Drop unnecessary die from emake

Signed-off-by: Justin Lecher <jlec@gentoo.org>

1 files changed, 156 insertions, 1 deletions

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 9f0bb27fc..734e32d77 120000..100644
--- a/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
+++ b/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild
@@ -1 +1,156 @@
-ngs_backbone-9999.ebuild
\ No newline at end of file
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_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/"${P}".tar.gz"
+	KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${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"
+}