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 <mmokr...@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>mmokr...@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"; +}
