex"
src_prepare() {
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/augustus/
@ 2015-05-25 19:07 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2015-05-25 19:07 UTC (permalink / raw
To: gentoo-commits
commit: 474dc964e9ffb57968a6fc0393ca8dda8524ff53
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 25 19:06:52 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 25 19:06:52 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=474dc964
sci-biology/augustus: version bump
Package-Manager: portage-2.2.18
sci-biology/augustus/ChangeLog | 6 ++++++
sci-biology/augustus/{augustus-3.0.3.ebuild => augustus-3.1.ebuild} | 0
2 files changed, 6 insertions(+)
diff --git a/sci-biology/augustus/ChangeLog b/sci-biology/augustus/ChangeLog
index ae9f1c6..d24d31d 100644
--- a/sci-biology/augustus/ChangeLog
+++ b/sci-biology/augustus/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/ChangeLog,v 1.19 2013/03/11 14:37:00 jlec Exp $
+*augustus-3.1 (25 May 2015)
+
+ 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +augustus-3.1.ebuild, -augustus-3.0.3.ebuild:
+ sci-biology/augustus: version bump
+
16 Apr 2015; Justin Lecher <jlec@gentoo.org> augustus-3.0.3.ebuild:
sci-biology/augustus: Switch RDEPEND - DEPEND
diff --git a/sci-biology/augustus/augustus-3.0.3.ebuild b/sci-biology/augustus/augustus-3.1.ebuild
similarity index 100%
rename from sci-biology/augustus/augustus-3.0.3.ebuild
rename to sci-biology/augustus/augustus-3.1.ebuild
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/augustus/
@ 2015-09-23 12:48 Justin Lecher
0 siblings, 0 replies; 13+ messages in thread
From: Justin Lecher @ 2015-09-23 12:48 UTC (permalink / raw
To: gentoo-commits
commit: e71d7ff2098227500cd475827ab40d0a79fccca1
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 23 12:47:23 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep 23 12:47:23 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e71d7ff2
sci-biology/augustus: Use default functions
Package-Manager: portage-2.2.21
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/augustus/augustus-3.1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/augustus/augustus-3.1.ebuild b/sci-biology/augustus/augustus-3.1.ebuild
index 6e18831..e67723d 100644
--- a/sci-biology/augustus/augustus-3.1.ebuild
+++ b/sci-biology/augustus/augustus-3.1.ebuild
@@ -32,7 +32,7 @@ src_prepare() {
}
src_compile() {
- emake clean && emake
+ emake clean && default
}
src_install() {
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/augustus/
@ 2016-12-01 18:44 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2016-12-01 18:44 UTC (permalink / raw
To: gentoo-commits
commit: f27843ff427867921374d9b23f9f074be211e191
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Dec 1 18:44:01 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Dec 1 18:44:01 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f27843ff
sci-biology/augustus: zap -O3 CFLAG from src/Makefile
Package-Manager: portage-2.3.2
sci-biology/augustus/augustus-3.1.ebuild | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/sci-biology/augustus/augustus-3.1.ebuild b/sci-biology/augustus/augustus-3.1.ebuild
index e67723d..f18c6fc 100644
--- a/sci-biology/augustus/augustus-3.1.ebuild
+++ b/sci-biology/augustus/augustus-3.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -29,6 +29,7 @@ src_prepare() {
# TODO: do we need anything from the 2.5.5 patch?
# epatch "${FILESDIR}"/${P}-sane-build.patch
tc-export CC CXX
+ sed -e 's/ -O3//g' -i src/Makefile || die
}
src_compile() {
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/augustus/
@ 2018-01-08 13:54 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2018-01-08 13:54 UTC (permalink / raw
To: gentoo-commits
commit: f1edfa4859b565410b78bbde88c93185b68dfe43
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jan 8 13:53:47 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jan 8 13:53:47 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f1edfa48
sci-biology/augustus: version bump
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/augustus/{augustus-3.1.ebuild => augustus-3.3.ebuild} | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/sci-biology/augustus/augustus-3.1.ebuild b/sci-biology/augustus/augustus-3.3.ebuild
similarity index 95%
rename from sci-biology/augustus/augustus-3.1.ebuild
rename to sci-biology/augustus/augustus-3.3.ebuild
index a0e452caf..08d0687ab 100644
--- a/sci-biology/augustus/augustus-3.1.ebuild
+++ b/sci-biology/augustus/augustus-3.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
@@ -23,6 +23,7 @@ RDEPEND="
sys-libs/zlib"
DEPEND="${RDEPEND}
sys-devel/flex"
+S="${WORKDIR}/${PN}"
src_prepare() {
# TODO: do we need anything from the 2.5.5 patch?
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/augustus/
@ 2018-03-23 0:22 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2018-03-23 0:22 UTC (permalink / raw
To: gentoo-commits
commit: cf04df0e7dad1b7779e01e24071a3c3600e2cebf
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 23 00:22:22 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 23 00:22:22 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cf04df0e
sci-biology/augustus: respect EPREFIX and enable comparative gene prediction
Package-Manager: Portage-2.3.24, Repoman-2.3.6
sci-biology/augustus/augustus-3.3.ebuild | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/sci-biology/augustus/augustus-3.3.ebuild b/sci-biology/augustus/augustus-3.3.ebuild
index 08d0687ab..b050f1da2 100644
--- a/sci-biology/augustus/augustus-3.3.ebuild
+++ b/sci-biology/augustus/augustus-3.3.ebuild
@@ -30,6 +30,10 @@ src_prepare() {
# epatch "${FILESDIR}"/${P}-sane-build.patch
tc-export CC CXX
sed -e 's/ -O3//g' -i src/Makefile || die
+ # enable comparative gene prediction (needs c++11 compiler)
+ sed -e 's/^# COMPGENEPRED/COMPGENEPRED/' -i common.mk || die
+ # respect $EPREFIX
+ sed -e 's#^INCLUDES = /usr/include/bamtools#INCLUDES = ${EPREFIX}/usr/include/bamtools#' -i auxprogs/bam2hints/Makefile || die
}
src_compile() {
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/augustus/
@ 2018-03-23 0:47 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2018-03-23 0:47 UTC (permalink / raw
To: gentoo-commits
commit: edf1cd8c7acd0369e94308ab5cdbcfea6c81e50b
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 23 00:47:46 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 23 00:47:46 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=edf1cd8c
sci-biology/augustus: respect EPREFIX and new DEPENDency
The dependency is brought in through the comparative gene prediction
code.
Package-Manager: Portage-2.3.24, Repoman-2.3.6
sci-biology/augustus/augustus-3.3.ebuild | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
diff --git a/sci-biology/augustus/augustus-3.3.ebuild b/sci-biology/augustus/augustus-3.3.ebuild
index b050f1da2..b2b19a04e 100644
--- a/sci-biology/augustus/augustus-3.3.ebuild
+++ b/sci-biology/augustus/augustus-3.3.ebuild
@@ -17,7 +17,10 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="examples"
+# TODO: provide USE for mysql and sqlite, edit src/Makefile to reflect paths
+# and common.mk
RDEPEND="
+ sci-mathematics/lpsolve
sci-libs/gsl
dev-libs/boost
sys-libs/zlib"
@@ -30,10 +33,13 @@ src_prepare() {
# epatch "${FILESDIR}"/${P}-sane-build.patch
tc-export CC CXX
sed -e 's/ -O3//g' -i src/Makefile || die
- # enable comparative gene prediction (needs c++11 compiler)
+ # enable comparative gene prediction (needs c++11 compiler),
+ # this needs sci-mathematics/lpsolve
sed -e 's/^# COMPGENEPRED/COMPGENEPRED/' -i common.mk || die
- # respect $EPREFIX
- sed -e 's#^INCLUDES = /usr/include/bamtools#INCLUDES = ${EPREFIX}/usr/include/bamtools#' -i auxprogs/bam2hints/Makefile || die
+ # respect $EPREFIX at src/Makefile, auxprogs/bam2hints/Makefile, more?
+ find . -name Makefile | while read f; do \
+ sed -s 's#/usr/include#${EPREFIX}/usr/include#' -i $f || die;
+ done
}
src_compile() {
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/augustus/
@ 2019-03-29 13:00 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2019-03-29 13:00 UTC (permalink / raw
To: gentoo-commits
commit: f291cafdf1bac38dea4e9781f08ee7cc171a6dc4
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 29 13:00:21 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 29 13:00:21 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f291cafd
sci-biology/augustus: version bump, fix awful Makefile's
Do not require static libraries. Only bamtools are really needed.
htslib is not needed. For bam2wig samtools-0.2 series is needed.
I decided to blindly install some of the binaries created but not
copied into `./bin/`.
`src/Makefile` will gladly define mysql and sqlite together, probably
a non-sense. We force mysql as we check for it first. Not sure if
sqlite should be preferred.
I documented in the augustus-3.3.2.ebuild other "forgotten" files,
like gbrowse.conf and a template for gff2ps.
I dropped `-O3` but left in `-ggdb` in the `CXXFLAGS`.
https://github.com/Gaius-Augustus/Augustus/issues/14
https://github.com/Gaius-Augustus/Augustus/issues/50
https://github.com/Gaius-Augustus/Augustus/issues/51
https://github.com/Gaius-Augustus/Augustus/issues/52
https://github.com/Gaius-Augustus/Augustus/issues/53
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/augustus/augustus-3.3.2.ebuild | 115 +++++++++++++++++++++++++++++
sci-biology/augustus/augustus-3.3.ebuild | 70 ------------------
sci-biology/augustus/metadata.xml | 4 +
3 files changed, 119 insertions(+), 70 deletions(-)
diff --git a/sci-biology/augustus/augustus-3.3.2.ebuild b/sci-biology/augustus/augustus-3.3.2.ebuild
new file mode 100644
index 000000000..f28fb4e93
--- /dev/null
+++ b/sci-biology/augustus/augustus-3.3.2.ebuild
@@ -0,0 +1,115 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Eukaryotic gene predictor"
+HOMEPAGE="http://bioinf.uni-greifswald.de/augustus
+ https://github.com/Gaius-Augustus/Augustus"
+SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/3.3.2.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+# temporary drop in licensing scheme, see http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/HISTORY.TXT
+# http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/LICENCE.TXT
+# LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="bam2wig examples man mysql sqlite"
+
+RDEPEND="
+ bam2wig? ( sci-biology/samtools:0.1-legacy )
+ sci-biology/bamtools
+ >=sci-mathematics/lpsolve-5.5
+ sci-libs/gsl
+ sci-libs/suitesparse
+ sqlite? ( dev-db/sqlite:3 )
+ mysql? ( dev-db/mysql++ )
+ >=dev-libs/boost-1.49.0
+ sys-libs/zlib"
+DEPEND="${RDEPEND}
+ sys-devel/flex"
+S="${WORKDIR}/Augustus-${PV}"
+
+src_prepare() {
+ # TODO: do we need anything from the 2.5.5 patch?
+ # epatch "${FILESDIR}"/${P}-sane-build.patch
+ default
+ tc-export CC CXX
+ # lets respect upstream's wish and keep -ggdb
+ sed -e 's#-ggdb -O3#-ggdb#' -i src/Makefile || die
+ sed -e 's#TOOLDIR=$(HOME)/tools#TOOLDIR='"${EPREFIX}/usr/include#" \
+ -i auxprogs/bam2wig/Makefile || die
+ sed -e "s#INCLUDES=#INCLUDES=-I${EPREFIX}/usr/include/bam-0.1-legacy #" \
+ -i auxprogs/bam2wig/Makefile || die
+ # https://github.com/Gaius-Augustus/Augustus/issues/53
+ sed -e 's#$(SAMTOOLS)/libbam.a $(HTSLIB)/libhts.a -lcurses -lm -lz -lpthread -lcurl -lssl -lcrypto#-lbam-0.1-legacy#' -i auxprogs/bam2wig/Makefile || die
+ sed -e 's#-lbz2 -llzma##' -i auxprogs/bam2wig/Makefile || die
+ # enable comparative gene prediction (CGP, needs c++11 compiler),
+ # this needs sci-mathematics/lpsolve
+ sed -e 's/^# COMPGENEPRED/COMPGENEPRED/' -i common.mk || die
+ # enable compressed gzip input
+ sed -e 's/^#ZIPINPUT/ZIPINPUT/' -i common.mk || die
+ # comparative (multi-species, CGP) AUGUSTUS with MySQL or SQLite
+ # supposedly pick only either a single-one
+ if use mysql; then
+ sed -e 's/^#MYSQL/MYSQL/' -i common.mk || die
+ elif use sqlite; then
+ # comparative (mutli-species, CGP) AUGUSTUS with SQLite
+ sed -e 's/^# SQLITE/SQLITE/' -i common.mk || die
+ fi
+ # respect $EPREFIX in all Makefile's
+ find . -name Makefile | while read f; do \
+ sed -s "s#/usr/include#${EPREFIX}/usr/include#g" -i $f || die;
+ done
+}
+
+src_compile() {
+ emake clean && default
+
+ # compile stuff not compiled by default
+ # https://github.com/Gaius-Augustus/Augustus/issues/52
+ cd auxprogs/aln2wig || die
+ emake
+}
+
+src_install() {
+ dobin bin/*
+
+ exeinto /usr/libexec/${PN}
+ doexe scripts/*.{pl,pm,py} scripts/checkUTR
+ insinto /usr/libexec/${PN}
+ doins scripts/*.conf
+
+ insinto /usr/share/${PN}
+ doins -r config
+
+ echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}"
+ doenvd "${S}/99${PN}"
+
+ insinto /usr/libexec/${PN}/gbrowse
+ doins scripts/gbrowse.conf
+ insinto /usr/libexec/${PN}/gfftools
+ doins scripts/gff2ps_mycustom # config setting
+
+ dodoc README.md README-cgp.txt HISTORY.TXT auxprogs/homGeneMapping/README.TXT
+ dodoc -r docs/*.{pdf,txt}
+
+ if use examples; then
+ insinto /usr/share/${PN}/
+ doins -r docs/tutorial examples
+ fi
+
+ use man && doman mansrc/*.1
+
+ # install stuff not compiled but not written into bin/
+ # https://github.com/Gaius-Augustus/Augustus/issues/14
+ dobin auxprogs/utrrnaseq/Debug/utrrnaseq
+ dodoc auxprogs/utrrnaseq/doc/reference.pdf
+ # https://github.com/Gaius-Augustus/Augustus/issues/51
+ dobin auxprogs/checkTargetSortedness/checkTargetSortedness \
+ auxprogs/compileSpliceCands/compileSpliceCands
+
+ # ./augustus-training/ contains web application and setup
+}
diff --git a/sci-biology/augustus/augustus-3.3.ebuild b/sci-biology/augustus/augustus-3.3.ebuild
deleted file mode 100644
index b2b19a04e..000000000
--- a/sci-biology/augustus/augustus-3.3.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Eukaryotic gene predictor"
-HOMEPAGE="http://augustus.gobics.de/"
-SRC_URI="http://bioinf.uni-greifswald.de/augustus/binaries/${P}.tar.gz"
-
-LICENSE="GPL-3"
-# temporary drop in licensing scheme, see http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/HISTORY.TXT
-# http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/LICENCE.TXT
-# LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="examples"
-
-# TODO: provide USE for mysql and sqlite, edit src/Makefile to reflect paths
-# and common.mk
-RDEPEND="
- sci-mathematics/lpsolve
- sci-libs/gsl
- dev-libs/boost
- sys-libs/zlib"
-DEPEND="${RDEPEND}
- sys-devel/flex"
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
- # TODO: do we need anything from the 2.5.5 patch?
- # epatch "${FILESDIR}"/${P}-sane-build.patch
- tc-export CC CXX
- sed -e 's/ -O3//g' -i src/Makefile || die
- # enable comparative gene prediction (needs c++11 compiler),
- # this needs sci-mathematics/lpsolve
- sed -e 's/^# COMPGENEPRED/COMPGENEPRED/' -i common.mk || die
- # respect $EPREFIX at src/Makefile, auxprogs/bam2hints/Makefile, more?
- find . -name Makefile | while read f; do \
- sed -s 's#/usr/include#${EPREFIX}/usr/include#' -i $f || die;
- done
-}
-
-src_compile() {
- emake clean && default
-}
-
-src_install() {
- dobin bin/*
-# dobin src/{augustus,etraining,consensusFinder,curve2hints,fastBlockSearch,prepareAlign}
-
- exeinto /usr/libexec/${PN}
- doexe scripts/*.p*
- insinto /usr/libexec/${PN}
- doins scripts/*.conf
-
- insinto /usr/share/${PN}
- doins -r config
-
- echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}"
- doenvd "${S}/99${PN}"
-
- dodoc -r README.TXT HISTORY.TXT docs/*.{pdf,txt}
-
- if use examples; then
- insinto /usr/share/${PN}/
- doins -r docs/tutorial examples
- fi
-}
diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml
index 8417d1580..6b4a3e5b5 100644
--- a/sci-biology/augustus/metadata.xml
+++ b/sci-biology/augustus/metadata.xml
@@ -5,4 +5,8 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <use>
+ <flag name="man">install preformatted manual pages</flag>
+ <flag name="bam2wig">compile and install bam2wig conversion utility</flag>
+ </use>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/augustus/
@ 2019-03-29 13:05 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2019-03-29 13:05 UTC (permalink / raw
To: gentoo-commits
commit: dad62d03f97e438406e58011f360195638297858
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 29 13:05:38 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 29 13:05:38 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=dad62d03
sci-biology/augustus: adjust to current LICENSE, use ${PV}
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/augustus/augustus-3.3.2.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/augustus/augustus-3.3.2.ebuild b/sci-biology/augustus/augustus-3.3.2.ebuild
index f28fb4e93..2326d9c92 100644
--- a/sci-biology/augustus/augustus-3.3.2.ebuild
+++ b/sci-biology/augustus/augustus-3.3.2.ebuild
@@ -8,12 +8,12 @@ inherit eutils toolchain-funcs
DESCRIPTION="Eukaryotic gene predictor"
HOMEPAGE="http://bioinf.uni-greifswald.de/augustus
https://github.com/Gaius-Augustus/Augustus"
-SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/3.3.2.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/${PV}.tar.gz -> ${P}.tar.gz"
-LICENSE="GPL-3"
+# LICENSE="GPL-3"
# temporary drop in licensing scheme, see http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/HISTORY.TXT
# http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/LICENCE.TXT
-# LICENSE="Artistic"
+LICENSE="Artistic"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="bam2wig examples man mysql sqlite"
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/augustus/
@ 2019-03-29 13:07 Martin Mokrejs
0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2019-03-29 13:07 UTC (permalink / raw
To: gentoo-commits
commit: 7e11364f3429ea8e4662a5c245c23e53a498326c
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 29 13:07:02 2019 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 29 13:07:02 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7e11364f
sci-biology/augustus: fix typo in a comment line
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/augustus/augustus-3.3.2.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/augustus/augustus-3.3.2.ebuild b/sci-biology/augustus/augustus-3.3.2.ebuild
index 2326d9c92..a959252a0 100644
--- a/sci-biology/augustus/augustus-3.3.2.ebuild
+++ b/sci-biology/augustus/augustus-3.3.2.ebuild
@@ -103,7 +103,7 @@ src_install() {
use man && doman mansrc/*.1
- # install stuff not compiled but not written into bin/
+ # install stuff compiled but not written into bin/
# https://github.com/Gaius-Augustus/Augustus/issues/14
dobin auxprogs/utrrnaseq/Debug/utrrnaseq
dodoc auxprogs/utrrnaseq/doc/reference.pdf
^ permalink raw reply related [flat|nested] 13+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/augustus/
@ 2020-09-22 11:12 Aisha Tammy
0 siblings, 0 replies; 13+ messages in thread
From: Aisha Tammy @ 2020-09-22 11:12 UTC (permalink / raw
To: gentoo-commits
commit: cd2304b0b4b65067df0d3ca9a117696f416b01ac
Author: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Tue Sep 22 10:44:43 2020 +0000
Commit: Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Tue Sep 22 10:46:01 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cd2304b0
sci-biology/augustus: drop package
present in ::gentoo
Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>
sci-biology/augustus/augustus-3.3.2.ebuild | 115 -----------------------------
sci-biology/augustus/metadata.xml | 12 ---
2 files changed, 127 deletions(-)
diff --git a/sci-biology/augustus/augustus-3.3.2.ebuild b/sci-biology/augustus/augustus-3.3.2.ebuild
deleted file mode 100644
index a959252a0..000000000
--- a/sci-biology/augustus/augustus-3.3.2.ebuild
+++ /dev/null
@@ -1,115 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="Eukaryotic gene predictor"
-HOMEPAGE="http://bioinf.uni-greifswald.de/augustus
- https://github.com/Gaius-Augustus/Augustus"
-SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-# LICENSE="GPL-3"
-# temporary drop in licensing scheme, see http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/HISTORY.TXT
-# http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/LICENCE.TXT
-LICENSE="Artistic"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="bam2wig examples man mysql sqlite"
-
-RDEPEND="
- bam2wig? ( sci-biology/samtools:0.1-legacy )
- sci-biology/bamtools
- >=sci-mathematics/lpsolve-5.5
- sci-libs/gsl
- sci-libs/suitesparse
- sqlite? ( dev-db/sqlite:3 )
- mysql? ( dev-db/mysql++ )
- >=dev-libs/boost-1.49.0
- sys-libs/zlib"
-DEPEND="${RDEPEND}
- sys-devel/flex"
-S="${WORKDIR}/Augustus-${PV}"
-
-src_prepare() {
- # TODO: do we need anything from the 2.5.5 patch?
- # epatch "${FILESDIR}"/${P}-sane-build.patch
- default
- tc-export CC CXX
- # lets respect upstream's wish and keep -ggdb
- sed -e 's#-ggdb -O3#-ggdb#' -i src/Makefile || die
- sed -e 's#TOOLDIR=$(HOME)/tools#TOOLDIR='"${EPREFIX}/usr/include#" \
- -i auxprogs/bam2wig/Makefile || die
- sed -e "s#INCLUDES=#INCLUDES=-I${EPREFIX}/usr/include/bam-0.1-legacy #" \
- -i auxprogs/bam2wig/Makefile || die
- # https://github.com/Gaius-Augustus/Augustus/issues/53
- sed -e 's#$(SAMTOOLS)/libbam.a $(HTSLIB)/libhts.a -lcurses -lm -lz -lpthread -lcurl -lssl -lcrypto#-lbam-0.1-legacy#' -i auxprogs/bam2wig/Makefile || die
- sed -e 's#-lbz2 -llzma##' -i auxprogs/bam2wig/Makefile || die
- # enable comparative gene prediction (CGP, needs c++11 compiler),
- # this needs sci-mathematics/lpsolve
- sed -e 's/^# COMPGENEPRED/COMPGENEPRED/' -i common.mk || die
- # enable compressed gzip input
- sed -e 's/^#ZIPINPUT/ZIPINPUT/' -i common.mk || die
- # comparative (multi-species, CGP) AUGUSTUS with MySQL or SQLite
- # supposedly pick only either a single-one
- if use mysql; then
- sed -e 's/^#MYSQL/MYSQL/' -i common.mk || die
- elif use sqlite; then
- # comparative (mutli-species, CGP) AUGUSTUS with SQLite
- sed -e 's/^# SQLITE/SQLITE/' -i common.mk || die
- fi
- # respect $EPREFIX in all Makefile's
- find . -name Makefile | while read f; do \
- sed -s "s#/usr/include#${EPREFIX}/usr/include#g" -i $f || die;
- done
-}
-
-src_compile() {
- emake clean && default
-
- # compile stuff not compiled by default
- # https://github.com/Gaius-Augustus/Augustus/issues/52
- cd auxprogs/aln2wig || die
- emake
-}
-
-src_install() {
- dobin bin/*
-
- exeinto /usr/libexec/${PN}
- doexe scripts/*.{pl,pm,py} scripts/checkUTR
- insinto /usr/libexec/${PN}
- doins scripts/*.conf
-
- insinto /usr/share/${PN}
- doins -r config
-
- echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}"
- doenvd "${S}/99${PN}"
-
- insinto /usr/libexec/${PN}/gbrowse
- doins scripts/gbrowse.conf
- insinto /usr/libexec/${PN}/gfftools
- doins scripts/gff2ps_mycustom # config setting
-
- dodoc README.md README-cgp.txt HISTORY.TXT auxprogs/homGeneMapping/README.TXT
- dodoc -r docs/*.{pdf,txt}
-
- if use examples; then
- insinto /usr/share/${PN}/
- doins -r docs/tutorial examples
- fi
-
- use man && doman mansrc/*.1
-
- # install stuff compiled but not written into bin/
- # https://github.com/Gaius-Augustus/Augustus/issues/14
- dobin auxprogs/utrrnaseq/Debug/utrrnaseq
- dodoc auxprogs/utrrnaseq/doc/reference.pdf
- # https://github.com/Gaius-Augustus/Augustus/issues/51
- dobin auxprogs/checkTargetSortedness/checkTargetSortedness \
- auxprogs/compileSpliceCands/compileSpliceCands
-
- # ./augustus-training/ contains web application and setup
-}
diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml
deleted file mode 100644
index 6b4a3e5b5..000000000
--- a/sci-biology/augustus/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <use>
- <flag name="man">install preformatted manual pages</flag>
- <flag name="bam2wig">compile and install bam2wig conversion utility</flag>
- </use>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 13+ messages in thread
end of thread, other threads:[~2020-09-22 11:12 UTC | newest]
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2019-03-29 13:07 Martin Mokrejs
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2018-03-23 0:47 Martin Mokrejs
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2016-12-01 18:44 Martin Mokrejs
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