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commit: a7bf4e9d7d31c5c27213f618b1160b0d7006ac1c |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Sun Mar 23 18:15:12 2014 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Sun Mar 23 18:15:12 2014 +0000 |
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URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=a7bf4e9d |
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|
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sci-biology/bambino: a new package, maybe should have -bin in its name?; needs decent inspection from java team for sure |
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|
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Package-Manager: portage-2.2.7 |
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|
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--- |
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sci-biology/bambino/ChangeLog | 11 ++++++++++ |
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sci-biology/bambino/bambino-1.02.ebuild | 36 +++++++++++++++++++++++++++++++++ |
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sci-biology/bambino/bambino-1.06.ebuild | 36 +++++++++++++++++++++++++++++++++ |
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sci-biology/bambino/metadata.xml | 9 +++++++++ |
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4 files changed, 92 insertions(+) |
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|
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diff --git a/sci-biology/bambino/ChangeLog b/sci-biology/bambino/ChangeLog |
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new file mode 100644 |
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index 0000000..1cc049f |
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--- /dev/null |
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+++ b/sci-biology/bambino/ChangeLog |
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@@ -0,0 +1,11 @@ |
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+# ChangeLog for sci-biology/bambino |
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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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+*bambino-1.02 (23 Mar 2014) |
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+*bambino-1.06 (23 Mar 2014) |
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+ |
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+ 23 Mar 2014; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
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+ +bambino-1.02.ebuild, +bambino-1.06.ebuild, +metadata.xml: |
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+ sci-biology/bambino: a new package, maybe should have -bin in its name?; needs |
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+ decent inspection from java team for sure |
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|
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diff --git a/sci-biology/bambino/bambino-1.02.ebuild b/sci-biology/bambino/bambino-1.02.ebuild |
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new file mode 100644 |
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index 0000000..4ea6c9d |
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--- /dev/null |
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+++ b/sci-biology/bambino/bambino-1.02.ebuild |
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@@ -0,0 +1,36 @@ |
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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=3 |
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+ |
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+inherit java-pkg-2 eutils |
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+ |
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+DESCRIPTION="Bambino / BAMview / bam_utils to display SAM/BAM files and for SNP/indel detection, report coverage in .wig files" |
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+HOMEPAGE="https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html" |
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+ |
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+# bug #377305 |
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+SRC_URI="https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=bundle -> bambino_core_1.02.jar |
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+ https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=core -> bambino_bundle_1.02.jar" |
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+ |
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+LICENSE="bambino" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86" |
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+IUSE="" |
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+ |
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+DEPEND="" |
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+RDEPEND="${DEPEND} |
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+ >=virtual/jdk-1.6 |
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+ sci-biology/picard |
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+ dev-java/jdbc-mysql" |
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+ |
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+src_install(){ |
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+ insinto "${DESTDIR}"/usr/share/"${PN}"/lib |
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+ doins "${DISTDIR}"/bambino_core_"${PV}".jar || die |
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+ doins "${DISTDIR}"/bambino_bundle_"${PV}".jar || die |
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+ |
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+ einfo "bambino can be run using 'java -jar /usr/share/bambino/lib/bambino_bundle_1.02.jar'" |
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+ einfo " or 'java -jar /usr/share/bambino/lib/bambino_core_1.02.jar'" |
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+ einfo "More info at "${HOMEPAGE} |
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+ |
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+} |
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|
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diff --git a/sci-biology/bambino/bambino-1.06.ebuild b/sci-biology/bambino/bambino-1.06.ebuild |
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new file mode 100644 |
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index 0000000..864beee |
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--- /dev/null |
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+++ b/sci-biology/bambino/bambino-1.06.ebuild |
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@@ -0,0 +1,36 @@ |
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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=3 |
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+ |
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+inherit java-pkg-2 eutils |
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+ |
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+DESCRIPTION="Bambino / BAMview / bam_utils to display SAM/BAM files and for SNP/indel detection, report coverage in .wig files" |
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+HOMEPAGE="https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html" |
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+ |
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+# bug #377305 |
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+SRC_URI="https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=bundle -> bambino_core_1.06.jar |
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+ https://cgwb.nci.nih.gov/cgi-bin/bambino?download_bambino_jar=core -> bambino_bundle_1.06.jar" |
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+ |
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+LICENSE="bambino" |
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+SLOT="0" |
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+KEYWORDS="~amd64 ~x86" |
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+IUSE="" |
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+ |
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+DEPEND="" |
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+RDEPEND="${DEPEND} |
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+ >=virtual/jdk-1.6 |
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+ sci-biology/picard |
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+ dev-java/jdbc-mysql" |
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+ |
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+src_install(){ |
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+ insinto "${DESTDIR}"/usr/share/"${PN}"/lib |
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+ doins "${DISTDIR}"/bambino_core_"${PV}".jar || die |
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+ doins "${DISTDIR}"/bambino_bundle_"${PV}".jar || die |
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+ |
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+ einfo "bambino can be run using 'java -jar /usr/share/bambino/lib/bambino_bundle_1.06.jar'" |
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+ einfo " or 'java -jar /usr/share/bambino/lib/bambino_core_1.06.jar'" |
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+ einfo "More info at "${HOMEPAGE} |
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+ |
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+} |
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|
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diff --git a/sci-biology/bambino/metadata.xml b/sci-biology/bambino/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/bambino/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> |