From 59cbe00f7e3f09edbe45448df2f75cbcf2d0e0c0 Mon Sep 17 00:00:00 2001 From: Martin Mokrejš Date: Sat, 30 May 2015 19:50:55 +0200 Subject: sci-biology/fastqc: version bump, added perl dependency, Apache ant-building does not work still Package-Manager: portage-2.2.18 --- sci-biology/fastqc/ChangeLog | 7 ++++++ sci-biology/fastqc/Manifest | 2 +- sci-biology/fastqc/fastqc-0.11.2.ebuild | 37 ---------------------------- sci-biology/fastqc/fastqc-0.11.3.ebuild | 43 +++++++++++++++++++++++++++++++++ 4 files changed, 51 insertions(+), 38 deletions(-) delete mode 100644 sci-biology/fastqc/fastqc-0.11.2.ebuild create mode 100644 sci-biology/fastqc/fastqc-0.11.3.ebuild (limited to 'sci-biology/fastqc') diff --git a/sci-biology/fastqc/ChangeLog b/sci-biology/fastqc/ChangeLog index b828a60ff..3510855fa 100644 --- a/sci-biology/fastqc/ChangeLog +++ b/sci-biology/fastqc/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*fastqc-0.11.3 (30 May 2015) + + 30 May 2015; Martin Mokrejs + +fastqc-0.11.3.ebuild, -fastqc-0.11.2.ebuild: + sci-biology/fastqc: version bump, added perl dependency, Apache ant-building + does not work still + 05 Mar 2015; Martin Mokrejs +files/build.xml, fastqc-0.11.2.ebuild: added build.xml exported by author from Eclipse IDE (it doesn't work under ant diff --git a/sci-biology/fastqc/Manifest b/sci-biology/fastqc/Manifest index c8dd062ca..4e8207292 100644 --- a/sci-biology/fastqc/Manifest +++ b/sci-biology/fastqc/Manifest @@ -1 +1 @@ -DIST fastqc_v0.11.2_source.zip 996798 SHA256 efee48358830f5120b5a39311d5f50352b1476e89bf5ea4ad6ce1ab831ee7eee SHA512 c0443d7b8313b488090832c7697662d6fccbe8bddf42d7941bb8a3f50e55c104cfa06e2edbd0e04c5fc5de02eadd61830ceddf2c944228a1ce9479d846a750b3 WHIRLPOOL 2aeae03c18595a7a56b88f353b2490d7a826aa7130451e3fc05faf111c1aeea67f5ea617225cedc1d11172ee5c3f823b1f0793278ef5910b8bec00468de76ce9 +DIST fastqc_v0.11.3_source.zip 10073593 SHA256 b62b1aea957af9051b30d306183df239b095eac4f8d281478c372b25c61fe44d SHA512 bab27d6997ad6525b7804ba9a3a54eec1cdb835d548c2840ae882334902d12eea4bbff549370669176ade76633a5f1d7dc6f7ee865a25f1a41b525764660b471 WHIRLPOOL 843039e115aa0101e687ad9fe9b40d4e658e96f6dbebe87a9f4074c1f3ea46910f3dac1a3426ec329a194a542580ca16ce5d22c348500453ba357c27f15a7f06 diff --git a/sci-biology/fastqc/fastqc-0.11.2.ebuild b/sci-biology/fastqc/fastqc-0.11.2.ebuild deleted file mode 100644 index dadc2881d..000000000 --- a/sci-biology/fastqc/fastqc-0.11.2.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit java-pkg-2 eutils java-ant-2 - -DESCRIPTION="Perl-based wrapper around java apps to quality control FASTA/FASTQ sequence files" -HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" -SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"${PV}"_source.zip" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND="sci-biology/picard - >=virtual/jre-1.5:*" -RDEPEND="${DEPEND} - >=virtual/jdk-1.5:* - dev-java/ant-core" - -S="${WORKDIR}"/FastQC - -src_prepare(){ - cp "${FILESDIR}"/build.xml . || die -} - -src_install(){ - dobin fastqc run_fastqc.bat - dodoc README.txt RELEASE_NOTES.txt - - # TODO: need to compile java in uk/ac/babraham/FastQC/ - # and decide whether jbzip2-0.9.jar is a standard java lib or not - # ignore the sam-1.32.jar, that is likely library already in sci-biology/picard -} diff --git a/sci-biology/fastqc/fastqc-0.11.3.ebuild b/sci-biology/fastqc/fastqc-0.11.3.ebuild new file mode 100644 index 000000000..d2ae40e59 --- /dev/null +++ b/sci-biology/fastqc/fastqc-0.11.3.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 eutils java-ant-2 + +DESCRIPTION="Perl-based wrapper around java apps to quality control FASTA/FASTQ sequence files" +HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" +SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"${PV}"_source.zip" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="sci-biology/picard + >=virtual/jre-1.5:*" +RDEPEND="${DEPEND} + dev-lang/perl + >=virtual/jdk-1.5:* + dev-java/ant-core" + +S="${WORKDIR}"/FastQC + +src_prepare(){ + cp "${FILESDIR}"/build.xml . || die +} + +src_compile(){ + ant build || die # TODO: this does not work somehow +} + +src_install(){ + dobin fastqc run_fastqc.bat + dodoc README.txt RELEASE_NOTES.txt + + # TODO: need to compile java in uk/ac/babraham/FastQC/ + # and decide whether jbzip2-0.9.jar is a standard java lib or not + # ignore the sam-1.103.jar, that is likely library already in sci-biology/picard + # cisd-jhdf5.jar +} -- cgit v1.2.3-65-gdbad