[gentoo-commits] proj/sci:master commit in: sci-biology/ngs_backbone/

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

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"
+}