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>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</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 [email protected]. -# * 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 [email protected]. -# * 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"; -}
