* [gentoo-commits] proj/sci:master commit in: sci-biology/exomiser-bin/
@ 2015-05-05 14:49 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2015-05-05 14:49 UTC (permalink / raw
To: gentoo-commits
commit: f60deed79963ffc7f97ea68afdfce84c891a2e58
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May 5 14:39:21 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May 5 14:39:21 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f60deed7
sci-biology/exomiser-bin: new package
Package-Manager: portage-2.2.18
sci-biology/exomiser-bin/ChangeLog | 9 +++++++++
sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild | 23 ++++++++++++++++++++++
sci-biology/exomiser-bin/metadata.xml | 9 +++++++++
3 files changed, 41 insertions(+)
diff --git a/sci-biology/exomiser-bin/ChangeLog b/sci-biology/exomiser-bin/ChangeLog
new file mode 100644
index 0000000..0948caa
--- /dev/null
+++ b/sci-biology/exomiser-bin/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/exomiser-bin
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*exomiser-bin-7.0.0 (05 May 2015)
+
+ 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +exomiser-bin-7.0.0.ebuild, +metadata.xml:
+ sci-biology/exomiser-bin: new package
diff --git a/sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild b/sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild
new file mode 100644
index 0000000..875db0e
--- /dev/null
+++ b/sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Annotate VCF files from whole-exome sequencing (Jannovar, UCSC KnownGenes, hg19)"
+HOMEPAGE="http://www.sanger.ac.uk/resources/software/exomiser"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-${PV}.BETA-distribution.zip"
+# 1.16GB !
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sci-biology/Jannovar-bin"
+RDEPEND="${DEPEND}"
+
+pkg_postinst(){
+ einfo "Please download 3.7GB file from ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/h2_db_dumps/exomiser-${PV}.BETA.h2.db.gz"
+ einfo "and follow README.md"
+}
diff --git a/sci-biology/exomiser-bin/metadata.xml b/sci-biology/exomiser-bin/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/exomiser-bin/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>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/exomiser-bin/
@ 2016-03-30 16:33 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2016-03-30 16:33 UTC (permalink / raw
To: gentoo-commits
commit: 4215f67e0da1eb2a2600f0b30a9e6032ddea342c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 30 16:30:41 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 30 16:30:41 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4215f67e
sci-biology/exomiser-bin: improve ebuild, fix LICENSE, a 19GB files should be fetched manually but the ebuild should get access to it, unpack it and install as the files make grounding for a usable workspace
Package-Manager: portage-2.2.28
sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild | 23 ----------------
sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild | 31 ++++++++++++++++++++++
2 files changed, 31 insertions(+), 23 deletions(-)
diff --git a/sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild b/sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild
deleted file mode 100644
index c58cabf..0000000
--- a/sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-DESCRIPTION="Annotate VCF files from whole-exome sequencing (Jannovar, UCSC KnownGenes, hg19)"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/exomiser"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-${PV}.BETA-distribution.zip"
-# 1.16GB !
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="sci-biology/Jannovar-bin"
-RDEPEND="${DEPEND}"
-
-pkg_postinst(){
- einfo "Please download 3.7GB file from ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/h2_db_dumps/exomiser-${PV}.BETA.h2.db.gz"
- einfo "and follow README.md"
-}
diff --git a/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild b/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild
new file mode 100644
index 0000000..1346fd2
--- /dev/null
+++ b/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+DESCRIPTION="Annotate VCF files and prioritize genome/exome mutations (Jannovar, UCSC KnownGenes, hg19)"
+HOMEPAGE="http://www.sanger.ac.uk/science/tools/exomiser"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-${PV}-distribution.zip
+ ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/GenomiserREADME -> ${PN}.README
+ ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/README.md -> ${PN}.README.md"
+# 1.16GB !
+
+LICENSE="AGPL-3+"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sci-biology/Jannovar-bin"
+RDEPEND="${DEPEND}"
+
+src_install(){
+ dodoc "${DISTDIR}"/${PN}.README "${DISTDIR}"/${PN}.README.md
+}
+
+pkg_postinst(){
+ einfo "Please download 3.7GB file from ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/h2_db_dumps/exomiser-${PV}.BETA.h2.db.gz"
+ einfo "and follow README.md"
+ einfo "The is also 19GB file ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-7.2.1-data.zip"
+ einfo "with test data"
+}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/exomiser-bin/
@ 2020-09-27 21:24 Horea Christian
0 siblings, 0 replies; 3+ messages in thread
From: Horea Christian @ 2020-09-27 21:24 UTC (permalink / raw
To: gentoo-commits
commit: e2f2334b11f6a99c17b945ccdbcdc3f029879db1
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 21:03:36 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 21:03:36 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e2f2334b
sci-biology/exomiser-bin: removed unmaintained package
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild | 30 ----------------------
sci-biology/exomiser-bin/metadata.xml | 12 ---------
2 files changed, 42 deletions(-)
diff --git a/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild b/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild
deleted file mode 100644
index 87434fa8a..000000000
--- a/sci-biology/exomiser-bin/exomiser-bin-7.2.1.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Annotate VCF files and prioritize genome/exome mutations"
-HOMEPAGE="http://www.sanger.ac.uk/science/tools/exomiser"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-${PV}-distribution.zip
- ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/GenomiserREADME -> ${PN}.README
- ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/README.md -> ${PN}.README.md"
-# 1.16GB !
-
-LICENSE="AGPL-3+"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="sci-biology/Jannovar-bin"
-RDEPEND="${DEPEND}"
-
-src_install(){
- dodoc "${DISTDIR}"/${PN}.README "${DISTDIR}"/${PN}.README.md
-}
-
-pkg_postinst(){
- einfo "Please download 3.7GB file from ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/h2_db_dumps/exomiser-${PV}.BETA.h2.db.gz"
- einfo "and follow README.md"
- einfo "The is also 19GB file ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-7.2.1-data.zip"
- einfo "with test data"
-}
diff --git a/sci-biology/exomiser-bin/metadata.xml b/sci-biology/exomiser-bin/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/exomiser-bin/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>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] 3+ messages in thread
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