* [gentoo-commits] proj/sci:master commit in: sci-biology/fastx_toolkit/
@ 2013-08-29 15:35 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2013-08-29 15:35 UTC (permalink / raw
To: gentoo-commits
commit: 3500e988a9231e0bb79e3de3daaf48ac1e7d1d9a
Author: Martin Mokrejš <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Thu Aug 29 15:34:26 2013 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Aug 29 15:34:26 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3500e988
New package for FASTA/FASTQ preprocessing
---
sci-biology/fastx_toolkit/ChangeLog | 10 +++++++++
.../fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild | 26 ++++++++++++++++++++++
2 files changed, 36 insertions(+)
diff --git a/sci-biology/fastx_toolkit/ChangeLog b/sci-biology/fastx_toolkit/ChangeLog
new file mode 100644
index 0000000..907109e
--- /dev/null
+++ b/sci-biology/fastx_toolkit/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/fastx_toolkit
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*fastx_toolkit-0.0.13.2 (29 Aug 2013)
+
+ 29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +fastx_toolkit-0.0.13.2.ebuild:
+ New package for FASTA/FASTQ preprocessing.
+
diff --git a/sci-biology/fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild b/sci-biology/fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild
new file mode 100644
index 0000000..ed24005
--- /dev/null
+++ b/sci-biology/fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+DESCRIPTION="Tools for Short Read FASTA/FASTQ file processing"
+HOMEPAGE="http://hannonlab.cshl.edu/fastx_toolkit"
+SRC_URI="http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit-"${PV}".tar.bz2"
+
+LICENSE="AGPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=sci-biology/libgtextutils-0.6.1"
+RDEPEND="${DEPEND}
+ dev-perl/PerlIO-gzip
+ dev-perl/GDGraph
+ sys-apps/sed
+ sci-visualization/gnuplot"
+
+src_install(){
+ emake install DESTDIR="${D}"
+}
+
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fastx_toolkit/
@ 2014-01-06 19:57 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2014-01-06 19:57 UTC (permalink / raw
To: gentoo-commits
commit: 1234bf674eb566e5b914235f996e047f7e221149
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 6 19:41:43 2014 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan 6 19:41:43 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1234bf67
sci-biology/fastx_toolkit: Bump to EAPI=5 and add missing metadata.xml
Package-Manager: portage-2.2.8
---
sci-biology/fastx_toolkit/ChangeLog | 6 +++++-
sci-biology/fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild | 9 ++-------
sci-biology/fastx_toolkit/metadata.xml | 5 +++++
3 files changed, 12 insertions(+), 8 deletions(-)
diff --git a/sci-biology/fastx_toolkit/ChangeLog b/sci-biology/fastx_toolkit/ChangeLog
index 907109e..112f562 100644
--- a/sci-biology/fastx_toolkit/ChangeLog
+++ b/sci-biology/fastx_toolkit/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/fastx_toolkit
-# Copyright 1999-2013 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> fastx_toolkit-0.0.13.2.ebuild,
+ +metadata.xml:
+ Bump to EAPI=5 and add missing metadata.xml
+
*fastx_toolkit-0.0.13.2 (29 Aug 2013)
29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild b/sci-biology/fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild
index ed24005..c3f6276 100644
--- a/sci-biology/fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild
+++ b/sci-biology/fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=3
+EAPI=5
DESCRIPTION="Tools for Short Read FASTA/FASTQ file processing"
HOMEPAGE="http://hannonlab.cshl.edu/fastx_toolkit"
@@ -19,8 +19,3 @@ RDEPEND="${DEPEND}
dev-perl/GDGraph
sys-apps/sed
sci-visualization/gnuplot"
-
-src_install(){
- emake install DESTDIR="${D}"
-}
-
diff --git a/sci-biology/fastx_toolkit/metadata.xml b/sci-biology/fastx_toolkit/metadata.xml
new file mode 100644
index 0000000..897aa2e
--- /dev/null
+++ b/sci-biology/fastx_toolkit/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</herd>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fastx_toolkit/
@ 2014-01-20 17:27 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2014-01-20 17:27 UTC (permalink / raw
To: gentoo-commits
commit: 3131ca1e4d9c1729f40e4e40a0f10d65e270105c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jan 20 17:26:54 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jan 20 17:26:54 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3131ca1e
Moved dependency on gtextlib
Package-Manager: portage-2.2.7
---
sci-biology/fastx_toolkit/ChangeLog | 5 ++++-
sci-biology/fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild | 5 +++--
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/sci-biology/fastx_toolkit/ChangeLog b/sci-biology/fastx_toolkit/ChangeLog
index 112f562..be96788 100644
--- a/sci-biology/fastx_toolkit/ChangeLog
+++ b/sci-biology/fastx_toolkit/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 20 Jan 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ fastx_toolkit-0.0.13.2.ebuild:
+ Moved dependency on gtextlib
+
06 Jan 2014; Justin Lecher <jlec@gentoo.org> fastx_toolkit-0.0.13.2.ebuild,
+metadata.xml:
Bump to EAPI=5 and add missing metadata.xml
@@ -11,4 +15,3 @@
29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+fastx_toolkit-0.0.13.2.ebuild:
New package for FASTA/FASTQ preprocessing.
-
diff --git a/sci-biology/fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild b/sci-biology/fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild
index c3f6276..2bbbdfc 100644
--- a/sci-biology/fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild
+++ b/sci-biology/fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild
@@ -13,9 +13,10 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
-DEPEND=">=sci-biology/libgtextutils-0.6.1"
+DEPEND=""
RDEPEND="${DEPEND}
dev-perl/PerlIO-gzip
dev-perl/GDGraph
sys-apps/sed
- sci-visualization/gnuplot"
+ sci-visualization/gnuplot
+ sci-biology/libgtextutils"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fastx_toolkit/
@ 2014-01-20 18:06 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2014-01-20 18:06 UTC (permalink / raw
To: gentoo-commits
commit: b88f7dc28fec5858ddcb5e1c287ef402407e7915
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jan 20 18:05:29 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jan 20 18:05:29 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b88f7dc2
Version bump, releases were moved to github
Package-Manager: portage-2.2.7
---
sci-biology/fastx_toolkit/ChangeLog | 6 ++++++
.../{fastx_toolkit-0.0.13.2.ebuild => fastx_toolkit-0.0.14.ebuild} | 2 +-
2 files changed, 7 insertions(+), 1 deletion(-)
diff --git a/sci-biology/fastx_toolkit/ChangeLog b/sci-biology/fastx_toolkit/ChangeLog
index be96788..f233c54 100644
--- a/sci-biology/fastx_toolkit/ChangeLog
+++ b/sci-biology/fastx_toolkit/ChangeLog
@@ -2,6 +2,12 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*fastx_toolkit-0.0.14 (20 Jan 2014)
+
+ 20 Jan 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +fastx_toolkit-0.0.14.ebuild, -fastx_toolkit-0.0.13.2.ebuild:
+ Version bump, releases were moved to github
+
20 Jan 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
fastx_toolkit-0.0.13.2.ebuild:
Moved dependency on gtextlib
diff --git a/sci-biology/fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild b/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14.ebuild
similarity index 82%
rename from sci-biology/fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild
rename to sci-biology/fastx_toolkit/fastx_toolkit-0.0.14.ebuild
index 2bbbdfc..171ca41 100644
--- a/sci-biology/fastx_toolkit/fastx_toolkit-0.0.13.2.ebuild
+++ b/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14.ebuild
@@ -6,7 +6,7 @@ EAPI=5
DESCRIPTION="Tools for Short Read FASTA/FASTQ file processing"
HOMEPAGE="http://hannonlab.cshl.edu/fastx_toolkit"
-SRC_URI="http://hannonlab.cshl.edu/fastx_toolkit/fastx_toolkit-"${PV}".tar.bz2"
+SRC_URI="https://github.com/agordon/fastx_toolkit/releases/download/"${PV}"/"${P}".tar.bz2"
LICENSE="AGPL-3"
SLOT="0"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fastx_toolkit/
@ 2015-06-06 10:23 Justin Lecher
0 siblings, 0 replies; 6+ messages in thread
From: Justin Lecher @ 2015-06-06 10:23 UTC (permalink / raw
To: gentoo-commits
commit: a0e617fddc5df49cb970854865e09fa677d3d306
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun 6 10:10:34 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun 6 10:10:34 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a0e617fd
sci-biology/fastx_toolkit: Add github to remote-id in metadata.xml
Package-Manager: portage-2.2.20
sci-biology/fastx_toolkit/ChangeLog | 5 ++++-
sci-biology/fastx_toolkit/metadata.xml | 3 +++
2 files changed, 7 insertions(+), 1 deletion(-)
diff --git a/sci-biology/fastx_toolkit/ChangeLog b/sci-biology/fastx_toolkit/ChangeLog
index f233c54..931fa79 100644
--- a/sci-biology/fastx_toolkit/ChangeLog
+++ b/sci-biology/fastx_toolkit/ChangeLog
@@ -1,7 +1,10 @@
# ChangeLog for sci-biology/fastx_toolkit
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
+ sci-biology/fastx_toolkit: Add github to remote-id in metadata.xml
+
*fastx_toolkit-0.0.14 (20 Jan 2014)
20 Jan 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/fastx_toolkit/metadata.xml b/sci-biology/fastx_toolkit/metadata.xml
index 897aa2e..bd98b58 100644
--- a/sci-biology/fastx_toolkit/metadata.xml
+++ b/sci-biology/fastx_toolkit/metadata.xml
@@ -2,4 +2,7 @@
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<herd>sci</herd>
+ <upstream>
+ <remote-id type="github">agordon/fastx_toolkit</remote-id>
+ </upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/fastx_toolkit/
@ 2018-01-10 9:59 David Seifert
0 siblings, 0 replies; 6+ messages in thread
From: David Seifert @ 2018-01-10 9:59 UTC (permalink / raw
To: gentoo-commits
commit: 9f4aad23ebad4a4cbbf5c94eddd52c0ec59370c7
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Wed Jan 10 09:58:38 2018 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Wed Jan 10 09:59:22 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9f4aad23
sci-biology/fastx_toolkit: Moved to main tree
.../fastx_toolkit/fastx_toolkit-0.0.14.ebuild | 32 ----------------------
sci-biology/fastx_toolkit/metadata.xml | 11 --------
2 files changed, 43 deletions(-)
diff --git a/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14.ebuild b/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14.ebuild
deleted file mode 100644
index 64feb239d..000000000
--- a/sci-biology/fastx_toolkit/fastx_toolkit-0.0.14.ebuild
+++ /dev/null
@@ -1,32 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools
-
-DESCRIPTION="Tools for Short Read FASTA/FASTQ file processing"
-HOMEPAGE="http://hannonlab.cshl.edu/fastx_toolkit"
-SRC_URI="https://github.com/agordon/fastx_toolkit/releases/download/"${PV}"/"${P}".tar.bz2"
-
-LICENSE="AGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
- dev-perl/PerlIO-gzip
- dev-perl/GDGraph
- sys-apps/sed
- sci-visualization/gnuplot
- sci-biology/libgtextutils"
-
-src_prepare() {
- # remove pointless installation of generic autoconf-archive m4 macros
- # causing file collisions with sys-devel/autoconf-archive
- rm m4/Makefile.am || die
- sed -i -e 's/m4 //g' Makefile.am || die
-
- eautoreconf
-}
diff --git a/sci-biology/fastx_toolkit/metadata.xml b/sci-biology/fastx_toolkit/metadata.xml
deleted file mode 100644
index 880cea016..000000000
--- a/sci-biology/fastx_toolkit/metadata.xml
+++ /dev/null
@@ -1,11 +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@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">agordon/fastx_toolkit</remote-id>
- </upstream>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread
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2014-01-06 19:57 Justin Lecher
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