* [gentoo-commits] proj/sci:master commit in: sci-biology/gap2caf/
@ 2011-03-06 21:16 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2011-03-06 21:16 UTC (permalink / raw
To: gentoo-commits
commit: 96e413d2cda39af886222c35398a7d6f0db1c89f
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 6 21:09:46 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 6 21:09:46 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=96e413d2
sci-biology/gap2caf-2.1.0: ebuild cleanup
(Portage version: 2.1.9.28/git/Linux i686, unsigned Manifest commit)
---
sci-biology/gap2caf/gap2caf-2.1.0.ebuild | 76 ++++++++++++++++++++++++++++++
sci-biology/gap2caf/metadata.xml | 9 ++++
2 files changed, 85 insertions(+), 0 deletions(-)
diff --git a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
new file mode 100644
index 0000000..5aae263
--- /dev/null
+++ b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
@@ -0,0 +1,76 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit eutils autotools
+
+DESCRIPTION="GAP4 file format to CAF v2 format converter for genomic assembly data"
+HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/gap2caf-2.1.0.tar.gz
+ http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz"
+
+LICENSE="as-is staden"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+DEPEND="sci-biology/staden
+ >=dev-lang/tcl-8.5"
+RDEPEND="${DEPEND}"
+
+#src_prepare(){
+# epatch "${FILESDIR}"/Makefile.in-"${PV}".patch || die
+#}
+
+src_prepare(){
+ sed -i 's:/include/tcl8.4:/include:' configure.ac || die
+ sed -i 's:libtcl8.4:libtcl8.5:' configure.ac || die
+ sed -i 's:tcl8.4:tcl8.5:' src/Makefile.am || die
+ eaclocal
+ eautomake
+ eautoconf
+ sed -i 's:/include/tcl8.4:/include:' configure
+ sed -i 's:libtcl8.4:libtcl8.5:' configure
+}
+
+src_configure(){
+ # STADENROOT=/usr is used to find $STADENROOT/lib/staden/staden.profile and staden_config.h
+ # STADENSRC is used to locate gap4/IO.h
+ #CPPFLAGS="$CPPFLAGS -I/home/mmokrejs/proj/staden/staden/trunk/src" \
+ #LDFLAGS="$LDFLAGS -L/usr/lib/staden -lmutlib -lprimer3 -lg -lmisc" \
+ # STADENROOT=/usr/share/staden \
+ # STADENSRC="${WORKDIR}"/staden-2.0.0b8-src \
+ econf --with-stadenroot=/usr \
+ --with-tcl=/usr \
+ --with-stadensrc="${WORKDIR}"/staden-2.0.0b8-src || die
+ #sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' Makefile || die
+ #sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' src/Makefile || die
+ sed -i 's:tcl8.4:tcl8.5:' src/Makefile || die
+
+ # The below tricks in overall do not help, only for -ltk_utils somehow
+ sed -i 's:-ltk_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -ltk_utils -rpath-link:' src/Makefile || die
+ sed -i 's:-lgap:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -lgap:' src/Makefile || die
+ sed -i 's:-lseq_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -lseq_utils:' src/Makefile || die
+}
+
+# TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME
+# The man/Makefile.in is screwed in 2.0.2 so we cannot use it to install the manpage files,
+# not even copying over whole caftools-2.0/man/ to caftools-2.0.2/man does not help.
+src_install(){
+ # do not use upstream's install it just install shell wrapper into /usr/bin/gap2caf
+ # calling "LD_LIBRARY_PATH=/usr/lib/staden /usr/lib/gap2caf/gap2caf $@"
+ # emake install DESTDIR="${D}" || die
+ #
+ # Instead, we rely on sci-biology/staden providind /etc/env.d/99staden file providing LDPATH=/usr/lib/staden
+ dobin src/gap2caf
+ dodoc README || die
+}
+
+# BUG #259848
+# A working ebuild which needs some files from staden source tree. That is ugly,
+# am sorting out with upstream how to get around in a clean way.
diff --git a/sci-biology/gap2caf/metadata.xml b/sci-biology/gap2caf/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/gap2caf/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] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gap2caf/
@ 2011-06-24 17:09 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2011-06-24 17:09 UTC (permalink / raw
To: gentoo-commits
commit: 916eb94e8ec844b4a65da44700c972c16fcda090
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 24 12:55:05 2011 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 24 12:55:05 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=916eb94e
Sort inherit and/or USE
(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)
---
sci-biology/gap2caf/gap2caf-2.1.0.ebuild | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
diff --git a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
index 5aae263..861bbc8 100644
--- a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
+++ b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
@@ -4,7 +4,7 @@
EAPI=3
-inherit eutils autotools
+inherit autotools eutils
DESCRIPTION="GAP4 file format to CAF v2 format converter for genomic assembly data"
HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gap2caf/
@ 2014-07-04 13:42 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2014-07-04 13:42 UTC (permalink / raw
To: gentoo-commits
commit: 2542105e4b6e51e9631b29c40f4d3c8174883db3
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 4 13:38:13 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 4 13:38:13 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2542105e
sci-biology/gap2caf: remove -rpath-link from src/Makefile
Package-Manager: portage-2.2.7
---
sci-biology/gap2caf/ChangeLog | 7 +++++--
sci-biology/gap2caf/gap2caf-2.1.0.ebuild | 1 +
2 files changed, 6 insertions(+), 2 deletions(-)
diff --git a/sci-biology/gap2caf/ChangeLog b/sci-biology/gap2caf/ChangeLog
index 8e35f86..f2a9c63 100644
--- a/sci-biology/gap2caf/ChangeLog
+++ b/sci-biology/gap2caf/ChangeLog
@@ -1,8 +1,11 @@
# ChangeLog for sci-biology/gap2caf
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 04 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ gap2caf-2.1.0.ebuild:
+ sci-biology/gap2caf: remove -rpath-link from src/Makefile
+
16 Jun 2013; Justin Lecher <jlec@gentoo.org> gap2caf-2.1.0.ebuild,
metadata.xml:
Bump to EAPI=5 and fix license; make it build with eautoreconf
-
diff --git a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
index 338c3a3..726ca2d 100644
--- a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
+++ b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
@@ -57,6 +57,7 @@ src_configure(){
sed -i 's:-ltk_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -ltk_utils -rpath-link:' src/Makefile || die
sed -i 's:-lgap:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -lgap:' src/Makefile || die
sed -i 's:-lseq_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -lseq_utils:' src/Makefile || die
+ sed -i 's:-rpath-link::' src/Makefile || die
}
# TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gap2caf/
@ 2015-09-21 17:44 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2015-09-21 17:44 UTC (permalink / raw
To: gentoo-commits
commit: f499ae186b9f75e1a17f245eed8c59681a78fb52
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Sep 21 17:22:28 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Sep 21 17:22:28 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f499ae18
sci-biology/gap2caf: Add subslot operators
Package-Manager: portage-2.2.20.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/gap2caf/gap2caf-2.1.0.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
index bb1fa50..167733c 100644
--- a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
+++ b/sci-biology/gap2caf/gap2caf-2.1.0.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
# $Id$
@@ -19,7 +19,7 @@ IUSE=""
DEPEND="
sci-biology/staden
- >=dev-lang/tcl-8.5"
+ >=dev-lang/tcl-8.5:0="
RDEPEND="${DEPEND}"
#src_prepare(){
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gap2caf/
@ 2016-04-01 14:40 Marius Brehler
0 siblings, 0 replies; 6+ messages in thread
From: Marius Brehler @ 2016-04-01 14:40 UTC (permalink / raw
To: gentoo-commits
commit: 51dd0781500bdcff1c6eb3b13fae52b7c1ed3451
Author: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Fri Apr 1 14:39:33 2016 +0000
Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Fri Apr 1 14:39:33 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=51dd0781
sci-biology/gap2caf: Drop keywords
Package-Manager: portage-2.2.26
sci-biology/gap2caf/gap2caf-2.1.0.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
index 167733c..ea03551 100644
--- a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
+++ b/sci-biology/gap2caf/gap2caf-2.1.0.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
# $Id$
@@ -14,7 +14,7 @@ SRC_URI="
LICENSE="GRL staden"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
IUSE=""
DEPEND="
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gap2caf/
@ 2021-01-19 13:38 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 13:38 UTC (permalink / raw
To: gentoo-commits
commit: 4811dbace02e39fc810456ddbc683dbafbe4a521
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 13:38:21 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 13:38:21 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4811dbac
sci-biology/gap2caf: remove pack, upstream gone
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/gap2caf/gap2caf-2.1.0.ebuild | 77 --------------------------------
sci-biology/gap2caf/metadata.xml | 15 -------
2 files changed, 92 deletions(-)
diff --git a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
deleted file mode 100644
index 90a117a8c..000000000
--- a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools eutils
-
-DESCRIPTION="GAP4 file format to CAF v2 format converter for genomic assembly data"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/"
-SRC_URI="
- ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/gap2caf-2.1.0.tar.gz
- http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz"
-
-LICENSE="GRL staden"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
- sci-biology/staden
- >=dev-lang/tcl-8.5:0="
-RDEPEND="${DEPEND}"
-
-#src_prepare(){
-# epatch "${FILESDIR}"/Makefile.in-"${PV}".patch || die
-#}
-
-src_prepare(){
- sed -i 's:/include/tcl8.4:/include:' configure.ac || die
- sed -i 's:libtcl8.4:libtcl:' configure.ac || die
- sed \
- -e 's:tcl8.4:tcl:' \
- -e 's:pkglib_PROGRAMS:pkglibexec_PROGRAMS:g' \
- -i src/Makefile.am || die
- eautoreconf
- sed -i 's:/include/tcl8.4:/include:' configure || die
- sed -i 's:libtcl8.4:libtcl:' configure || die
-}
-
-src_configure(){
- # STADENROOT=/usr is used to find $STADENROOT/lib/staden/staden.profile and staden_config.h
- # STADENSRC is used to locate gap4/IO.h
- #CPPFLAGS="$CPPFLAGS -I/home/mmokrejs/proj/staden/staden/trunk/src" \
- #LDFLAGS="$LDFLAGS -L/usr/lib/staden -lmutlib -lprimer3 -lg -lmisc" \
- # STADENROOT=/usr/share/staden \
- # STADENSRC="${WORKDIR}"/staden-2.0.0b8-src \
- econf \
- --with-stadenroot=/usr \
- --with-tcl=/usr \
- --with-stadensrc="${WORKDIR}"/staden-2.0.0b8-src
- #sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' Makefile || die
- #sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' src/Makefile || die
- sed -i 's:tcl8.4:tcl:' src/Makefile || die
-
- # The below tricks in overall do not help, only for -ltk_utils somehow
- sed -i 's:-ltk_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -ltk_utils -rpath-link:' src/Makefile || die
- sed -i 's:-lgap:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -lgap:' src/Makefile || die
- sed -i 's:-lseq_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -lseq_utils:' src/Makefile || die
- sed -i 's:-rpath-link::' src/Makefile || die
-}
-
-# TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME
-# The man/Makefile.in is screwed in 2.0.2 so we cannot use it to install the manpage files,
-# not even copying over whole caftools-2.0/man/ to caftools-2.0.2/man does not help.
-src_install(){
- # do not use upstream's install it just install shell wrapper into /usr/bin/gap2caf
- # calling "LD_LIBRARY_PATH=/usr/lib/staden /usr/lib/gap2caf/gap2caf $@"
- # emake install DESTDIR="${D}" || die
- #
- # Instead, we rely on sci-biology/staden providind /etc/env.d/99staden file providing LDPATH=/usr/lib/staden
- dobin src/gap2caf
- dodoc README
-}
-
-# BUG #259848
-# A working ebuild which needs some files from staden source tree. That is ugly,
-# am sorting out with upstream how to get around in a clean way.
diff --git a/sci-biology/gap2caf/metadata.xml b/sci-biology/gap2caf/metadata.xml
deleted file mode 100644
index 0f267b755..000000000
--- a/sci-biology/gap2caf/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">downloads</remote-id>
- </upstream>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread
end of thread, other threads:[~2021-01-19 13:38 UTC | newest]
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2011-06-24 17:09 [gentoo-commits] proj/sci:master commit in: sci-biology/gap2caf/ Justin Lecher
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2021-01-19 13:38 Andrew Ammerlaan
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