| 1 |
commit: 3bdd3d1c35c9e23cbc13e86dcb8c4b2321fd2620 |
| 2 |
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
| 3 |
AuthorDate: Fri Jul 29 20:47:12 2016 +0000 |
| 4 |
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
| 5 |
CommitDate: Fri Jul 29 20:47:12 2016 +0000 |
| 6 |
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3bdd3d1c |
| 7 |
|
| 8 |
sci-biology/ensembl-tools: new package, needs more fixes, upstream contacted |
| 9 |
|
| 10 |
Package-Manager: portage-2.3.0 |
| 11 |
|
| 12 |
sci-biology/ensembl-tools/ensembl-tools-85.ebuild | 47 +++++++++++++++++++++++ |
| 13 |
sci-biology/ensembl-tools/metadata.xml | 12 ++++++ |
| 14 |
2 files changed, 59 insertions(+) |
| 15 |
|
| 16 |
diff --git a/sci-biology/ensembl-tools/ensembl-tools-85.ebuild b/sci-biology/ensembl-tools/ensembl-tools-85.ebuild |
| 17 |
new file mode 100644 |
| 18 |
index 0000000..642caf8 |
| 19 |
--- /dev/null |
| 20 |
+++ b/sci-biology/ensembl-tools/ensembl-tools-85.ebuild |
| 21 |
@@ -0,0 +1,47 @@ |
| 22 |
+# Copyright 1999-2016 Gentoo Foundation |
| 23 |
+# Distributed under the terms of the GNU General Public License v2 |
| 24 |
+# $Id$ |
| 25 |
+ |
| 26 |
+EAPI=5 |
| 27 |
+ |
| 28 |
+PERL_EXPORT_PHASE_FUNCTIONS=no |
| 29 |
+inherit perl-module |
| 30 |
+ |
| 31 |
+DESCRIPTION="Bioinformatics tools incl. Variant Effect Predictor (VEP)" |
| 32 |
+HOMEPAGE="http://grch37.ensembl.org/info/docs/tools/vep/script/index.html" |
| 33 |
+SRC_URI="https://github.com/Ensembl/ensembl-tools/archive/release/${PV}.zip -> ${P}.zip" |
| 34 |
+ |
| 35 |
+LICENSE="Apache-2.0" |
| 36 |
+SLOT="0" |
| 37 |
+KEYWORDS="" # BUG: needs Bio::EnsEMBL::Registry |
| 38 |
+IUSE="" |
| 39 |
+ |
| 40 |
+DEPEND="" |
| 41 |
+#DEPEND="dev-perl/Perl-XS |
| 42 |
+# dev-perl/Bio-DB-HTS" |
| 43 |
+RDEPEND="${DEPEND}" |
| 44 |
+ |
| 45 |
+S="${WORKDIR}/ensembl-tools-release-${PV}" |
| 46 |
+ |
| 47 |
+src_install(){ |
| 48 |
+ perl_set_version |
| 49 |
+ insinto ${VENDOR_LIB}/${PN} |
| 50 |
+ cd scripts/variant_effect_predictor || die |
| 51 |
+ perl INSTALL.pl --DESTDIR="${EPREFIX}"/"${DESTDIR}" --AUTO ac |
| 52 |
+ newdoc README.txt variant_effect_predictor.txt |
| 53 |
+ cd ../../scripts/region_reporter || die |
| 54 |
+ dobin *.pl |
| 55 |
+ newdoc README.txt region_reporter.txt |
| 56 |
+ cd ../../scripts/assembly_converter |
| 57 |
+ dobin *.pl |
| 58 |
+ insinto ${VENDOR_LIB}/${PN} |
| 59 |
+ doins *.pm |
| 60 |
+ newdoc README.txt assembly_converter.txt |
| 61 |
+ insinto /usr/share/"${PN}"/examples |
| 62 |
+ doins assemblymapper.in |
| 63 |
+ cd ../../scripts/id_history_converter |
| 64 |
+ dobin *.pl |
| 65 |
+ newdoc README.txt id_history_converter.txt |
| 66 |
+ insinto /usr/share/"${PN}"/examples |
| 67 |
+ doins idmapper.in |
| 68 |
+} |
| 69 |
|
| 70 |
diff --git a/sci-biology/ensembl-tools/metadata.xml b/sci-biology/ensembl-tools/metadata.xml |
| 71 |
new file mode 100644 |
| 72 |
index 0000000..f68a1b6 |
| 73 |
--- /dev/null |
| 74 |
+++ b/sci-biology/ensembl-tools/metadata.xml |
| 75 |
@@ -0,0 +1,12 @@ |
| 76 |
+<?xml version="1.0" encoding="UTF-8"?> |
| 77 |
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> |
| 78 |
+<pkgmetadata> |
| 79 |
+ <maintainer type="person"> |
| 80 |
+ <email>mmokrejs@×××××××××××××××.cz</email> |
| 81 |
+ <name>Martin Mokrejs</name> |
| 82 |
+ </maintainer> |
| 83 |
+ <maintainer type="project"> |
| 84 |
+ <email>sci-biology@g.o</email> |
| 85 |
+ <name>Gentoo Biology Project</name> |
| 86 |
+ </maintainer> |
| 87 |
+</pkgmetadata> |
Archives