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| author |   Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-01-28 17:51:03 +0100 |
|---|---|---|
| committer | Martin Mokrejš <mmokrejs@fold.natur.cuni.cz> | 2017-01-28 17:51:03 +0100 |
| commit | 64a0c52245b6062bae5382c4776c99ef3194befe (patch) | |
| tree | c25cf1e2739ceded0041b2d3a19255954471d805 | |
| parent | sci-libs/clblas: apply previous fix also to the other ebuilds (diff) | |
| download | sci-64a0c522.tar.gz sci-64a0c522.tar.bz2 sci-64a0c522.zip | |
sci-biology/BBmap: version bump
Package-Manager: Portage-2.3.3, Repoman-2.3.1
| -rw-r--r-- | sci-biology/BBmap/BBmap-34.97.ebuild | 2 | ||||
| -rw-r--r-- | sci-biology/BBmap/BBmap-35.92.ebuild | 2 | ||||
| -rw-r--r-- | sci-biology/BBmap/BBmap-36.02.ebuild | 2 | ||||
| -rw-r--r-- | sci-biology/BBmap/BBmap-36.86.ebuild | 43 | ||||
| -rw-r--r-- | sci-biology/BBmap/Manifest | 1 |
5 files changed, 47 insertions, 3 deletions
diff --git a/sci-biology/BBmap/BBmap-34.97.ebuild b/sci-biology/BBmap/BBmap-34.97.ebuild index 10cdcb313..d2bad053d 100644 --- a/sci-biology/BBmap/BBmap-34.97.ebuild +++ b/sci-biology/BBmap/BBmap-34.97.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ diff --git a/sci-biology/BBmap/BBmap-35.92.ebuild b/sci-biology/BBmap/BBmap-35.92.ebuild index fa463a306..8f8b0b3c0 100644 --- a/sci-biology/BBmap/BBmap-35.92.ebuild +++ b/sci-biology/BBmap/BBmap-35.92.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ diff --git a/sci-biology/BBmap/BBmap-36.02.ebuild b/sci-biology/BBmap/BBmap-36.02.ebuild index fa463a306..8f8b0b3c0 100644 --- a/sci-biology/BBmap/BBmap-36.02.ebuild +++ b/sci-biology/BBmap/BBmap-36.02.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ diff --git a/sci-biology/BBmap/BBmap-36.86.ebuild b/sci-biology/BBmap/BBmap-36.86.ebuild new file mode 100644 index 000000000..8f8b0b3c0 --- /dev/null +++ b/sci-biology/BBmap/BBmap-36.86.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="Short read aligner, K-mer-based error-correct and normalize, FASTA/Q tool" +HOMEPAGE="http://sourceforge.net/projects/bbmap/" +SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND=" + sys-cluster/openmpi[java] + >=virtual/jdk-1.7:* + dev-java/ant-core" +RDEPEND="${DEPEND} + >=virtual/jre-1.7:*" + +S="${WORKDIR}"/bbmap + +src_prepare(){ + # fix the line in build.xml to point to mpi.jar location + # <property name="mpijar" location="/tmp/mpi.jar" ></property> + # see bug #542700 + sed -e 's#/usr/common/usg/hpc/openmpi/gnu4.6/sge/1.8.1/ib_2.1-1.0.0/lib/mpi.jar#/usr/share/openmpi/lib/mpi.jar#' -i build.xml + sed -e 's#compiler="${jcompiler}" ##' -i build.xml +} + +src_compile(){ + ant dist || die +} + +src_install(){ + dobin *.sh + dodoc docs/readme.txt + java-pkg_dojar dist/lib/BBTools.jar +} diff --git a/sci-biology/BBmap/Manifest b/sci-biology/BBmap/Manifest index c9c39e012..21526d4c4 100644 --- a/sci-biology/BBmap/Manifest +++ b/sci-biology/BBmap/Manifest @@ -1,3 +1,4 @@ DIST BBMap_34.97.tar.gz 3986036 SHA256 46e9de558d5a7cb9f9db024ee59adaaee8fad28e5dbf1323cd619691f7ad8e53 SHA512 ddc43fe281af775946a8688805ec352431340a1e28ae0e8bd90dc8f2ef51435d03af73d3d90f2c0d04cf932d744acb43576bf89cd392e79f02393f9a6188598a WHIRLPOOL 21f73c14d4714024c7c68547da06037eef014e967c02ffc93f86887700366385d9edbfb67c67a648c314170bd2876c0ddb81e000c478138a706dd69f82e9d22a DIST BBMap_35.92.tar.gz 4481029 SHA256 d15b1e42537f2cd947c4f1941e2be5a7d3584d632da5c0a372c84efed3d72ccb SHA512 d9d43d40d8791826ad9d9a639a2cf9f08fd92460d37a19564ca460b9c5ace988c91052bb4e7c7ca49eb807efa2d3869153bdd5615df0f5900d623a3aae930dc5 WHIRLPOOL 544e6227321fd70529b0c49c1e2029061368b3909baf17d76b09cc44b5af48dbe36835b0f82bd97f29a20eda16e0c7f5efcd79026ed95cd3a7f0596cb0512d7e DIST BBMap_36.02.tar.gz 4545396 SHA256 05dcee9a3b89f665449b6e48b4828557d6474d00616c8c035d4f73e02efe0760 SHA512 4e960bd8d3b665333bbcd2c8f1b74e5b40a8172ef3b92f0512f1f9ea26cd83116f1284147e3f2e4f7340f7fb472159b47442c082336d3c45bf42ecb99f911fad WHIRLPOOL f4ba6bd9d7153b62f52a0f717074664ac943853ea1f1806cd80273cb9026a9cee1a4b4f5194f9a4b4135de85e0072c8c92c22a12366e6308ed49263d5e1c6e70 +DIST BBMap_36.86.tar.gz 5290221 SHA256 4f2fa2b139b67b57136e1b61df8de00d8b9fb75e1a1cdf5e5f28259a9743b6a8 SHA512 fc263572d8d3ecd8096594643cb4b955d48daf3c44538393c9f2f212838503ad00b5dfab969121e80091b1079752dd3e35428ca658959dd8549bda667396e8b0 WHIRLPOOL c503c3e77dba232547de792c6e219cb4275b4d0ec6806f5885abc03bc15e7bb2ebd683d4f5655dd16d3e480cb5b24799109388abc6f8abb3607454dcbe104115 |