* [gentoo-commits] proj/sci:master commit in: sci-biology/mosaik/
@ 2012-03-15 19:02 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2012-03-15 19:02 UTC (permalink / raw
To: gentoo-commits
commit: e51c8cf94d007438cd703266317fd41e863dc3bd
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 15 18:17:36 2012 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 15 18:17:36 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e51c8cf9
version bump, added the pdf documentation to SRC_URI, the compile process leaks through many 'Fastq.cpp:224: error: conditional expression between distinct pointer types 'gzFile_s*' and 'FILE*' lacks a cast' messages in Fastq.cpp:224, Fastq.cpp:226, Fasta.cpp:258, Fasta.cpp:260, Fasta.cpp:266, Fasta.cpp:268, but the package itself installs and executes at least
(Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)
---
sci-biology/mosaik/ChangeLog | 16 +++++++++++
sci-biology/mosaik/metadata.xml | 9 ++++++
sci-biology/mosaik/mosaik-1.1.0021.ebuild | 40 +++++++++++++++++++++++++++++
sci-biology/mosaik/mosaik-2.1.33.ebuild | 39 ++++++++++++++++++++++++++++
4 files changed, 104 insertions(+), 0 deletions(-)
diff --git a/sci-biology/mosaik/ChangeLog b/sci-biology/mosaik/ChangeLog
new file mode 100644
index 0000000..0b8561a
--- /dev/null
+++ b/sci-biology/mosaik/ChangeLog
@@ -0,0 +1,16 @@
+# ChangeLog for sci-biology/mosaik
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*mosaik-2.1.33 (15 Mar 2012)
+*mosaik-1.1.0021 (15 Mar 2012)
+
+ 15 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +mosaik-1.1.0021.ebuild, +mosaik-2.1.33.ebuild:
+ version bump, added the pdf documentation to SRC_URI, the compile process
+ leaks through many 'Fastq.cpp:224: error: conditional expression between
+ distinct pointer types 'gzFile_s*' and 'FILE*' lacks a cast' messages in
+ Fastq.cpp:224, Fastq.cpp:226, Fasta.cpp:258, Fasta.cpp:260, Fasta.cpp:266,
+ Fasta.cpp:268, but the package itself installs and executes at least
+ mosaik-1.1.0021.ebuild
+
diff --git a/sci-biology/mosaik/metadata.xml b/sci-biology/mosaik/metadata.xml
new file mode 100644
index 0000000..3302123
--- /dev/null
+++ b/sci-biology/mosaik/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer>
+ <email>weaver@gentoo.org</email>
+ <name>Andrey Kislyuk</name>
+ </maintainer>
+ <herd>sci-biology</herd>
+</pkgmetadata>
diff --git a/sci-biology/mosaik/mosaik-1.1.0021.ebuild b/sci-biology/mosaik/mosaik-1.1.0021.ebuild
new file mode 100644
index 0000000..932c5d0
--- /dev/null
+++ b/sci-biology/mosaik/mosaik-1.1.0021.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mosaik/mosaik-1.0.1388.ebuild,v 1.1 2010/04/11 17:29:40 weaver Exp $
+
+EAPI="2"
+
+DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
+HOMEPAGE="http://code.google.com/p/mosaik-aligner/"
+SRC_URI="http://mosaik-aligner.googlecode.com/files/Mosaik-${PV}-source.tar.bz2
+ http://code.google.com/p/mosaik-aligner/downloads/detail?name=Mosaik%201.0%20Documentation.pdf -> Mosaik-1.0-Documentation.pdf"
+
+LICENSE="GPL-2"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="dev-lang/swig"
+RDEPEND=""
+
+S="${WORKDIR}/mosaik-aligner"
+
+src_prepare() {
+ sed -i 's/-static//' src/includes/linux.inc || die
+}
+
+src_compile() {
+ emake -C src || die
+ emake -C MosaikTools/c++ || die
+ export PERL_CORE_DIR=/usr/lib64/perl5/5.12.4/x86_64-linux/CORE
+ emake -C MosaikTools/perl PERL_CORE_DIR=/usr/lib64/perl5/5.12.4/x86_64-linux/CORE || die
+}
+
+src_install() {
+ dobin bin/* || die
+
+ insinto /usr/share/${PN}
+ doins -r MosaikTools || die
+
+ dodoc README "${DISTDIR}"/Mosaik-1.0-Documentation.pdf
+}
diff --git a/sci-biology/mosaik/mosaik-2.1.33.ebuild b/sci-biology/mosaik/mosaik-2.1.33.ebuild
new file mode 100644
index 0000000..353ecb5
--- /dev/null
+++ b/sci-biology/mosaik/mosaik-2.1.33.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mosaik/mosaik-1.0.1388.ebuild,v 1.1 2010/04/11 17:29:40 weaver Exp $
+
+EAPI="2"
+
+DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
+HOMEPAGE="http://code.google.com/p/mosaik-aligner/"
+SRC_URI="http://mosaik-aligner.googlecode.com/files/MOSAIK-${PV}-source.tar"
+
+LICENSE="GPL-2 || ( MIT )"
+SLOT="0"
+IUSE=""
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND=""
+
+S="${WORKDIR}/MOSAIK-${PV}-source"
+
+src_prepare() {
+ #sed -i 's/-static//' src/includes/linux.inc || die
+ echo
+}
+
+src_compile() {
+ emake || die
+# emake -C MosaikTools/c++ || die
+# emake -C MosaikTools/perl || die
+}
+
+src_install() {
+ dobin bin/* || die
+
+ insinto /usr/share/${PN}
+ doins -r MosaikTools || die
+
+ dodoc README Mosaik-1.0-Documentation.pdf
+}
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mosaik/
@ 2012-03-15 19:42 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2012-03-15 19:42 UTC (permalink / raw
To: gentoo-commits
commit: e60260d0cfac4c0834f36777c589e87f43d08c62
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 15 19:42:12 2012 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 15 19:42:12 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=e60260d0
sci-biology/mosaik: version bump for 2.1.33 and GIT HEAD, neither compiles so far; upstream re-contacted
(Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)
---
sci-biology/mosaik/ChangeLog | 7 +++++
sci-biology/mosaik/mosaik-2.1.33.ebuild | 33 +++++++++++++---------
sci-biology/mosaik/mosaik-9999.ebuild | 45 +++++++++++++++++++++++++++++++
3 files changed, 71 insertions(+), 14 deletions(-)
diff --git a/sci-biology/mosaik/ChangeLog b/sci-biology/mosaik/ChangeLog
index 0b8561a..51f8658 100644
--- a/sci-biology/mosaik/ChangeLog
+++ b/sci-biology/mosaik/ChangeLog
@@ -2,6 +2,13 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*mosaik-9999 (15 Mar 2012)
+
+ 15 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ mosaik-2.1.33.ebuild, +mosaik-9999.ebuild:
+ version bump for 2.1.33 and GIT HEAD, neither compiles so far; upstream
+ re-contacted mosaik-2.1.33.ebuild mosaik-9999.ebuild
+
*mosaik-2.1.33 (15 Mar 2012)
*mosaik-1.1.0021 (15 Mar 2012)
diff --git a/sci-biology/mosaik/mosaik-2.1.33.ebuild b/sci-biology/mosaik/mosaik-2.1.33.ebuild
index 353ecb5..172bed2 100644
--- a/sci-biology/mosaik/mosaik-2.1.33.ebuild
+++ b/sci-biology/mosaik/mosaik-2.1.33.ebuild
@@ -4,9 +4,19 @@
EAPI="2"
+if [ "$PV" == "9999" ]; then
+ inherit git-2
+fi
+
DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
HOMEPAGE="http://code.google.com/p/mosaik-aligner/"
-SRC_URI="http://mosaik-aligner.googlecode.com/files/MOSAIK-${PV}-source.tar"
+
+if [ "$PV" == "9999" ]; then
+ EGIT_REPO_URI="http://code.google.com/p/mosaik-aligner"
+else
+ SRC_URI="http://mosaik-aligner.googlecode.com/files/MOSAIK-${PV}-source.tar
+ http://code.google.com/p/mosaik-aligner/downloads/detail?name=Mosaik%201.0%20Documentation.pdf -> Mosaik-1.0-Documentation.pdf"
+fi
LICENSE="GPL-2 || ( MIT )"
SLOT="0"
@@ -16,24 +26,19 @@ KEYWORDS="~amd64 ~x86"
DEPEND=""
RDEPEND=""
-S="${WORKDIR}/MOSAIK-${PV}-source"
-
-src_prepare() {
- #sed -i 's/-static//' src/includes/linux.inc || die
- echo
-}
+if [ ! "$PV" == "9999" ]; then
+ S="${WORKDIR}/MOSAIK-${PV}-source"
+fi
src_compile() {
+ if [ "$PV" == "9999" ]; then
+ cd src || die
+ fi
emake || die
-# emake -C MosaikTools/c++ || die
-# emake -C MosaikTools/perl || die
}
src_install() {
- dobin bin/* || die
-
- insinto /usr/share/${PN}
- doins -r MosaikTools || die
+ dobin "${WORKDIR}"/bin/* || die
- dodoc README Mosaik-1.0-Documentation.pdf
+ dodoc README "${DISTDIR}"/Mosaik-1.0-Documentation.pdf
}
diff --git a/sci-biology/mosaik/mosaik-9999.ebuild b/sci-biology/mosaik/mosaik-9999.ebuild
new file mode 100644
index 0000000..3564bc3
--- /dev/null
+++ b/sci-biology/mosaik/mosaik-9999.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/mosaik/mosaik-1.0.1388.ebuild,v 1.1 2010/04/11 17:29:40 weaver Exp $
+
+EAPI="2"
+
+if [ "$PV" == "9999" ]; then
+ inherit git-2
+fi
+
+DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
+HOMEPAGE="http://code.google.com/p/mosaik-aligner/"
+
+if [ "$PV" == "9999" ]; then
+ EGIT_REPO_URI="http://code.google.com/p/mosaik-aligner"
+ KEYWORDS=""
+else
+ SRC_URI="http://mosaik-aligner.googlecode.com/files/MOSAIK-${PV}-source.tar
+ http://code.google.com/p/mosaik-aligner/downloads/detail?name=Mosaik%201.0%20Documentation.pdf -> Mosaik-1.0-Documentation.pdf"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="GPL-2 || ( MIT )"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND=""
+
+if [ ! "$PV" == "9999" ]; then
+ S="${WORKDIR}/MOSAIK-${PV}-source"
+fi
+
+src_compile() {
+ if [ "$PV" == "9999" ]; then
+ cd src || die
+ fi
+ emake || die
+}
+
+src_install() {
+ dobin "${WORKDIR}"/bin/* || die
+
+ dodoc README "${DISTDIR}"/Mosaik-1.0-Documentation.pdf
+}
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mosaik/
@ 2012-03-16 0:27 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2012-03-16 0:27 UTC (permalink / raw
To: gentoo-commits
commit: a4961e21d3f7154fa9ca7a121e39345ae1a7cebc
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 16 00:26:37 2012 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 16 00:26:37 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a4961e21
sci-biology/mosaik: masking mosaik-2.1.33 mosaik-9999
(Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)
---
sci-biology/mosaik/ChangeLog | 4 ++++
sci-biology/mosaik/mosaik-2.1.33.ebuild | 4 +++-
sci-biology/mosaik/mosaik-9999.ebuild | 3 ++-
3 files changed, 9 insertions(+), 2 deletions(-)
diff --git a/sci-biology/mosaik/ChangeLog b/sci-biology/mosaik/ChangeLog
index 51f8658..2b974bd 100644
--- a/sci-biology/mosaik/ChangeLog
+++ b/sci-biology/mosaik/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 16 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ mosaik-2.1.33.ebuild, mosaik-9999.ebuild:
+ sci-biology/mosaik: masking mosaik-2.1.33 mosaik-9999
+
*mosaik-9999 (15 Mar 2012)
15 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/mosaik/mosaik-2.1.33.ebuild b/sci-biology/mosaik/mosaik-2.1.33.ebuild
index 172bed2..aaed122 100644
--- a/sci-biology/mosaik/mosaik-2.1.33.ebuild
+++ b/sci-biology/mosaik/mosaik-2.1.33.ebuild
@@ -13,15 +13,17 @@ HOMEPAGE="http://code.google.com/p/mosaik-aligner/"
if [ "$PV" == "9999" ]; then
EGIT_REPO_URI="http://code.google.com/p/mosaik-aligner"
+ KEYWORDS=""
else
SRC_URI="http://mosaik-aligner.googlecode.com/files/MOSAIK-${PV}-source.tar
http://code.google.com/p/mosaik-aligner/downloads/detail?name=Mosaik%201.0%20Documentation.pdf -> Mosaik-1.0-Documentation.pdf"
+ #KEYWORDS="~amd64 ~x86"
+ KEYWORDS=""
fi
LICENSE="GPL-2 || ( MIT )"
SLOT="0"
IUSE=""
-KEYWORDS="~amd64 ~x86"
DEPEND=""
RDEPEND=""
diff --git a/sci-biology/mosaik/mosaik-9999.ebuild b/sci-biology/mosaik/mosaik-9999.ebuild
index 3564bc3..aaed122 100644
--- a/sci-biology/mosaik/mosaik-9999.ebuild
+++ b/sci-biology/mosaik/mosaik-9999.ebuild
@@ -17,7 +17,8 @@ if [ "$PV" == "9999" ]; then
else
SRC_URI="http://mosaik-aligner.googlecode.com/files/MOSAIK-${PV}-source.tar
http://code.google.com/p/mosaik-aligner/downloads/detail?name=Mosaik%201.0%20Documentation.pdf -> Mosaik-1.0-Documentation.pdf"
- KEYWORDS="~amd64 ~x86"
+ #KEYWORDS="~amd64 ~x86"
+ KEYWORDS=""
fi
LICENSE="GPL-2 || ( MIT )"
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mosaik/
@ 2012-06-01 9:28 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2012-06-01 9:28 UTC (permalink / raw
To: gentoo-commits
commit: 1c622b5751c7828f39d82ee578f30ea083cabfce
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jun 1 09:28:05 2012 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jun 1 09:28:05 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1c622b57
improved die() message to inform user that gcc-4.5.3 does not work while gcc-4.3.6 does
(Portage version: 2.1.10.63/git/Linux x86_64, unsigned Manifest commit)
---
sci-biology/mosaik/ChangeLog | 5 +++++
sci-biology/mosaik/mosaik-1.1.0021.ebuild | 2 +-
2 files changed, 6 insertions(+), 1 deletions(-)
diff --git a/sci-biology/mosaik/ChangeLog b/sci-biology/mosaik/ChangeLog
index 2b974bd..8c892a5 100644
--- a/sci-biology/mosaik/ChangeLog
+++ b/sci-biology/mosaik/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 01 Jun 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ mosaik-1.1.0021.ebuild:
+ improved die() message to inform user that gcc-4.5.3 does not work while
+ gcc-4.3.6 does
+
16 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
mosaik-2.1.33.ebuild, mosaik-9999.ebuild:
sci-biology/mosaik: masking mosaik-2.1.33 mosaik-9999
diff --git a/sci-biology/mosaik/mosaik-1.1.0021.ebuild b/sci-biology/mosaik/mosaik-1.1.0021.ebuild
index 932c5d0..853835e 100644
--- a/sci-biology/mosaik/mosaik-1.1.0021.ebuild
+++ b/sci-biology/mosaik/mosaik-1.1.0021.ebuild
@@ -27,7 +27,7 @@ src_compile() {
emake -C src || die
emake -C MosaikTools/c++ || die
export PERL_CORE_DIR=/usr/lib64/perl5/5.12.4/x86_64-linux/CORE
- emake -C MosaikTools/perl PERL_CORE_DIR=/usr/lib64/perl5/5.12.4/x86_64-linux/CORE || die
+ emake -C MosaikTools/perl PERL_CORE_DIR=/usr/lib64/perl5/5.12.4/x86_64-linux/CORE || die "Please use gcc-4.3.6 while not 4.5.3 if the latter exits at MosaikAlignment.cpp"
}
src_install() {
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mosaik/
@ 2014-01-06 19:27 Justin Lecher
0 siblings, 0 replies; 9+ messages in thread
From: Justin Lecher @ 2014-01-06 19:27 UTC (permalink / raw
To: gentoo-commits
commit: 153f5827acd59206bee5de4d135e46a8db78e55b
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 6 18:57:37 2014 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan 6 18:57:37 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=153f5827
sci-biology/mosaik: Switch from git-2 to git-r3
Package-Manager: portage-2.2.8
---
sci-biology/mosaik/ChangeLog | 6 ++++-
sci-biology/mosaik/metadata.xml | 10 ++++----
sci-biology/mosaik/mosaik-1.1.0021.ebuild | 40 -------------------------------
sci-biology/mosaik/mosaik-2.1.33.ebuild | 38 +++++++----------------------
sci-biology/mosaik/mosaik-9999.ebuild | 36 +++++++---------------------
5 files changed, 27 insertions(+), 103 deletions(-)
diff --git a/sci-biology/mosaik/ChangeLog b/sci-biology/mosaik/ChangeLog
index 8c892a5..5fa0b1e 100644
--- a/sci-biology/mosaik/ChangeLog
+++ b/sci-biology/mosaik/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/mosaik
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mosaik-1.1.0021.ebuild,
+ mosaik-2.1.33.ebuild, mosaik-9999.ebuild, metadata.xml:
+ Switch from git-2 to git-r3
+
01 Jun 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
mosaik-1.1.0021.ebuild:
improved die() message to inform user that gcc-4.5.3 does not work while
diff --git a/sci-biology/mosaik/metadata.xml b/sci-biology/mosaik/metadata.xml
index 3302123..fc7c769 100644
--- a/sci-biology/mosaik/metadata.xml
+++ b/sci-biology/mosaik/metadata.xml
@@ -1,9 +1,9 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer>
- <email>weaver@gentoo.org</email>
- <name>Andrey Kislyuk</name>
- </maintainer>
- <herd>sci-biology</herd>
+ <maintainer>
+ <email>weaver@gentoo.org</email>
+ <name>Andrey Kislyuk</name>
+ </maintainer>
+ <herd>sci-biology</herd>
</pkgmetadata>
diff --git a/sci-biology/mosaik/mosaik-1.1.0021.ebuild b/sci-biology/mosaik/mosaik-1.1.0021.ebuild
deleted file mode 100644
index 853835e..0000000
--- a/sci-biology/mosaik/mosaik-1.1.0021.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mosaik/mosaik-1.0.1388.ebuild,v 1.1 2010/04/11 17:29:40 weaver Exp $
-
-EAPI="2"
-
-DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
-HOMEPAGE="http://code.google.com/p/mosaik-aligner/"
-SRC_URI="http://mosaik-aligner.googlecode.com/files/Mosaik-${PV}-source.tar.bz2
- http://code.google.com/p/mosaik-aligner/downloads/detail?name=Mosaik%201.0%20Documentation.pdf -> Mosaik-1.0-Documentation.pdf"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86"
-
-DEPEND="dev-lang/swig"
-RDEPEND=""
-
-S="${WORKDIR}/mosaik-aligner"
-
-src_prepare() {
- sed -i 's/-static//' src/includes/linux.inc || die
-}
-
-src_compile() {
- emake -C src || die
- emake -C MosaikTools/c++ || die
- export PERL_CORE_DIR=/usr/lib64/perl5/5.12.4/x86_64-linux/CORE
- emake -C MosaikTools/perl PERL_CORE_DIR=/usr/lib64/perl5/5.12.4/x86_64-linux/CORE || die "Please use gcc-4.3.6 while not 4.5.3 if the latter exits at MosaikAlignment.cpp"
-}
-
-src_install() {
- dobin bin/* || die
-
- insinto /usr/share/${PN}
- doins -r MosaikTools || die
-
- dodoc README "${DISTDIR}"/Mosaik-1.0-Documentation.pdf
-}
diff --git a/sci-biology/mosaik/mosaik-2.1.33.ebuild b/sci-biology/mosaik/mosaik-2.1.33.ebuild
index aaed122..f2a6954 100644
--- a/sci-biology/mosaik/mosaik-2.1.33.ebuild
+++ b/sci-biology/mosaik/mosaik-2.1.33.ebuild
@@ -1,46 +1,24 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/mosaik/mosaik-1.0.1388.ebuild,v 1.1 2010/04/11 17:29:40 weaver Exp $
-EAPI="2"
-
-if [ "$PV" == "9999" ]; then
- inherit git-2
-fi
+EAPI=5
DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
HOMEPAGE="http://code.google.com/p/mosaik-aligner/"
-
-if [ "$PV" == "9999" ]; then
- EGIT_REPO_URI="http://code.google.com/p/mosaik-aligner"
- KEYWORDS=""
-else
- SRC_URI="http://mosaik-aligner.googlecode.com/files/MOSAIK-${PV}-source.tar
- http://code.google.com/p/mosaik-aligner/downloads/detail?name=Mosaik%201.0%20Documentation.pdf -> Mosaik-1.0-Documentation.pdf"
- #KEYWORDS="~amd64 ~x86"
- KEYWORDS=""
-fi
+SRC_URI="
+ http://mosaik-aligner.googlecode.com/files/MOSAIK-${PV}-source.tar
+ http://code.google.com/p/mosaik-aligner/downloads/detail?name=Mosaik%201.0%20Documentation.pdf -> Mosaik-1.0-Documentation.pdf"
LICENSE="GPL-2 || ( MIT )"
SLOT="0"
IUSE=""
+KEYWORDS="~amd64 ~x86"
-DEPEND=""
-RDEPEND=""
-
-if [ ! "$PV" == "9999" ]; then
- S="${WORKDIR}/MOSAIK-${PV}-source"
-fi
-
-src_compile() {
- if [ "$PV" == "9999" ]; then
- cd src || die
- fi
- emake || die
-}
+S="${WORKDIR}/MOSAIK-${PV}-source"
src_install() {
- dobin "${WORKDIR}"/bin/* || die
+ dobin "${WORKDIR}"/bin/*
dodoc README "${DISTDIR}"/Mosaik-1.0-Documentation.pdf
}
diff --git a/sci-biology/mosaik/mosaik-9999.ebuild b/sci-biology/mosaik/mosaik-9999.ebuild
index aaed122..70d048f 100644
--- a/sci-biology/mosaik/mosaik-9999.ebuild
+++ b/sci-biology/mosaik/mosaik-9999.ebuild
@@ -1,46 +1,28 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/mosaik/mosaik-1.0.1388.ebuild,v 1.1 2010/04/11 17:29:40 weaver Exp $
-EAPI="2"
+EAPI=5
-if [ "$PV" == "9999" ]; then
- inherit git-2
-fi
+inherit git-r3
DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
HOMEPAGE="http://code.google.com/p/mosaik-aligner/"
-
-if [ "$PV" == "9999" ]; then
- EGIT_REPO_URI="http://code.google.com/p/mosaik-aligner"
- KEYWORDS=""
-else
- SRC_URI="http://mosaik-aligner.googlecode.com/files/MOSAIK-${PV}-source.tar
- http://code.google.com/p/mosaik-aligner/downloads/detail?name=Mosaik%201.0%20Documentation.pdf -> Mosaik-1.0-Documentation.pdf"
- #KEYWORDS="~amd64 ~x86"
- KEYWORDS=""
-fi
+SRC_URI=""
+EGIT_REPO_URI="http://code.google.com/p/mosaik-aligner"
LICENSE="GPL-2 || ( MIT )"
SLOT="0"
IUSE=""
-
-DEPEND=""
-RDEPEND=""
-
-if [ ! "$PV" == "9999" ]; then
- S="${WORKDIR}/MOSAIK-${PV}-source"
-fi
+KEYWORDS=""
src_compile() {
- if [ "$PV" == "9999" ]; then
- cd src || die
- fi
- emake || die
+ cd src || die
+ emake
}
src_install() {
- dobin "${WORKDIR}"/bin/* || die
+ dobin "${WORKDIR}"/bin/*
dodoc README "${DISTDIR}"/Mosaik-1.0-Documentation.pdf
}
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mosaik/
@ 2014-01-07 7:45 Justin Lecher
0 siblings, 0 replies; 9+ messages in thread
From: Justin Lecher @ 2014-01-07 7:45 UTC (permalink / raw
To: gentoo-commits
commit: f5ee8018d5d66f091fde1582bc86594a621b45c4
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 7 07:44:39 2014 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jan 7 07:44:39 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f5ee8018
sci-biology/mosaik: Readd ebuild
Package-Manager: portage-2.2.8
---
sci-biology/mosaik/ChangeLog | 6 +++---
sci-biology/mosaik/mosaik-2.1.33.ebuild | 2 +-
sci-biology/mosaik/mosaik-9999.ebuild | 4 ++--
3 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/sci-biology/mosaik/ChangeLog b/sci-biology/mosaik/ChangeLog
index 5fa0b1e..87f4c4b 100644
--- a/sci-biology/mosaik/ChangeLog
+++ b/sci-biology/mosaik/ChangeLog
@@ -2,9 +2,9 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
- 06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mosaik-1.1.0021.ebuild,
- mosaik-2.1.33.ebuild, mosaik-9999.ebuild, metadata.xml:
- Switch from git-2 to git-r3
+ 07 Jan 2014; Justin Lecher <jlec@gentoo.org> mosaik-2.1.33.ebuild,
+ mosaik-9999.ebuild, metadata.xml:
+ Readd ebuild
01 Jun 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
mosaik-1.1.0021.ebuild:
diff --git a/sci-biology/mosaik/mosaik-2.1.33.ebuild b/sci-biology/mosaik/mosaik-2.1.33.ebuild
index f2a6954..daf0a60 100644
--- a/sci-biology/mosaik/mosaik-2.1.33.ebuild
+++ b/sci-biology/mosaik/mosaik-2.1.33.ebuild
@@ -15,7 +15,7 @@ SLOT="0"
IUSE=""
KEYWORDS="~amd64 ~x86"
-S="${WORKDIR}/MOSAIK-${PV}-source"
+S="${WORKDIR}"/MOSAIK-${PV}-source
src_install() {
dobin "${WORKDIR}"/bin/*
diff --git a/sci-biology/mosaik/mosaik-9999.ebuild b/sci-biology/mosaik/mosaik-9999.ebuild
index 70d048f..f7d680d 100644
--- a/sci-biology/mosaik/mosaik-9999.ebuild
+++ b/sci-biology/mosaik/mosaik-9999.ebuild
@@ -8,7 +8,7 @@ inherit git-r3
DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
HOMEPAGE="http://code.google.com/p/mosaik-aligner/"
-SRC_URI=""
+SRC_URI="http://code.google.com/p/mosaik-aligner/downloads/detail?name=Mosaik%201.0%20Documentation.pdf -> Mosaik-1.0-Documentation.pdf"
EGIT_REPO_URI="http://code.google.com/p/mosaik-aligner"
LICENSE="GPL-2 || ( MIT )"
@@ -18,7 +18,7 @@ KEYWORDS=""
src_compile() {
cd src || die
- emake
+ default
}
src_install() {
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mosaik/
@ 2015-01-15 9:57 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2015-01-15 9:57 UTC (permalink / raw
To: gentoo-commits
commit: 016a54a18482b9ade330b819a0c772a2ff74da8e
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan 15 09:54:09 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan 15 09:54:09 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=016a54a1
version bump, masking a crappy package until at least the Makefile's propagate an error code back to upstream caller, https://code.google.com/p/mosaik-aligner/issues/detail?id=135
Package-Manager: portage-2.2.7
---
sci-biology/mosaik/ChangeLog | 11 +++++++++--
.../mosaik/{mosaik-2.1.33.ebuild => mosaik-2.2.3.ebuild} | 10 ++++++++--
2 files changed, 17 insertions(+), 4 deletions(-)
diff --git a/sci-biology/mosaik/ChangeLog b/sci-biology/mosaik/ChangeLog
index 87f4c4b..5116021 100644
--- a/sci-biology/mosaik/ChangeLog
+++ b/sci-biology/mosaik/ChangeLog
@@ -1,7 +1,15 @@
# ChangeLog for sci-biology/mosaik
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*mosaik-2.2.3 (15 Jan 2015)
+
+ 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +mosaik-2.2.3.ebuild, -mosaik-2.1.33.ebuild:
+ version bump, masking a crappy package until at least the Makefile's
+ propagate an error code back to upstream caller, https://code.google.com/p
+ /mosaik-aligner/issues/detail?id=135
+
07 Jan 2014; Justin Lecher <jlec@gentoo.org> mosaik-2.1.33.ebuild,
mosaik-9999.ebuild, metadata.xml:
Readd ebuild
@@ -33,4 +41,3 @@
Fastq.cpp:224, Fastq.cpp:226, Fasta.cpp:258, Fasta.cpp:260, Fasta.cpp:266,
Fasta.cpp:268, but the package itself installs and executes at least
mosaik-1.1.0021.ebuild
-
diff --git a/sci-biology/mosaik/mosaik-2.1.33.ebuild b/sci-biology/mosaik/mosaik-2.2.3.ebuild
similarity index 75%
rename from sci-biology/mosaik/mosaik-2.1.33.ebuild
rename to sci-biology/mosaik/mosaik-2.2.3.ebuild
index bc26a05..6bd994b 100644
--- a/sci-biology/mosaik/mosaik-2.1.33.ebuild
+++ b/sci-biology/mosaik/mosaik-2.2.3.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: $
@@ -13,10 +13,16 @@ SRC_URI="
LICENSE="GPL-2 || ( MIT )"
SLOT="0"
IUSE=""
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
+
+# https://code.google.com/p/mosaik-aligner/issues/detail?id=135
S="${WORKDIR}"/MOSAIK-${PV}-source
+src_prepare(){
+ sed -e "s@export LDFLAGS = -Wl@#export LDFLAGS = -Wl@" -i Makefile
+}
+
src_install() {
dobin "${WORKDIR}"/bin/*
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mosaik/
@ 2016-12-19 19:55 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2016-12-19 19:55 UTC (permalink / raw
To: gentoo-commits
commit: 3e1bdc7058b39e6b61004c093714cf6a83a18764
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Dec 19 19:55:48 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Dec 19 19:55:48 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3e1bdc70
sci-biology/mosaik: removing old since newer landed in main tree
sci-biology/mosaik/mosaik-2.2.3.ebuild | 30 ------------------------------
1 file changed, 30 deletions(-)
diff --git a/sci-biology/mosaik/mosaik-2.2.3.ebuild b/sci-biology/mosaik/mosaik-2.2.3.ebuild
deleted file mode 100644
index 9e6800f..0000000
--- a/sci-biology/mosaik/mosaik-2.2.3.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
-HOMEPAGE="http://code.google.com/p/mosaik-aligner/"
-SRC_URI="
- http://mosaik-aligner.googlecode.com/files/MOSAIK-${PV}-source.tar
- http://code.google.com/p/mosaik-aligner/downloads/detail?name=Mosaik%201.0%20Documentation.pdf -> Mosaik-1.0-Documentation.pdf"
-
-LICENSE="GPL-2 || ( MIT )"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-# https://code.google.com/p/mosaik-aligner/issues/detail?id=135
-
-S="${WORKDIR}"/MOSAIK-${PV}-source
-
-src_prepare(){
- sed -e "s@export LDFLAGS = -Wl@#export LDFLAGS = -Wl@" -i Makefile
-}
-
-src_install() {
- dobin "${WORKDIR}"/bin/*
-
- dodoc README "${DISTDIR}"/Mosaik-1.0-Documentation.pdf
-}
^ permalink raw reply related [flat|nested] 9+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/mosaik/
@ 2016-12-19 20:02 Martin Mokrejs
0 siblings, 0 replies; 9+ messages in thread
From: Martin Mokrejs @ 2016-12-19 20:02 UTC (permalink / raw
To: gentoo-commits
commit: b1515f9599b10c8b079f95cef4aaa52cbdb520dc
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Dec 19 20:02:27 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Dec 19 20:02:27 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b1515f95
sci-biology/mosaik: removing since latest version landed in main tree
sci-biology/mosaik/metadata.xml | 8 --------
sci-biology/mosaik/mosaik-9999.ebuild | 28 ----------------------------
2 files changed, 36 deletions(-)
diff --git a/sci-biology/mosaik/metadata.xml b/sci-biology/mosaik/metadata.xml
deleted file mode 100644
index 004c995..0000000
--- a/sci-biology/mosaik/metadata.xml
+++ /dev/null
@@ -1,8 +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>
- </pkgmetadata>
diff --git a/sci-biology/mosaik/mosaik-9999.ebuild b/sci-biology/mosaik/mosaik-9999.ebuild
deleted file mode 100644
index 8a68a16..0000000
--- a/sci-biology/mosaik/mosaik-9999.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit git-r3
-
-DESCRIPTION="A reference-guided aligner for next-generation sequencing technologies"
-HOMEPAGE="http://code.google.com/p/mosaik-aligner/"
-SRC_URI="http://code.google.com/p/mosaik-aligner/downloads/detail?name=Mosaik%201.0%20Documentation.pdf -> Mosaik-1.0-Documentation.pdf"
-EGIT_REPO_URI="http://code.google.com/p/mosaik-aligner"
-
-LICENSE="GPL-2 || ( MIT )"
-SLOT="0"
-IUSE=""
-KEYWORDS=""
-
-src_compile() {
- cd src || die
- default
-}
-
-src_install() {
- dobin "${WORKDIR}"/bin/*
-
- dodoc README "${DISTDIR}"/Mosaik-1.0-Documentation.pdf
-}
^ permalink raw reply related [flat|nested] 9+ messages in thread
end of thread, other threads:[~2016-12-19 20:02 UTC | newest]
Thread overview: 9+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2015-01-15 9:57 [gentoo-commits] proj/sci:master commit in: sci-biology/mosaik/ Martin Mokrejs
-- strict thread matches above, loose matches on Subject: below --
2016-12-19 20:02 Martin Mokrejs
2016-12-19 19:55 Martin Mokrejs
2014-01-07 7:45 Justin Lecher
2014-01-06 19:27 Justin Lecher
2012-06-01 9:28 Martin Mokrejs
2012-03-16 0:27 Martin Mokrejs
2012-03-15 19:42 Martin Mokrejs
2012-03-15 19:02 Martin Mokrejs
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox