* [gentoo-commits] proj/sci:master commit in: sci-biology/ensembl-tools/
@ 2016-07-29 20:47 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2016-07-29 20:47 UTC (permalink / raw
To: gentoo-commits
commit: 3bdd3d1c35c9e23cbc13e86dcb8c4b2321fd2620
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 29 20:47:12 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 29 20:47:12 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=3bdd3d1c
sci-biology/ensembl-tools: new package, needs more fixes, upstream contacted
Package-Manager: portage-2.3.0
sci-biology/ensembl-tools/ensembl-tools-85.ebuild | 47 +++++++++++++++++++++++
sci-biology/ensembl-tools/metadata.xml | 12 ++++++
2 files changed, 59 insertions(+)
diff --git a/sci-biology/ensembl-tools/ensembl-tools-85.ebuild b/sci-biology/ensembl-tools/ensembl-tools-85.ebuild
new file mode 100644
index 0000000..642caf8
--- /dev/null
+++ b/sci-biology/ensembl-tools/ensembl-tools-85.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module
+
+DESCRIPTION="Bioinformatics tools incl. Variant Effect Predictor (VEP)"
+HOMEPAGE="http://grch37.ensembl.org/info/docs/tools/vep/script/index.html"
+SRC_URI="https://github.com/Ensembl/ensembl-tools/archive/release/${PV}.zip -> ${P}.zip"
+
+LICENSE="Apache-2.0"
+SLOT="0"
+KEYWORDS="" # BUG: needs Bio::EnsEMBL::Registry
+IUSE=""
+
+DEPEND=""
+#DEPEND="dev-perl/Perl-XS
+# dev-perl/Bio-DB-HTS"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}/ensembl-tools-release-${PV}"
+
+src_install(){
+ perl_set_version
+ insinto ${VENDOR_LIB}/${PN}
+ cd scripts/variant_effect_predictor || die
+ perl INSTALL.pl --DESTDIR="${EPREFIX}"/"${DESTDIR}" --AUTO ac
+ newdoc README.txt variant_effect_predictor.txt
+ cd ../../scripts/region_reporter || die
+ dobin *.pl
+ newdoc README.txt region_reporter.txt
+ cd ../../scripts/assembly_converter
+ dobin *.pl
+ insinto ${VENDOR_LIB}/${PN}
+ doins *.pm
+ newdoc README.txt assembly_converter.txt
+ insinto /usr/share/"${PN}"/examples
+ doins assemblymapper.in
+ cd ../../scripts/id_history_converter
+ dobin *.pl
+ newdoc README.txt id_history_converter.txt
+ insinto /usr/share/"${PN}"/examples
+ doins idmapper.in
+}
diff --git a/sci-biology/ensembl-tools/metadata.xml b/sci-biology/ensembl-tools/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/ensembl-tools/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ensembl-tools/
@ 2016-07-29 20:50 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2016-07-29 20:50 UTC (permalink / raw
To: gentoo-commits
commit: 2a0ec3bd65fd0ea4410056138b43ef380a605efa
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 29 20:50:38 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 29 20:50:38 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2a0ec3bd
sci-biology/ensembl-tools: add another link to a HOMEPAGE
Package-Manager: portage-2.3.0
sci-biology/ensembl-tools/ensembl-tools-85.ebuild | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/sci-biology/ensembl-tools/ensembl-tools-85.ebuild b/sci-biology/ensembl-tools/ensembl-tools-85.ebuild
index 642caf8..9fb2a60 100644
--- a/sci-biology/ensembl-tools/ensembl-tools-85.ebuild
+++ b/sci-biology/ensembl-tools/ensembl-tools-85.ebuild
@@ -8,7 +8,8 @@ PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module
DESCRIPTION="Bioinformatics tools incl. Variant Effect Predictor (VEP)"
-HOMEPAGE="http://grch37.ensembl.org/info/docs/tools/vep/script/index.html"
+HOMEPAGE="http://grch37.ensembl.org/info/docs/tools/vep/script/index.html
+ http://grch37.ensembl.org/info/docs/tools/vep/script/vep_plugins.html"
SRC_URI="https://github.com/Ensembl/ensembl-tools/archive/release/${PV}.zip -> ${P}.zip"
LICENSE="Apache-2.0"
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ensembl-tools/
@ 2016-08-01 12:27 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2016-08-01 12:27 UTC (permalink / raw
To: gentoo-commits
commit: 7f5e7cc373b0e2c7ae838deaf4aec115e6362013
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Aug 1 12:26:49 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Aug 1 12:26:49 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7f5e7cc3
sci-biology/ensembl-tools: there are no *.pm to be installed, install example
Package-Manager: portage-2.3.0
sci-biology/ensembl-tools/ensembl-tools-85.ebuild | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/sci-biology/ensembl-tools/ensembl-tools-85.ebuild b/sci-biology/ensembl-tools/ensembl-tools-85.ebuild
index 9fb2a60..0ed40bb 100644
--- a/sci-biology/ensembl-tools/ensembl-tools-85.ebuild
+++ b/sci-biology/ensembl-tools/ensembl-tools-85.ebuild
@@ -35,8 +35,10 @@ src_install(){
newdoc README.txt region_reporter.txt
cd ../../scripts/assembly_converter
dobin *.pl
- insinto ${VENDOR_LIB}/${PN}
- doins *.pm
+ insinto /usr/share/"${PN}"/examples
+ doins assemblymapper.in
+ #insinto ${VENDOR_LIB}/${PN}
+ #doins *.pm
newdoc README.txt assembly_converter.txt
insinto /usr/share/"${PN}"/examples
doins assemblymapper.in
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ensembl-tools/
@ 2016-08-01 12:44 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2016-08-01 12:44 UTC (permalink / raw
To: gentoo-commits
commit: 51323d9c686f7a9bd5ec8b04d003353f8829e520
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Aug 1 12:43:09 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Aug 1 12:43:09 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=51323d9c
sci-biology/ensembl-tools: add more dependencies
Package-Manager: portage-2.3.0
sci-biology/ensembl-tools/ensembl-tools-85.ebuild | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/sci-biology/ensembl-tools/ensembl-tools-85.ebuild b/sci-biology/ensembl-tools/ensembl-tools-85.ebuild
index 0ed40bb..ffa1b63 100644
--- a/sci-biology/ensembl-tools/ensembl-tools-85.ebuild
+++ b/sci-biology/ensembl-tools/ensembl-tools-85.ebuild
@@ -17,7 +17,8 @@ SLOT="0"
KEYWORDS="" # BUG: needs Bio::EnsEMBL::Registry
IUSE=""
-DEPEND=""
+DEPEND="dev-perl/File-Copy-Recursive
+ dev-perl/Archive-Extract"
#DEPEND="dev-perl/Perl-XS
# dev-perl/Bio-DB-HTS"
RDEPEND="${DEPEND}"
@@ -28,7 +29,8 @@ src_install(){
perl_set_version
insinto ${VENDOR_LIB}/${PN}
cd scripts/variant_effect_predictor || die
- perl INSTALL.pl --DESTDIR="${EPREFIX}"/"${DESTDIR}" --AUTO ac
+ # FIXME: INSTALL.pl does not exit upon error
+ ./INSTALL.pl --DESTDIR="${DESTDIR}"/"${EPREFIX}" --AUTO=ac || die
newdoc README.txt variant_effect_predictor.txt
cd ../../scripts/region_reporter || die
dobin *.pl
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ensembl-tools/
@ 2016-08-01 13:02 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2016-08-01 13:02 UTC (permalink / raw
To: gentoo-commits
commit: 7fd7c5b187f194bd656233e7b671eaa3badcbb60
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Aug 1 13:02:36 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Aug 1 13:02:36 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7fd7c5b1
sci-biology/ensembl-tools: tune HOMEPAGE URL
Package-Manager: portage-2.3.0
sci-biology/ensembl-tools/ensembl-tools-85.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/ensembl-tools/ensembl-tools-85.ebuild b/sci-biology/ensembl-tools/ensembl-tools-85.ebuild
index ffa1b63..ad17777 100644
--- a/sci-biology/ensembl-tools/ensembl-tools-85.ebuild
+++ b/sci-biology/ensembl-tools/ensembl-tools-85.ebuild
@@ -8,8 +8,8 @@ PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module
DESCRIPTION="Bioinformatics tools incl. Variant Effect Predictor (VEP)"
-HOMEPAGE="http://grch37.ensembl.org/info/docs/tools/vep/script/index.html
- http://grch37.ensembl.org/info/docs/tools/vep/script/vep_plugins.html"
+HOMEPAGE="http://www.ensembl.org/info/docs/tools/vep/script
+ http://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html"
SRC_URI="https://github.com/Ensembl/ensembl-tools/archive/release/${PV}.zip -> ${P}.zip"
LICENSE="Apache-2.0"
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ensembl-tools/
@ 2016-12-02 21:39 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2016-12-02 21:39 UTC (permalink / raw
To: gentoo-commits
commit: 89901ef8af86f09919417a38d7d2d79e349f6caf
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Dec 2 21:38:56 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Dec 2 21:38:56 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=89901ef8
sci-biology/ensembl-tools: note dependency not yet in science overlay
Package-Manager: portage-2.3.2
.../{ensembl-tools-85.ebuild => ensembl-tools-86.ebuild} | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/sci-biology/ensembl-tools/ensembl-tools-85.ebuild b/sci-biology/ensembl-tools/ensembl-tools-86.ebuild
similarity index 89%
rename from sci-biology/ensembl-tools/ensembl-tools-85.ebuild
rename to sci-biology/ensembl-tools/ensembl-tools-86.ebuild
index ad17777..cee1149 100644
--- a/sci-biology/ensembl-tools/ensembl-tools-85.ebuild
+++ b/sci-biology/ensembl-tools/ensembl-tools-86.ebuild
@@ -18,9 +18,11 @@ KEYWORDS="" # BUG: needs Bio::EnsEMBL::Registry
IUSE=""
DEPEND="dev-perl/File-Copy-Recursive
- dev-perl/Archive-Extract"
+ dev-perl/Archive-Extract
+ dev-perl/Bio-DB-HTS"
+# BUG: needs Bio::EnsEMBL::Registry from http://www.ensembl.org/info/docs/api/api_installation.html
+# dev-perl/Bio-EnsEMBL" #
#DEPEND="dev-perl/Perl-XS
-# dev-perl/Bio-DB-HTS"
RDEPEND="${DEPEND}"
S="${WORKDIR}/ensembl-tools-release-${PV}"
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ensembl-tools/
@ 2016-12-02 22:55 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2016-12-02 22:55 UTC (permalink / raw
To: gentoo-commits
commit: b0a99390c78474f28670d6e577b431fc7da77088
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Dec 2 22:55:23 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Dec 2 22:55:23 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b0a99390
sci-biology/ensembl-tools: add missing dependency
Package-Manager: portage-2.3.2
sci-biology/ensembl-tools/ensembl-tools-86.ebuild | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/sci-biology/ensembl-tools/ensembl-tools-86.ebuild b/sci-biology/ensembl-tools/ensembl-tools-86.ebuild
index cee1149..95e9525 100644
--- a/sci-biology/ensembl-tools/ensembl-tools-86.ebuild
+++ b/sci-biology/ensembl-tools/ensembl-tools-86.ebuild
@@ -19,9 +19,8 @@ IUSE=""
DEPEND="dev-perl/File-Copy-Recursive
dev-perl/Archive-Extract
- dev-perl/Bio-DB-HTS"
-# BUG: needs Bio::EnsEMBL::Registry from http://www.ensembl.org/info/docs/api/api_installation.html
-# dev-perl/Bio-EnsEMBL" #
+ dev-perl/Bio-DB-HTS
+ dev-perl/Bio-EnsEMBL"
#DEPEND="dev-perl/Perl-XS
RDEPEND="${DEPEND}"
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/ensembl-tools/
@ 2016-12-07 12:52 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2016-12-07 12:52 UTC (permalink / raw
To: gentoo-commits
commit: 5e2fcfa47bb951d319e95d9340bc724aeb045002
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Dec 7 12:52:28 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Dec 7 12:52:28 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5e2fcfa4
sci-biology/ensembl-tools: mimic upstream's INSTALL.pl so we can install on Gentoo
Seems the code fetching VEP plugins will need more reverse-engineering unless
this can be completed during run-time (do not know).
Package-Manager: portage-2.3.2
sci-biology/ensembl-tools/ensembl-tools-86.ebuild | 37 ++++++++++++++---------
1 file changed, 22 insertions(+), 15 deletions(-)
diff --git a/sci-biology/ensembl-tools/ensembl-tools-86.ebuild b/sci-biology/ensembl-tools/ensembl-tools-86.ebuild
index 95e9525..793f51e 100644
--- a/sci-biology/ensembl-tools/ensembl-tools-86.ebuild
+++ b/sci-biology/ensembl-tools/ensembl-tools-86.ebuild
@@ -7,14 +7,14 @@ EAPI=5
PERL_EXPORT_PHASE_FUNCTIONS=no
inherit perl-module
-DESCRIPTION="Bioinformatics tools incl. Variant Effect Predictor (VEP)"
+DESCRIPTION="Variant Effect Predictor (VEP), AssemblyMapper, IDMapper, RegionReporter tools"
HOMEPAGE="http://www.ensembl.org/info/docs/tools/vep/script
http://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html"
SRC_URI="https://github.com/Ensembl/ensembl-tools/archive/release/${PV}.zip -> ${P}.zip"
LICENSE="Apache-2.0"
SLOT="0"
-KEYWORDS="" # BUG: needs Bio::EnsEMBL::Registry
+KEYWORDS=""
IUSE=""
DEPEND="dev-perl/File-Copy-Recursive
@@ -28,26 +28,33 @@ S="${WORKDIR}/ensembl-tools-release-${PV}"
src_install(){
perl_set_version
- insinto ${VENDOR_LIB}/${PN}
- cd scripts/variant_effect_predictor || die
- # FIXME: INSTALL.pl does not exit upon error
- ./INSTALL.pl --DESTDIR="${DESTDIR}"/"${EPREFIX}" --AUTO=ac || die
+ pushd scripts/variant_effect_predictor || die
+ # BUG1: the INSTALL.pl does not exit upon error with non-zero exit code
+ # BUG2: it complains if ${VENDOR_LIB}/${PN} is not in PERL5LIB
+ # perl INSTALL.pl --AUTO=acf --NO_HTSLIB --PLUGINS all --DESTDIR ${VENDOR_LIB}/${PN} || die
newdoc README.txt variant_effect_predictor.txt
- cd ../../scripts/region_reporter || die
+ dobin variant_effect_predictor.pl gtf2vep.pl filter_vep.pl convert_cache.pl
+ insinto /usr/share/"${PN}"/examples
+ doins example_*
+ popd
+ pushd scripts/region_reporter || die
dobin *.pl
newdoc README.txt region_reporter.txt
- cd ../../scripts/assembly_converter
+ popd
+ pushd scripts/assembly_converter
dobin *.pl
- insinto /usr/share/"${PN}"/examples
doins assemblymapper.in
- #insinto ${VENDOR_LIB}/${PN}
- #doins *.pm
newdoc README.txt assembly_converter.txt
- insinto /usr/share/"${PN}"/examples
- doins assemblymapper.in
- cd ../../scripts/id_history_converter
+ popd
+ pushd scripts/id_history_converter
dobin *.pl
newdoc README.txt id_history_converter.txt
- insinto /usr/share/"${PN}"/examples
doins idmapper.in
+ popd
+}
+
+pkg_postinst(){
+ einfo "Probably you want to download some of the files from ftp://ftp.ensembl.org/pub/release-86/variation/VEP/"
}
+# TODO The INSTALL.pl fetches https://raw.githubusercontent.com/Ensembl/VEP_plugins/release/86/plugin_config.txt
+# and calls eval on its contents
^ permalink raw reply related [flat|nested] 8+ messages in thread
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