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commit: 2a7c1e996ce33b74683db0c59252f91351f0b0af |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Mon Mar 24 11:57:13 2014 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Mon Mar 24 11:57:13 2014 +0000 |
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URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2a7c1e99 |
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|
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sci-biology/ngs_backbone: added an ebuild for latest release |
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|
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--- |
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sci-biology/ngs_backbone/ChangeLog | 11 ++ |
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sci-biology/ngs_backbone/metadata.xml | 9 ++ |
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sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild | 1 + |
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sci-biology/ngs_backbone/ngs_backbone-9999.ebuild | 157 +++++++++++++++++++++ |
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4 files changed, 178 insertions(+) |
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|
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diff --git a/sci-biology/ngs_backbone/ChangeLog b/sci-biology/ngs_backbone/ChangeLog |
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new file mode 100644 |
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index 0000000..a1e165c |
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--- /dev/null |
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+++ b/sci-biology/ngs_backbone/ChangeLog |
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@@ -0,0 +1,11 @@ |
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+# ChangeLog for sci-biology/ngs_backbone |
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+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 |
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+# $Header: $ |
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+ |
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+*ngs_backbone-9999 (24 Mar 2014) |
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+ |
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+ 24 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
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+ +ngs_backbone-9999.ebuild, +metadata.xml: |
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+ Initial ebuild, external optional but highly recommended dependency on |
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+ blast2GO aka b2g4pipe is not resolved |
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+ |
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|
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diff --git a/sci-biology/ngs_backbone/metadata.xml b/sci-biology/ngs_backbone/metadata.xml |
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new file mode 100644 |
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index 0000000..07b5255 |
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--- /dev/null |
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+++ b/sci-biology/ngs_backbone/metadata.xml |
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@@ -0,0 +1,9 @@ |
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+<?xml version="1.0" encoding="UTF-8"?> |
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+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
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+<pkgmetadata> |
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+ <herd>sci-biology</herd> |
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+ <maintainer> |
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+ <email>mmokrejs@×××××××××××××××.cz</email> |
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+ <name>Martin Mokrejs</name> |
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+ </maintainer> |
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+</pkgmetadata> |
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|
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diff --git a/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild b/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild |
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new file mode 120000 |
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index 0000000..9f0bb27 |
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--- /dev/null |
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+++ b/sci-biology/ngs_backbone/ngs_backbone-1.4.0.ebuild |
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@@ -0,0 +1 @@ |
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+ngs_backbone-9999.ebuild |
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\ No newline at end of file |
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|
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diff --git a/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild b/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild |
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new file mode 100644 |
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index 0000000..8c2bf6f |
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--- /dev/null |
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+++ b/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild |
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@@ -0,0 +1,157 @@ |
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+# Copyright 1999-2014 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Header: $ |
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+ |
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+EAPI=5 |
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+ |
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+PYTHON_COMPAT=( python{2_6,2_7} ) |
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+ |
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+inherit distutils-r1 |
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+ |
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+[ "$PV" == "9999" ] && inherit git-2 |
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+ |
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+DESCRIPTION="Assembly and annotation pipeline with web interface for EST/chromosomal sequences" |
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+HOMEPAGE="http://bioinf.comav.upv.es/ngs_backbone/index.html" |
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+if [ "$PV" == "9999" ]; then |
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+ EGIT_REPO_URI="https://github.com/JoseBlanca/franklin" |
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+ KEYWORDS="" |
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+else |
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+ SRC_URI="http://bioinf.comav.upv.es/_downloads/"${P}".tar.gz" |
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+ KEYWORDS="~amd64 ~x86" |
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+fi |
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+ |
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+LICENSE="GPL-3" |
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+SLOT="0" |
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+IUSE="" |
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+ |
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+DEPEND="" |
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+RDEPEND="${DEPEND} |
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+ sci-biology/biopython |
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+ sci-biology/samtools |
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+ sci-biology/picard |
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+ sci-biology/mira |
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+ sci-biology/bwa |
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+ sci-biology/gatk |
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+ sci-biology/pysam |
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+ sci-biology/estscan |
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+ sci-biology/ncbi-tools |
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+ sci-biology/lucy |
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+ sci-biology/gmap |
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+ sci-biology/emboss |
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+ dev-python/matplotlib |
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+ dev-python/psubprocess |
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+ dev-python/configobj" |
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+ # ( blast2GO || b2g4pipe ) |
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+ # sci-biology/sputnik |
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+ # sci-biology/gsnap |
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+ |
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+# blast2GO is http://www.blast2go.org/home |
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+# a non-GUI pipeline is called b2g4pipe, see https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/b2g4pipe-2-5 |
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+ |
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+# TODO: drop the bundled binaries but ... |
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+# 1. the QA check did not find all bundled binaries, e.g. sputnik, lucy, trimpoly |
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+# 2. until we have them all, maybe keep the installed |
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+# |
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+# * QA Notice: The following files contain writable and executable sections |
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+# * Files with such sections will not work properly (or at all!) on some |
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+# * architectures/operating systems. A bug should be filed at |
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+# * http://bugs.gentoo.org/ to make sure the issue is fixed. |
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+# * For more information, see http://hardened.gentoo.org/gnu-stack.xml |
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+# * Please include the following list of files in your report: |
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+# * Note: Bugs should be filed for the respective maintainers |
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+# * of the package in question and not hardened@g.o. |
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+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastx |
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+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/makeblastdb |
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+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastx |
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+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastp |
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+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastn |
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+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastn |
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+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastx |
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+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/makeblastdb |
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+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastx |
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+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastp |
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+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastn |
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+# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastn |
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+ |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/bgzip |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastn |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastp |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastx |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/bwa |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/EBLOSUM62 |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/EDNAFULL |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/codes.english |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/est2genome.acd |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/knowntypes.standard |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/water.acd |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/est2genome |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/estscan |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/fa_coords |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_build |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_compress |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_process |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_reassemble |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_setup |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_uncompress |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmapindex |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gsnap |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gsnap_tally |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/lucy |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/makeblastdb |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/md_coords |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/mdust |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/samtools |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/sputnik |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tabix |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastn |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastx |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/trimpoly |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/water |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/bgzip |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastn |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastp |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastx |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/bwa |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/EBLOSUM62 |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/EDNAFULL |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/codes.english |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/est2genome.acd |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/knowntypes.standard |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/water.acd |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/est2genome |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/estscan |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/fa_coords |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_build |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_compress |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_process |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_reassemble |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_setup |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_uncompress |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmapindex |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gsnap |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gsnap_tally |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/lucy |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/makeblastdb |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/md_coords |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/mdust |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/samtools |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/sputnik |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tabix |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastn |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastx |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/trimpoly |
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+#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/water |
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+ |
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+ |
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+pkg_postinst(){ |
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+ einfo "It is highly recommended to install blast2GO. Either the commercial version with GUI" |
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+ einfo " or a non-GUI version called b2g4pipe. Either way, refer to http://www.blast2go.org" |
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+ einfo " Brief installation process is at http://bioinf.comav.upv.es/ngs_backbone/install.html" |
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+ 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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+} |