* [gentoo-commits] proj/sci:master commit in: sci-biology/ngs_backbone/
@ 2014-03-24 11:58 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2014-03-24 11:58 UTC (permalink / raw
To: gentoo-commits
commit: 2a7c1e996ce33b74683db0c59252f91351f0b0af
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Mar 24 11:57:13 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Mar 24 11:57:13 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2a7c1e99
sci-biology/ngs_backbone: added an ebuild for latest release
---
sci-biology/ngs_backbone/ChangeLog | 11 ++
sci-biology/ngs_backbone/metadata.xml | 9 ++
sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild | 1 +
sci-biology/ngs_backbone/ngs_backbone-9999.ebuild | 157 +++++++++++++++++++++
4 files changed, 178 insertions(+)
diff --git a/sci-biology/ngs_backbone/ChangeLog b/sci-biology/ngs_backbone/ChangeLog
new file mode 100644
index 0000000..a1e165c
--- /dev/null
+++ b/sci-biology/ngs_backbone/ChangeLog
@@ -0,0 +1,11 @@
+# ChangeLog for sci-biology/ngs_backbone
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*ngs_backbone-9999 (24 Mar 2014)
+
+ 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +ngs_backbone-9999.ebuild, +metadata.xml:
+ Initial ebuild, external optional but highly recommended dependency on
+ blast2GO aka b2g4pipe is not resolved
+
diff --git a/sci-biology/ngs_backbone/metadata.xml b/sci-biology/ngs_backbone/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/ngs_backbone/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>
diff --git a/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild b/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
new file mode 120000
index 0000000..9f0bb27
--- /dev/null
+++ b/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
@@ -0,0 +1 @@
+ngs_backbone-9999.ebuild
\ No newline at end of file
diff --git a/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild b/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild
new file mode 100644
index 0000000..8c2bf6f
--- /dev/null
+++ b/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild
@@ -0,0 +1,157 @@
+# 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 distutils-r1
+
+[ "$PV" == "9999" ] && inherit git-2
+
+DESCRIPTION="Assembly and annotation pipeline with web interface for EST/chromosomal sequences"
+HOMEPAGE="http://bioinf.comav.upv.es/ngs_backbone/index.html"
+if [ "$PV" == "9999" ]; then
+ EGIT_REPO_URI="https://github.com/JoseBlanca/franklin"
+ KEYWORDS=""
+else
+ SRC_URI="http://bioinf.comav.upv.es/_downloads/"${P}".tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ sci-biology/biopython
+ sci-biology/samtools
+ sci-biology/picard
+ sci-biology/mira
+ sci-biology/bwa
+ sci-biology/gatk
+ sci-biology/pysam
+ sci-biology/estscan
+ sci-biology/ncbi-tools
+ sci-biology/lucy
+ sci-biology/gmap
+ sci-biology/emboss
+ dev-python/matplotlib
+ dev-python/psubprocess
+ dev-python/configobj"
+ # ( blast2GO || b2g4pipe )
+ # sci-biology/sputnik
+ # sci-biology/gsnap
+
+# blast2GO is http://www.blast2go.org/home
+# a non-GUI pipeline is called b2g4pipe, see https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/b2g4pipe-2-5
+
+# TODO: drop the bundled binaries but ...
+# 1. the QA check did not find all bundled binaries, e.g. sputnik, lucy, trimpoly
+# 2. until we have them all, maybe keep the installed
+#
+# * QA Notice: The following files contain writable and executable sections
+# * Files with such sections will not work properly (or at all!) on some
+# * architectures/operating systems. A bug should be filed at
+# * http://bugs.gentoo.org/ to make sure the issue is fixed.
+# * For more information, see http://hardened.gentoo.org/gnu-stack.xml
+# * Please include the following list of files in your report:
+# * Note: Bugs should be filed for the respective maintainers
+# * of the package in question and not hardened@g.o.
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastx
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/makeblastdb
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastx
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastp
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastn
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastn
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastx
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/makeblastdb
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastx
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastp
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastn
+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastn
+
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/bgzip
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastn
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastp
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastx
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/bwa
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/EBLOSUM62
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/EDNAFULL
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/codes.english
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/est2genome.acd
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/knowntypes.standard
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/water.acd
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/est2genome
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/estscan
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/fa_coords
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_build
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_compress
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_process
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_reassemble
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_setup
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_uncompress
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmapindex
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gsnap
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gsnap_tally
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/lucy
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/makeblastdb
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/md_coords
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/mdust
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/samtools
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/sputnik
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tabix
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastn
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastx
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/trimpoly
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/water
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/bgzip
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastn
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastp
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastx
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/bwa
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/EBLOSUM62
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/EDNAFULL
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/codes.english
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/est2genome.acd
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/knowntypes.standard
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/water.acd
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/est2genome
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/estscan
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/fa_coords
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_build
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_compress
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_process
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_reassemble
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_setup
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_uncompress
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmapindex
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gsnap
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gsnap_tally
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/lucy
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/makeblastdb
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/md_coords
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/mdust
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/samtools
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/sputnik
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tabix
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastn
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastx
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/trimpoly
+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/water
+
+
+pkg_postinst(){
+ einfo "It is highly recommended to install blast2GO. Either the commercial version with GUI"
+ einfo " or a non-GUI version called b2g4pipe. Either way, refer to http://www.blast2go.org"
+ einfo " Brief installation process is at http://bioinf.comav.upv.es/ngs_backbone/install.html"
+ einfo "Alternatively, a VirtualBox image with ngs_bakbone is at http://bioinf.comav.upv.es/_downloads/ngs_machine_v3.tar.gz"
+}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ngs_backbone/
@ 2014-09-12 17:22 Christoph Junghans
0 siblings, 0 replies; 5+ messages in thread
From: Christoph Junghans @ 2014-09-12 17:22 UTC (permalink / raw
To: gentoo-commits
commit: 8cf080a70fe63bfb0b9cf43db154e2693ef30bcb
Author: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
AuthorDate: Fri Sep 12 16:45:47 2014 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Fri Sep 12 16:45:47 2014 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8cf080a7
drop ~x86 as deps are missing
Package-Manager: portage-2.2.8-r1
---
sci-biology/ngs_backbone/ChangeLog | 4 +++-
sci-biology/ngs_backbone/ngs_backbone-9999.ebuild | 3 +--
2 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/sci-biology/ngs_backbone/ChangeLog b/sci-biology/ngs_backbone/ChangeLog
index a1e165c..231e153 100644
--- a/sci-biology/ngs_backbone/ChangeLog
+++ b/sci-biology/ngs_backbone/ChangeLog
@@ -2,10 +2,12 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 12 Sep 2014; Christoph Junghans <ottxor@gentoo.org> ngs_backbone-9999.ebuild:
+ drop ~x86 as deps are missing
+
*ngs_backbone-9999 (24 Mar 2014)
24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ngs_backbone-9999.ebuild, +metadata.xml:
Initial ebuild, external optional but highly recommended dependency on
blast2GO aka b2g4pipe is not resolved
-
diff --git a/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild b/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild
index 8c2bf6f..7defc73 100644
--- a/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild
+++ b/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild
@@ -17,7 +17,7 @@ if [ "$PV" == "9999" ]; then
KEYWORDS=""
else
SRC_URI="http://bioinf.comav.upv.es/_downloads/"${P}".tar.gz"
- KEYWORDS="~amd64 ~x86"
+ KEYWORDS="~amd64"
fi
LICENSE="GPL-3"
@@ -148,7 +148,6 @@ RDEPEND="${DEPEND}
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/trimpoly
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/water
-
pkg_postinst(){
einfo "It is highly recommended to install blast2GO. Either the commercial version with GUI"
einfo " or a non-GUI version called b2g4pipe. Either way, refer to http://www.blast2go.org"
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ngs_backbone/
@ 2015-05-02 16:29 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2015-05-02 16:29 UTC (permalink / raw
To: gentoo-commits
commit: 7fb9ac3743cb1d1a58d5f79e27895985245dd11e
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat May 2 16:11:49 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat May 2 16:11:49 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7fb9ac37
added PYTHON_USEDEP
Package-Manager: portage-2.2.18
sci-biology/ngs_backbone/ChangeLog | 6 +++++-
sci-biology/ngs_backbone/ngs_backbone-9999.ebuild | 14 +++++++-------
2 files changed, 12 insertions(+), 8 deletions(-)
diff --git a/sci-biology/ngs_backbone/ChangeLog b/sci-biology/ngs_backbone/ChangeLog
index 231e153..463e8e5 100644
--- a/sci-biology/ngs_backbone/ChangeLog
+++ b/sci-biology/ngs_backbone/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/ngs_backbone
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ ngs_backbone-9999.ebuild:
+ added PYTHON_USEDEP
+
12 Sep 2014; Christoph Junghans <ottxor@gentoo.org> ngs_backbone-9999.ebuild:
drop ~x86 as deps are missing
diff --git a/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild b/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild
index 1b4b65b..b2de334 100644
--- a/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild
+++ b/sci-biology/ngs_backbone/ngs_backbone-9999.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: $
@@ -26,21 +26,21 @@ IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
- sci-biology/biopython
- sci-biology/samtools
+ sci-biology/biopython[${PYTHON_USEDEP}]
+ sci-biology/samtools[${PYTHON_USEDEP}]
sci-biology/picard
sci-biology/mira
sci-biology/bwa
sci-biology/gatk
- sci-biology/pysam
+ sci-biology/pysam[${PYTHON_USEDEP}]
sci-biology/estscan
sci-biology/ncbi-tools
sci-biology/lucy
sci-biology/gmap
sci-biology/emboss
- dev-python/matplotlib
- dev-python/psubprocess
- dev-python/configobj"
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/psubprocess[${PYTHON_USEDEP}]
+ dev-python/configobj[${PYTHON_USEDEP}]"
# ( blast2GO || b2g4pipe )
# sci-biology/sputnik
# sci-biology/gsnap
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ngs_backbone/
@ 2016-02-14 17:32 Justin Lecher
0 siblings, 0 replies; 5+ messages in thread
From: Justin Lecher @ 2016-02-14 17:32 UTC (permalink / raw
To: gentoo-commits
commit: 7d3c524cb9bd1de2d309b7d8bea1a5bd0d92598c
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 14 17:21:05 2016 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Feb 14 17:21:27 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7d3c524c
sci-biology/ngs_backbone: Bump to EAPI=6
* Use git-r3.eclass
Package-Manager: portage-2.2.27
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/ngs_backbone/metadata.xml | 2 +-
sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild | 17 +++++------------
sci-biology/ngs_backbone/ngs_backbone-9999.ebuild | 19 ++++++-------------
3 files changed, 12 insertions(+), 26 deletions(-)
diff --git a/sci-biology/ngs_backbone/metadata.xml b/sci-biology/ngs_backbone/metadata.xml
index 1d67411..138cb77 100644
--- a/sci-biology/ngs_backbone/metadata.xml
+++ b/sci-biology/ngs_backbone/metadata.xml
@@ -5,7 +5,7 @@
<email>mmokrejs@fold.natur.cuni.cz</email>
<name>Martin Mokrejs</name>
</maintainer>
-<maintainer type="project">
+ <maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
diff --git a/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild b/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
index 734e32d..edfc5b0 100644
--- a/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
+++ b/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
@@ -1,27 +1,20 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
PYTHON_COMPAT=( python2_7 )
inherit distutils-r1
-[ "$PV" == "9999" ] && inherit git-2
-
-DESCRIPTION="Assembly and annotation pipeline with web interface for EST/chromosomal sequences"
+DESCRIPTION="Assembly & annotation pipeline with web interface for EST/chromosomal sequences"
HOMEPAGE="http://bioinf.comav.upv.es/ngs_backbone/index.html"
-if [ "$PV" == "9999" ]; then
- EGIT_REPO_URI="https://github.com/JoseBlanca/franklin"
- KEYWORDS=""
-else
- SRC_URI="http://bioinf.comav.upv.es/_downloads/"${P}".tar.gz"
- KEYWORDS="~amd64"
-fi
+SRC_URI="http://bioinf.comav.upv.es/_downloads/"${P}".tar.gz"
LICENSE="GPL-3"
SLOT="0"
+KEYWORDS="~amd64"
IUSE=""
DEPEND=""
diff --git a/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild b/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild
index 734e32d..3319b16 100644
--- a/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild
+++ b/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild
@@ -1,27 +1,20 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
PYTHON_COMPAT=( python2_7 )
-inherit distutils-r1
+inherit distutils-r1 git-r3
-[ "$PV" == "9999" ] && inherit git-2
-
-DESCRIPTION="Assembly and annotation pipeline with web interface for EST/chromosomal sequences"
+DESCRIPTION="Assembly & annotation pipeline with web interface for EST/chromosomal sequences"
HOMEPAGE="http://bioinf.comav.upv.es/ngs_backbone/index.html"
-if [ "$PV" == "9999" ]; then
- EGIT_REPO_URI="https://github.com/JoseBlanca/franklin"
- KEYWORDS=""
-else
- SRC_URI="http://bioinf.comav.upv.es/_downloads/"${P}".tar.gz"
- KEYWORDS="~amd64"
-fi
+EGIT_REPO_URI="https://github.com/JoseBlanca/franklin"
LICENSE="GPL-3"
SLOT="0"
+KEYWORDS=""
IUSE=""
DEPEND=""
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ngs_backbone/
@ 2020-09-27 8:02 Horea Christian
0 siblings, 0 replies; 5+ messages in thread
From: Horea Christian @ 2020-09-27 8:02 UTC (permalink / raw
To: gentoo-commits
commit: 1c285519613a3729129b206b9a90f7534e14b73f
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 08:00:34 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 08:00:34 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1c285519
sci-biology/ngs_backbone: removed discontinued package
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/ngs_backbone/metadata.xml | 12 --
sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild | 148 ---------------------
sci-biology/ngs_backbone/ngs_backbone-9999.ebuild | 148 ---------------------
3 files changed, 308 deletions(-)
diff --git a/sci-biology/ngs_backbone/metadata.xml b/sci-biology/ngs_backbone/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/ngs_backbone/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>
diff --git a/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild b/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
deleted file mode 100644
index 6ea39e0ad..000000000
--- a/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
+++ /dev/null
@@ -1,148 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Assembly & annotation pipeline with web interface for EST/chromosomal sequences"
-HOMEPAGE="http://bioinf.comav.upv.es/ngs_backbone/index.html"
-SRC_URI="http://bioinf.comav.upv.es/_downloads/"${P}".tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
- sci-biology/biopython[${PYTHON_USEDEP}]
- sci-biology/samtools[${PYTHON_USEDEP}]
- sci-biology/picard
- sci-biology/mira
- sci-biology/bwa
- sci-biology/gatk
- sci-biology/pysam[${PYTHON_USEDEP}]
- sci-biology/estscan
- sci-biology/ncbi-tools
- sci-biology/lucy
- sci-biology/gmap
- sci-biology/emboss
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/psubprocess[${PYTHON_USEDEP}]
- dev-python/configobj[${PYTHON_USEDEP}]"
- # ( blast2GO || b2g4pipe )
- # sci-biology/sputnik
- # sci-biology/gsnap
-
-# blast2GO is http://www.blast2go.org/home
-# a non-GUI pipeline is called b2g4pipe, see https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/b2g4pipe-2-5
-
-# TODO: drop the bundled binaries but ...
-# 1. the QA check did not find all bundled binaries, e.g. sputnik, lucy, trimpoly
-# 2. until we have them all, maybe keep the installed
-#
-# * QA Notice: The following files contain writable and executable sections
-# * Files with such sections will not work properly (or at all!) on some
-# * architectures/operating systems. A bug should be filed at
-# * http://bugs.gentoo.org/ to make sure the issue is fixed.
-# * For more information, see http://hardened.gentoo.org/gnu-stack.xml
-# * Please include the following list of files in your report:
-# * Note: Bugs should be filed for the respective maintainers
-# * of the package in question and not hardened@g.o.
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastx
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/makeblastdb
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastx
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastp
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastn
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastn
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastx
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/makeblastdb
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastx
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastp
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastn
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastn
-
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/bgzip
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastn
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastp
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastx
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/bwa
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/EBLOSUM62
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/EDNAFULL
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/codes.english
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/est2genome.acd
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/knowntypes.standard
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/water.acd
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/est2genome
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/estscan
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/fa_coords
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_build
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_compress
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_process
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_reassemble
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_setup
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_uncompress
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmapindex
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gsnap
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gsnap_tally
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/lucy
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/makeblastdb
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/md_coords
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/mdust
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/samtools
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/sputnik
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tabix
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastn
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastx
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/trimpoly
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/water
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/bgzip
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastn
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastp
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastx
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/bwa
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/EBLOSUM62
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/EDNAFULL
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/codes.english
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/est2genome.acd
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/knowntypes.standard
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/water.acd
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/est2genome
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/estscan
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/fa_coords
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_build
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_compress
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_process
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_reassemble
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_setup
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_uncompress
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmapindex
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gsnap
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gsnap_tally
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/lucy
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/makeblastdb
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/md_coords
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/mdust
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/samtools
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/sputnik
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tabix
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastn
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastx
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/trimpoly
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/water
-
-pkg_postinst(){
- einfo "It is highly recommended to install blast2GO. Either the commercial version with GUI"
- einfo " or a non-GUI version called b2g4pipe. Either way, refer to http://www.blast2go.org"
- einfo " Brief installation process is at http://bioinf.comav.upv.es/ngs_backbone/install.html"
- einfo "Alternatively, a VirtualBox image with ngs_bakbone is at http://bioinf.comav.upv.es/_downloads/ngs_machine_v3.tar.gz"
-}
diff --git a/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild b/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild
deleted file mode 100644
index 03f606c31..000000000
--- a/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild
+++ /dev/null
@@ -1,148 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Assembly & annotation pipeline with web interface for EST/chromosomal sequences"
-HOMEPAGE="http://bioinf.comav.upv.es/ngs_backbone/index.html"
-EGIT_REPO_URI="https://github.com/JoseBlanca/franklin"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=""
-RDEPEND="${DEPEND}
- sci-biology/biopython[${PYTHON_USEDEP}]
- sci-biology/samtools[${PYTHON_USEDEP}]
- sci-biology/picard
- sci-biology/mira
- sci-biology/bwa
- sci-biology/gatk
- sci-biology/pysam[${PYTHON_USEDEP}]
- sci-biology/estscan
- sci-biology/ncbi-tools
- sci-biology/lucy
- sci-biology/gmap
- sci-biology/emboss
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/psubprocess[${PYTHON_USEDEP}]
- dev-python/configobj[${PYTHON_USEDEP}]"
- # ( blast2GO || b2g4pipe )
- # sci-biology/sputnik
- # sci-biology/gsnap
-
-# blast2GO is http://www.blast2go.org/home
-# a non-GUI pipeline is called b2g4pipe, see https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/b2g4pipe-2-5
-
-# TODO: drop the bundled binaries but ...
-# 1. the QA check did not find all bundled binaries, e.g. sputnik, lucy, trimpoly
-# 2. until we have them all, maybe keep the installed
-#
-# * QA Notice: The following files contain writable and executable sections
-# * Files with such sections will not work properly (or at all!) on some
-# * architectures/operating systems. A bug should be filed at
-# * http://bugs.gentoo.org/ to make sure the issue is fixed.
-# * For more information, see http://hardened.gentoo.org/gnu-stack.xml
-# * Please include the following list of files in your report:
-# * Note: Bugs should be filed for the respective maintainers
-# * of the package in question and not hardened@g.o.
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastx
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/makeblastdb
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastx
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastp
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastn
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastn
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastx
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/makeblastdb
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastx
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastp
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastn
-# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastn
-
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/bgzip
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastn
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastp
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastx
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/bwa
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/EBLOSUM62
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/EDNAFULL
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/codes.english
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/est2genome.acd
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/knowntypes.standard
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/water.acd
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/est2genome
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/estscan
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/fa_coords
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_build
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_compress
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_process
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_reassemble
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_setup
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_uncompress
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmapindex
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gsnap
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gsnap_tally
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/lucy
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/makeblastdb
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/md_coords
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/mdust
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/samtools
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/sputnik
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tabix
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastn
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastx
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/trimpoly
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/water
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/bgzip
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastn
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastp
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastx
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/bwa
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/EBLOSUM62
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/EDNAFULL
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/codes.english
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/est2genome.acd
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/knowntypes.standard
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/water.acd
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/est2genome
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/estscan
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/fa_coords
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_build
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_compress
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_process
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_reassemble
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_setup
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_uncompress
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmapindex
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gsnap
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gsnap_tally
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/lucy
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/makeblastdb
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/md_coords
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/mdust
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/samtools
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/sputnik
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tabix
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastn
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastx
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/trimpoly
-#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/water
-
-pkg_postinst(){
- einfo "It is highly recommended to install blast2GO. Either the commercial version with GUI"
- einfo " or a non-GUI version called b2g4pipe. Either way, refer to http://www.blast2go.org"
- einfo " Brief installation process is at http://bioinf.comav.upv.es/ngs_backbone/install.html"
- einfo "Alternatively, a VirtualBox image with ngs_bakbone is at http://bioinf.comav.upv.es/_downloads/ngs_machine_v3.tar.gz"
-}
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2014-03-24 11:58 [gentoo-commits] proj/sci:master commit in: sci-biology/ngs_backbone/ Martin Mokrejs
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2014-09-12 17:22 Christoph Junghans
2015-05-02 16:29 Martin Mokrejs
2016-02-14 17:32 Justin Lecher
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