* [gentoo-commits] proj/sci:master commit in: sci-biology/est2assembly/
@ 2015-01-07 21:44 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2015-01-07 21:44 UTC (permalink / raw
To: gentoo-commits
commit: 5c282c71bd4e760c0b99df0188a5ca339bdf8fc9
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 7 21:43:54 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 7 21:43:54 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5c282c71
updated checksum types
---
sci-biology/est2assembly/metadata.xml | 9 +++++++++
1 file changed, 9 insertions(+)
diff --git a/sci-biology/est2assembly/metadata.xml b/sci-biology/est2assembly/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/est2assembly/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] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/est2assembly/
@ 2015-01-07 21:44 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2015-01-07 21:44 UTC (permalink / raw
To: gentoo-commits
commit: 1a11e439862e745518e3ac576cfc67dc6f110331
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 7 21:43:37 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 7 21:43:37 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1a11e439
updated checksum types
---
sci-biology/est2assembly/est2assembly-1.08.ebuild | 26 +++++++++++++
sci-biology/est2assembly/est2assembly-9999.ebuild | 47 +++++++++++++++++++++++
2 files changed, 73 insertions(+)
diff --git a/sci-biology/est2assembly/est2assembly-1.08.ebuild b/sci-biology/est2assembly/est2assembly-1.08.ebuild
new file mode 100644
index 0000000..72fcd5d
--- /dev/null
+++ b/sci-biology/est2assembly/est2assembly-1.08.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+DESCRIPTION="EST assembly and annotation pipeline for chado/gbrowse2 display"
+HOMEPAGE="http://code.google.com/p/est2assembly/"
+SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_1.08.tar.gz"
+
+LICENSE="GPL-v3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="dev-lang/perl
+ app-portage/g-cpan
+ perl-gcpan/Time-Progress
+ sci-biology/fasta
+ sci-biology/ssaha2
+ sci-biology/mira
+ sci-biology/emboss
+ sci-biology/bioperl
+ app-arch/pbzip2"
+RDEPEND="${DEPEND}"
+
diff --git a/sci-biology/est2assembly/est2assembly-9999.ebuild b/sci-biology/est2assembly/est2assembly-9999.ebuild
new file mode 100644
index 0000000..11284c5
--- /dev/null
+++ b/sci-biology/est2assembly/est2assembly-9999.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit eutils distutils-r1
+
+[ "$PV" == "9999" ] && inherit subversion
+
+DESCRIPTION="EST assembly and annotation pipeline for chado/gbrowse2 display"
+HOMEPAGE="http://code.google.com/p/est2assembly/"
+ESVN_REPO_URI="http://est2assembly.googlecode.com/svn/trunk"
+
+if [ "$PV" == "9999" ]; then
+ ESVN_REPO_URI="http://est2assembly.googlecode.com/svn/trunk"
+ KEYWORDS="~amd64 ~x86"
+else
+ SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_"${PV}".tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+# still missing
+# annot8r http://nematodes.org/bioinformatics/annot8r/index.shtml and http://nematodes.org/bioinformatics/Annot8r_physprop/
+# prot4EST http://nematodes.org/bioinformatics/prot4EST/
+
+DEPEND="dev-lang/perl
+ dev-perl/Time-Progress
+ sci-biology/fasta
+ sci-biology/ssaha2-bin
+ sci-biology/mira
+ sci-biology/emboss
+ sci-biology/bioperl
+ app-arch/pbzip2"
+RDEPEND="${DEPEND}"
+
+# more install tricks in "${S}"/install.pl
+
+pkg_postinst(){
+ einfo "The package uses mira and newbler assemblers"
+}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/est2assembly/
@ 2015-01-10 14:07 Justin Lecher
0 siblings, 0 replies; 5+ messages in thread
From: Justin Lecher @ 2015-01-10 14:07 UTC (permalink / raw
To: gentoo-commits
commit: 6396d9dcc78b362596fc1ed13b8365589b3a6316
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 10 13:44:36 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jan 10 13:44:36 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6396d9dc
sci-biology/est2assembly: Bump EAPI; drop KEYWORDS from live ebuild; fix deps
Package-Manager: portage-2.2.15
---
sci-biology/est2assembly/ChangeLog | 8 +++++++
sci-biology/est2assembly/est2assembly-1.08.ebuild | 26 +++++++++++------------
sci-biology/est2assembly/est2assembly-9999.ebuild | 23 ++++++++++----------
3 files changed, 33 insertions(+), 24 deletions(-)
diff --git a/sci-biology/est2assembly/ChangeLog b/sci-biology/est2assembly/ChangeLog
new file mode 100644
index 0000000..9024848
--- /dev/null
+++ b/sci-biology/est2assembly/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/est2assembly
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 10 Jan 2015; Justin Lecher <jlec@gentoo.org> est2assembly-1.08.ebuild,
+ est2assembly-9999.ebuild:
+ Bump EAPI; drop KEYWORDS from live ebuild; fix deps
+
diff --git a/sci-biology/est2assembly/est2assembly-1.08.ebuild b/sci-biology/est2assembly/est2assembly-1.08.ebuild
index 72fcd5d..dcbcfb5 100644
--- a/sci-biology/est2assembly/est2assembly-1.08.ebuild
+++ b/sci-biology/est2assembly/est2assembly-1.08.ebuild
@@ -1,26 +1,26 @@
-# Copyright 1999-2011 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=3
+EAPI=5
DESCRIPTION="EST assembly and annotation pipeline for chado/gbrowse2 display"
HOMEPAGE="http://code.google.com/p/est2assembly/"
SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_1.08.tar.gz"
-LICENSE="GPL-v3"
+LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
-DEPEND="dev-lang/perl
- app-portage/g-cpan
- perl-gcpan/Time-Progress
- sci-biology/fasta
- sci-biology/ssaha2
- sci-biology/mira
- sci-biology/emboss
- sci-biology/bioperl
- app-arch/pbzip2"
+DEPEND="
+ app-arch/pbzip2
+ app-portage/g-cpan
+ dev-lang/perl
+ dev-perl/Time-Progress
+ sci-biology/fasta
+ sci-biology/ssaha2-bin
+ sci-biology/mira
+ sci-biology/emboss
+ sci-biology/bioperl"
RDEPEND="${DEPEND}"
-
diff --git a/sci-biology/est2assembly/est2assembly-9999.ebuild b/sci-biology/est2assembly/est2assembly-9999.ebuild
index 11284c5..c1c58a2 100644
--- a/sci-biology/est2assembly/est2assembly-9999.ebuild
+++ b/sci-biology/est2assembly/est2assembly-9999.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
EAPI=5
-PYTHON_COMPAT=( python{2_6,2_7} )
+PYTHON_COMPAT=( python2_7 )
inherit eutils distutils-r1
@@ -16,7 +16,7 @@ ESVN_REPO_URI="http://est2assembly.googlecode.com/svn/trunk"
if [ "$PV" == "9999" ]; then
ESVN_REPO_URI="http://est2assembly.googlecode.com/svn/trunk"
- KEYWORDS="~amd64 ~x86"
+ KEYWORDS=""
else
SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_"${PV}".tar.gz"
KEYWORDS="~amd64 ~x86"
@@ -30,14 +30,15 @@ IUSE=""
# annot8r http://nematodes.org/bioinformatics/annot8r/index.shtml and http://nematodes.org/bioinformatics/Annot8r_physprop/
# prot4EST http://nematodes.org/bioinformatics/prot4EST/
-DEPEND="dev-lang/perl
- dev-perl/Time-Progress
- sci-biology/fasta
- sci-biology/ssaha2-bin
- sci-biology/mira
- sci-biology/emboss
- sci-biology/bioperl
- app-arch/pbzip2"
+DEPEND="
+ app-arch/pbzip2
+ dev-lang/perl
+ dev-perl/Time-Progress
+ sci-biology/fasta
+ sci-biology/ssaha2-bin
+ sci-biology/mira
+ sci-biology/emboss
+ sci-biology/bioperl"
RDEPEND="${DEPEND}"
# more install tricks in "${S}"/install.pl
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/est2assembly/
@ 2015-05-25 19:35 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2015-05-25 19:35 UTC (permalink / raw
To: gentoo-commits
commit: 2c4dd52004a7a8e6bf8e2696014adf57a431df15
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 25 19:35:03 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 25 19:35:03 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2c4dd520
fix S variable, use PV in URI
sci-biology/est2assembly/ChangeLog | 4 ++++
sci-biology/est2assembly/est2assembly-1.08.ebuild | 4 +++-
2 files changed, 7 insertions(+), 1 deletion(-)
diff --git a/sci-biology/est2assembly/ChangeLog b/sci-biology/est2assembly/ChangeLog
index 9024848..19a53e1 100644
--- a/sci-biology/est2assembly/ChangeLog
+++ b/sci-biology/est2assembly/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ est2assembly-1.08.ebuild:
+ fix S variable, use PV in URI
+
10 Jan 2015; Justin Lecher <jlec@gentoo.org> est2assembly-1.08.ebuild,
est2assembly-9999.ebuild:
Bump EAPI; drop KEYWORDS from live ebuild; fix deps
diff --git a/sci-biology/est2assembly/est2assembly-1.08.ebuild b/sci-biology/est2assembly/est2assembly-1.08.ebuild
index dcbcfb5..e9878a7 100644
--- a/sci-biology/est2assembly/est2assembly-1.08.ebuild
+++ b/sci-biology/est2assembly/est2assembly-1.08.ebuild
@@ -6,7 +6,7 @@ EAPI=5
DESCRIPTION="EST assembly and annotation pipeline for chado/gbrowse2 display"
HOMEPAGE="http://code.google.com/p/est2assembly/"
-SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_1.08.tar.gz"
+SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_${PV}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
@@ -24,3 +24,5 @@ DEPEND="
sci-biology/emboss
sci-biology/bioperl"
RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/"${PN}"
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/est2assembly/
@ 2021-01-05 18:05 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2021-01-05 18:05 UTC (permalink / raw
To: gentoo-commits
commit: 9bf414e708ee3d3db14d61243a0d249b99331b73
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 5 14:03:09 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 5 18:01:27 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9bf414e7
sci-biology/est2assembly: drop package, latest update 2011, py2 only
Upstream has been archived: https://code.google.com/archive/p/est2assembly/
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/est2assembly/est2assembly-1.08.ebuild | 27 -------------
sci-biology/est2assembly/est2assembly-9999.ebuild | 47 -----------------------
sci-biology/est2assembly/metadata.xml | 12 ------
3 files changed, 86 deletions(-)
diff --git a/sci-biology/est2assembly/est2assembly-1.08.ebuild b/sci-biology/est2assembly/est2assembly-1.08.ebuild
deleted file mode 100644
index a481a425c..000000000
--- a/sci-biology/est2assembly/est2assembly-1.08.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="EST assembly and annotation pipeline for chado/gbrowse2 display"
-HOMEPAGE="http://code.google.com/p/est2assembly/"
-SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_${PV}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="
- app-arch/pbzip2
- app-portage/g-cpan
- dev-lang/perl
- dev-perl/Time-Progress
- sci-biology/fasta
- sci-biology/ssaha2-bin
- sci-biology/mira
- sci-biology/emboss
- sci-biology/bioperl"
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/"${PN}"
diff --git a/sci-biology/est2assembly/est2assembly-9999.ebuild b/sci-biology/est2assembly/est2assembly-9999.ebuild
deleted file mode 100644
index 5e71408a3..000000000
--- a/sci-biology/est2assembly/est2assembly-9999.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit eutils distutils-r1
-
-[ "$PV" == "9999" ] && inherit subversion
-
-DESCRIPTION="EST assembly and annotation pipeline for chado/gbrowse2 display"
-HOMEPAGE="http://code.google.com/p/est2assembly/"
-ESVN_REPO_URI="http://est2assembly.googlecode.com/svn/trunk"
-
-if [ "$PV" == "9999" ]; then
- ESVN_REPO_URI="http://est2assembly.googlecode.com/svn/trunk"
- KEYWORDS=""
-else
- SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_"${PV}".tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-
-# still missing
-# annot8r http://nematodes.org/bioinformatics/annot8r/index.shtml and http://nematodes.org/bioinformatics/Annot8r_physprop/
-# prot4EST http://nematodes.org/bioinformatics/prot4EST/
-
-DEPEND="
- app-arch/pbzip2
- dev-lang/perl
- dev-perl/Time-Progress
- sci-biology/fasta
- sci-biology/ssaha2-bin
- sci-biology/mira
- sci-biology/emboss
- sci-biology/bioperl"
-RDEPEND="${DEPEND}"
-
-# more install tricks in "${S}"/install.pl
-
-pkg_postinst(){
- einfo "The package uses mira and newbler assemblers"
-}
diff --git a/sci-biology/est2assembly/metadata.xml b/sci-biology/est2assembly/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/est2assembly/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="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>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 5+ messages in thread
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