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commit: d8114ce881aac5e2972066606955071fa0ae4fde |
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Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Tue Jul 12 16:04:10 2016 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Tue Jul 12 16:04:10 2016 +0000 |
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URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d8114ce8 |
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|
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sci-biology/cramtools: new package, not working yet |
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|
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will not compile with java8 until upstream issue #59 is fixed |
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|
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contains bundled dev-java/htsjdk (although other apps do not keep up |
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with the API changes in htsjdk so it does have a reason) |
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|
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Package-Manager: portage-2.2.28 |
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|
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sci-biology/cramtools/cramtools-3.0.ebuild | 32 ++++++++++++++++++++++++++++++ |
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sci-biology/cramtools/metadata.xml | 12 +++++++++++ |
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2 files changed, 44 insertions(+) |
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|
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diff --git a/sci-biology/cramtools/cramtools-3.0.ebuild b/sci-biology/cramtools/cramtools-3.0.ebuild |
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new file mode 100644 |
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index 0000000..9d903a2 |
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--- /dev/null |
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+++ b/sci-biology/cramtools/cramtools-3.0.ebuild |
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@@ -0,0 +1,32 @@ |
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+# Copyright 1999-2016 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Id$ |
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+ |
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+EAPI=5 |
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+ |
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+inherit java-pkg-2 java-ant-2 |
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+ |
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+DESCRIPTION="Java tools and APIs for efficient compression of sequence read data" |
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+HOMEPAGE="http://www.ebi.ac.uk/ena/software/cram-toolkit |
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+ https://github.com/enasequence/cramtools" |
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+SRC_URI="https://github.com/enasequence/cramtools/archive/v3.0.tar.gz -> ${P}.tar.gz" |
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+ |
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+LICENSE="Apache-2.0" |
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+SLOT="0" |
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+KEYWORDS="" |
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+IUSE="" |
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+ |
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+DEPEND=" |
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+ >=virtual/jdk-1.7:* |
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+ dev-java/ant-core |
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+ dev-java/htsjdk" |
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+RDEPEND=" |
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+ ${DEPEND} |
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+ >=virtual/jre-1.7:*" |
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+ |
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+# TODO: zap bundled htsjdk to ensure it uses dev-java/htsjdk? |
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+# https://github.com/enasequence/cramtools/issues/58 |
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+# https://github.com/enasequence/cramtools/issues/59 |
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+src_compile(){ |
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+ ant -f build/build.xml runnable || die |
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+} |
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|
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diff --git a/sci-biology/cramtools/metadata.xml b/sci-biology/cramtools/metadata.xml |
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new file mode 100644 |
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index 0000000..f68a1b6 |
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--- /dev/null |
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+++ b/sci-biology/cramtools/metadata.xml |
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@@ -0,0 +1,12 @@ |
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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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+ <maintainer type="person"> |
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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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+ <maintainer type="project"> |
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+ <email>sci-biology@g.o</email> |
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+ <name>Gentoo Biology Project</name> |
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+ </maintainer> |
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+</pkgmetadata> |
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