diff options
21 files changed, 240 insertions, 35 deletions
diff --git a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild index e3681243f..a8643695e 100644 --- a/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild +++ b/sci-biology/Atlas_GapFill/Atlas_GapFill-2.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2015 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Id$ @@ -18,7 +18,6 @@ IUSE="" # is there an ebuild for newbler so we could add it to DEPEND? RDEPEND=" dev-lang/perl - sys-cluster/torque sci-biology/phrap sci-biology/bwa sci-biology/velvet" diff --git a/sci-biology/Ray/Ray-2.3.0.ebuild b/sci-biology/Ray/Ray-2.3.0.ebuild index 352a5dd01..a74548fe5 100644 --- a/sci-biology/Ray/Ray-2.3.0.ebuild +++ b/sci-biology/Ray/Ray-2.3.0.ebuild @@ -19,5 +19,5 @@ RDEPEND="${DEPEND} src_install(){ dobin Ray - use statics-libs && dolib.a libRayPlatform.a libRay.a + use static-libs && dolib.a libRayPlatform.a libRay.a } diff --git a/sci-biology/SnpEff/Manifest b/sci-biology/SnpEff/Manifest index 17f39b3d2..05c15412b 100644 --- a/sci-biology/SnpEff/Manifest +++ b/sci-biology/SnpEff/Manifest @@ -1,2 +1,2 @@ -DIST SnpEff-4.3g.html 100934 SHA256 6893356e05d878a62b01352713ec04d5bae03829536d5788cda64e0e0f555e37 SHA512 ee72b2528dc81b6326c9b4472f335cdf8f8f99dc6a368a573fec95c0dc60f335d99c52bbdd397cea130d7b924606879228d073c1ba69746617862ccec331082b WHIRLPOOL 220e2268a44a9f1e2b81daaf65abfe89630e323d698bfb68af8057da4354e29ffacd1cb5368492f5929c0f15c784cea4e206c8924179aab29dc04221a4e43915 -DIST snpEff_v4_3g_core.zip 48454027 SHA256 31485950a6528f4f3a8c377ba4b4cbef39e9d34e11758481517a5adbca5513d4 SHA512 207801cc647a26308b4594a3652008e4742d4e6ecb5fe5fddfeb2b3a10bdebace1a47a26ae2225a87651da434a6bda67e1b9e3147ea01b1fdf9d83fb57889405 WHIRLPOOL a918efe87f431a2d116809411fd352e30acb3127c3d558a369cc6040c8bbb45e25ad7038d205a808ae4227fa8eb8c1cecae377efe67747c0db5d7c011aea61de +DIST SnpEff-4.3i.html 101923 SHA256 10e365b8567ecc11453eb123ab24a483a682223baeb269fbe66e7c81320e80c6 SHA512 ecf6c56508dff0abaec9dbc05677e958e10ad1df97ae0a29007b0748598de8f0982c298ea9a7e5d8692c5abe4adacd4afc1307137a92ea81e793577bc1e7ecaf WHIRLPOOL f503346a51461de107b05b047b5472b6739e264db1718afbf38c501ea2dc0ccb7a609eec38d383112790e1b4a6ac36680d5e198cd0d11f91b0f9d028c098fcf2 +DIST snpEff_v4_3i_core.zip 48456135 SHA256 ebd3d5bec106c3ebc68961b941d3420c44fe1febe4654eb2931eb100c4a33a44 SHA512 6eb90afe125022da48a0d70c445c362ea8f9138d7dcecbf5fff1bf4f2d6bdbba812591416669481890a0d8bc89518023c2e0d1ef2d91d5efa7cce61cdbb02676 WHIRLPOOL 74557c36a58c0cf29b82dcf3af9da2e7824195c805ae6c5a875c346fdaeef5021a92009d8fe003b20dbce3f2f728285e4af24c5c8ecdb588974578b5cb955dd7 diff --git a/sci-biology/SnpEff/SnpEff-4.3g.ebuild b/sci-biology/SnpEff/SnpEff-4.3i.ebuild index fb1189406..8d2a06821 100644 --- a/sci-biology/SnpEff/SnpEff-4.3g.ebuild +++ b/sci-biology/SnpEff/SnpEff-4.3i.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/VarScan-bin/Manifest b/sci-biology/VarScan-bin/Manifest index efdc31df9..cd23b534b 100644 --- a/sci-biology/VarScan-bin/Manifest +++ b/sci-biology/VarScan-bin/Manifest @@ -1 +1,2 @@ DIST VarScan.v2.4.2.jar 114840 SHA256 34ff6462f91fb6ed3f11e867ab4a179efae5dd8214b97fa261fc616f23d4d031 SHA512 a58c35412a3fb5a3750a4f3fea834e92bde3e0b98c6bbf48e677589a3d99dcd82a01d864ab0c5d19d2089cad1174ea9f70c8081fbc02fddfb3723c8c9af6de68 WHIRLPOOL adf7f4a149010a438438fb5c51a2ffa45709d22d72b94053803eb8d4e2341a4eebc3e9db5a6d7e9c175b691e8c72201fe30f0c995a94802603492b569b091a92 +DIST VarScan.v2.4.3.jar 115272 SHA256 dc0e908ebe6a429fdd2d0f80f26c428cfc71f65429dc1816d41230b649168ff3 SHA512 4ac1b35796923261e0273f8e761b391090b2bb6ca8555bd87ef2ba8386f72ad840e84380202516cf332e5efffe2bbb71c97b1f504933e46579ed0f7a48d55091 WHIRLPOOL a09766dbadcfaafd9c7c7995e71d5096b50d77564ccdfd3af8674a65d38a860895692e0056560a0adf566ed2f263ed98ffe0f17873b5362eeb4e811e81fbc3d1 diff --git a/sci-biology/VarScan-bin/VarScan-bin-2.4.3.ebuild b/sci-biology/VarScan-bin/VarScan-bin-2.4.3.ebuild new file mode 100644 index 000000000..ecf60c9ad --- /dev/null +++ b/sci-biology/VarScan-bin/VarScan-bin-2.4.3.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit java-pkg-2 + +MY_PN="VarScan" +DESCRIPTION="Variant detection (germline, multi-sample, somatic mut., CNA), SNP" +HOMEPAGE="http://dkoboldt.github.io/varscan" + +# binary +#http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.7.jar +#SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.jar" +SRC_URI="https://github.com/dkoboldt/varscan/blob/master/${MY_PN}.v${PV}.jar?raw=true -> ${MY_PN}.v${PV}.jar" + +LICENSE="Non-profit-OSL-3.0" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND=" + >=virtual/jdk-1.5:*" +RDEPEND=">=virtual/jre-1.5:*" + +S="${WORKDIR}"/net/sf/varscan + +src_install(){ + java-pkg_newjar "${DISTDIR}"/${MY_PN}.v${PV}.jar ${MY_PN}.jar + java-pkg_dolauncher VarScan +} diff --git a/sci-biology/VarScan/Manifest b/sci-biology/VarScan/Manifest index c0e3615fd..4596de996 100644 --- a/sci-biology/VarScan/Manifest +++ b/sci-biology/VarScan/Manifest @@ -1 +1,2 @@ DIST VarScan.v2.4.2.source.jar 205503 SHA256 d65c3a761ef3ed25544a62b0885373628d3f4f644dde165cd47448e5c175c791 SHA512 92a31b22574144fdb9800b6b3bf016d151119f7e147b47fb9063d1f772a817867265057cd7895fd5a450ef998956e0871d52fb929acf00866f4224586efdce4c WHIRLPOOL a6e3336a55109744dd307556909f105ac4ea6a6a7c9c6a28b657b2a38a0f6da0152519275f6078c667fe4c03fe56c4b86e452a3cbcd5170ff55855d9a859770c +DIST VarScan.v2.4.3.source.jar 206397 SHA256 926927b37bfab7ed7d33861c053b3204aaa211adf4260fdeb312624ae6aff00c SHA512 620a3a41b1e99fe7e1d6ca629287de26bff517efb70a42610abbc66092c935775dc4b2ad10a68c38e69b3063cdadb5794355219f6bf20809761804038713117c WHIRLPOOL c2ec6d5adf96f095b0d4b317d1c5f06ce905bb2bafcf8c75d09377bbacacadb565b7c9c4809f947c48eec220951b61f97645de044bab29c753348c96219a9938 diff --git a/sci-biology/VarScan/VarScan-2.4.3.ebuild b/sci-biology/VarScan/VarScan-2.4.3.ebuild new file mode 100644 index 000000000..3ef29a10c --- /dev/null +++ b/sci-biology/VarScan/VarScan-2.4.3.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +inherit java-pkg-2 + +DESCRIPTION="Variant detection (germline, multi-sample, somatic mutations, CNA, SNP calls)" +HOMEPAGE="http://varscan.sourceforge.net/" + +# binary +#https://github.com/dkoboldt/varscan/blob/master/VarScan.v2.4.3.jar +SRC_URI="https://github.com/dkoboldt/varscan/blob/master/VarScan.v2.4.3.source.jar?raw=true -> ${PN}.v${PV}.source.jar" + +LICENSE="Non-profit-OSL-3.0" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND=" + >=virtual/jdk-1.5:* + !sci-biology/VarScan-bin" +RDEPEND=">=virtual/jre-1.5:*" + +S="${WORKDIR}"/net/sf/varscan + +src_compile(){ + javac *.java +} + +src_install(){ + java-pkg_newjar "${DISTDIR}"/${PN}.v${PV}.source.jar ${PN}.source.jar + java-pkg_dolauncher VarScan +} diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild index 504b0ee4b..dfaa9493e 100644 --- a/sci-biology/bambus/bambus-2.33.ebuild +++ b/sci-biology/bambus/bambus-2.33.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 # $Id$ @@ -23,7 +23,6 @@ IUSE="" RDEPEND=" sci-biology/tigr-foundation-libs - dev-lang/perl dev-perl/XML-Parser dev-perl/Config-IniFiles dev-perl/GraphViz" diff --git a/sci-biology/genepop/Manifest b/sci-biology/genepop/Manifest index 68906abb4..4891decec 100644 --- a/sci-biology/genepop/Manifest +++ b/sci-biology/genepop/Manifest @@ -1 +1,3 @@ DIST genepop-4.2.1.tar.gz 136675 SHA256 08d82c6236814573086627305b47e201ec6abc6ce1a15fcebac9671f24f57f91 SHA512 f658f6ab82c1ef21bf15a9bd03335ea792e670ce7cf8f2eb3e1c4d75ae24ff099bde5580b310fdcd552dfb1dbb6df55352a8c06fedeeb7d46434a58767233882 WHIRLPOOL 20ac7ad1e9ff710e4ff420cdf67ba479019a020f5da9ac5f961a5937e7532c6e069f909e48074cd738d4d857a6c84331aca8972eb5cd3567c649c218b386cdb1 +DIST genepop-4.6.tar.gz 1872683 SHA256 1b6cbb4c133ea2bfb0bee728bad01e25bdd7e8574d21401d09fd93f34298ff14 SHA512 813040f43c3d0c1b41f4689c005f00e7593cb1c201182b202343b3dcafa63f141086e98b140056e0916d3383cb17166694e42277152436831139c1aa02532349 WHIRLPOOL a47312cb52dc8a28af46940f24acf55f5a3bbdd28d5b19f82ec28835e02cd39ee4e921fd88b8d6788331d43ec0a7472d189cda02209e4c3d86545e491d78df24 +DIST genepop.pdf 578521 SHA256 8d7477d182dc91b6b35a46831752ad90d06681572e272935b3d26ffb44a09db1 SHA512 48d1b951c3ab9896827c9f8dca2dbeb447db5a9af1559cb7c2bac2cf27c0c36e7b27268678258a81aacc925ac1346d9ed1b63b25b8517a9acc55177438ee885e WHIRLPOOL 6b422bf8b568261ff09e779c367e3b4fc33bf9a1f8f73cdb58a7482255afd0d380f4ddace24288213377fa5da0af7f1240a06c3c9035915ccc274a5a3bf3afd3 diff --git a/sci-biology/genepop/genepop-4.6.ebuild b/sci-biology/genepop/genepop-4.6.ebuild new file mode 100644 index 000000000..e42f57c82 --- /dev/null +++ b/sci-biology/genepop/genepop-4.6.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit cmake-utils + +DESCRIPTION="Population genetics analysis" +HOMEPAGE="http://genepop.curtin.edu.au/ http://kimura.univ-montp2.fr/~rousset/Genepop.htm" +SRC_URI="http://kimura.univ-montp2.fr/%7Erousset/GenepopV4.tar.gz -> ${P}.tar.gz + http://kimura.univ-montp2.fr/%7Erousset/Genepop.pdf -> ${PN}.pdf" + +LICENSE="CeCILL-2" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +S="${WORKDIR}" + +src_prepare() { + gzip -dc sources.tar.gz | tar xf - || die + mv Cpp/* . || die + rmdir Cpp || die + cat >> CMakeLists.txt <<- EOF + cmake_minimum_required (VERSION 2.6) + project (${PN} CXX) + + set(CMAKE_CXX_FLAGS "\${CMAKE_CXX_FLAGS} -DNO_MODULES") + + add_executable(Genepop GenepopS.cpp) + install(TARGETS Genepop DESTINATION bin) + EOF + cmake-utils_src_prepare + default +} + +src_install(){ + cmake-utils_src_install + dodoc "${DISTDIR}"/"${PN}".pdf +} diff --git a/sci-biology/picard/Manifest b/sci-biology/picard/Manifest index 0b6c7208b..ecaa3b85f 100644 --- a/sci-biology/picard/Manifest +++ b/sci-biology/picard/Manifest @@ -1,3 +1,3 @@ DIST picard-1.141.tar.gz 5692255 SHA256 128e761b4dbedda9a89cceb4d1648be213ec823ff105a35db9c9526955a42320 SHA512 5fed8ff0076ec5f096a5138b95ae07805f8f4d68db33b65f2e21325f49493c50f235519768823c2db981b2e543fbf05f55be7939d75cbd5d257ac84e633b9bf4 WHIRLPOOL 5716cc51da6e94b338aceb5a3d01da5ae048f011e3d3eee72a96144d4b6f80dddf898ea902fae08b127f93c771f521437bd299bdeaf005af6f24c76f9844b63d DIST picard-2.2.2.tar.gz 6565857 SHA256 1d858fde23aa9938a87cd96e6c2fbbfcdea669c9f30d524c107af26bce3798de SHA512 4ee97443397b45236a2481fa64c80edbd7761d6562cc134d65f1d95fa101ccc82402bbf21ed6b186e15324f2c189737790066e18cd0143bb50768c20ee4b156b WHIRLPOOL 69df60c171a5e531b78ad670b260d717a749012d05028e1afba2484eb3a84a71e61ade13c7298b0e9bc6ff526367ca886d9440b996882d3f19455f8f46e3bd4f -DIST picard-2.8.1.tar.gz 3851366 SHA256 780d43230f769e312ccc00b0a5bde4f0d8a2020e98e7447887f581550f4cb975 SHA512 897ec512b3bf66c25dd4f1cbb70306cdfd951c9a257f745ae23f7b8bf7125563460f90128b053977c13fa4fb509b5fa4ec6a11d410487fa0c8927b6ab1bd909a WHIRLPOOL 71b1a7c56f465c7afbdc9b8e0143ab2cb0f661edbaa425d07efe264c37cd58adf1f9f7d388e81fbc3a78efe06af5c1c2611feaeaea7bd64bb748709bf515dc43 +DIST picard-2.9.0.tar.gz 3860908 SHA256 a3d48d820d5e11d54ab78852df8b8221e992cefcea7dc0a4525fb0fd86e5adff SHA512 844303d6e420b20789f9c2e3232412ca16de0ae4d0409a2298f89f9c9c26a487ef356c91faf0eaa0fae009d0866d14481c6f1027d367cca830363c23cb5a0b96 WHIRLPOOL 15e715f812047972c3188e7dc6db83648c8d561d27fdecf4d194cb7ef8e4753a0ca051c492043c00fdd667219b2248d335fc09349e3a64f94acc5dd91621964d diff --git a/sci-biology/picard/picard-2.8.1.ebuild b/sci-biology/picard/picard-2.9.0.ebuild index e6495cd7f..e6495cd7f 100644 --- a/sci-biology/picard/picard-2.8.1.ebuild +++ b/sci-biology/picard/picard-2.9.0.ebuild diff --git a/sci-biology/sambamba/Manifest b/sci-biology/sambamba/Manifest new file mode 100644 index 000000000..ea0a83936 --- /dev/null +++ b/sci-biology/sambamba/Manifest @@ -0,0 +1 @@ +DIST sambamba-0.6.5.tar.gz 249275 SHA256 7ea356109543eb51066e46691e332d3f42f5d67e42db7f801baa9826e333079c SHA512 a0353523bb921a32e4f7601d9c5552b2103567cfa23fb622b213170028122f49cb6929942e9a630890ddd93b7ebf00f048344edb75d5f2d10b1c86bae018497c WHIRLPOOL 6a88cf07e18a07416bcafe3350ae7d168e6a10063eae072376e9228d36a686db6dfa0e7506ad7042f26ea4cbbfea40c12c4eab2c1c66795cb26953cb3133f248 diff --git a/sci-biology/sambamba/metadata.xml b/sci-biology/sambamba/metadata.xml new file mode 100644 index 000000000..f68a1b6fa --- /dev/null +++ b/sci-biology/sambamba/metadata.xml @@ -0,0 +1,12 @@ +<?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> diff --git a/sci-biology/sambamba/sambamba-0.6.5.ebuild b/sci-biology/sambamba/sambamba-0.6.5.ebuild new file mode 100644 index 000000000..2e8d062e0 --- /dev/null +++ b/sci-biology/sambamba/sambamba-0.6.5.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools" +HOMEPAGE="http://lomereiter.github.io/sambamba" +SRC_URI="https://github.com/lomereiter/sambamba/archive/v0.6.5.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-2+" +SLOT="0" +KEYWORDS="" +IUSE="debug" + +# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2 +# +# contains bundled htslib +DEPEND="" +RDEPEND="${DEPEND}" + +src_compile(){ + if use debug ; then + emake sambamba-ldmd2-debug + else + emake sambamba-ldmd2-64 + fi +} diff --git a/sci-biology/sambamba/sambamba-9999.ebuild b/sci-biology/sambamba/sambamba-9999.ebuild new file mode 100644 index 000000000..0ea89ba23 --- /dev/null +++ b/sci-biology/sambamba/sambamba-9999.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +inherit git-r3 + +DESCRIPTION="Parallell process SAM/BAM/CRAM files faster than samtools" +HOMEPAGE="http://lomereiter.github.io/sambamba" +EGIT_REPO_URI="https://github.com/lomereiter/sambamba.git" + +LICENSE="GPL-2+" +SLOT="0" +KEYWORDS="" +IUSE="debug" + +DEPEND="" +RDEPEND="${DEPEND}" + +# https://github.com/ldc-developers/gentoo-overlay/tree/master/dev-lang/ldc2 + +src_compile(){ + if use debug ; then + emake sambamba-ldmd2-debug + else + emake sambamba-ldmd2-64 + fi +} diff --git a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild b/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild index 5819aeed8..6fc765e54 100644 --- a/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild +++ b/sci-biology/tablet-bin/tablet-bin-1.16.09.06.ebuild @@ -39,6 +39,9 @@ DEPEND="${PYTHON_DEPS} >=virtual/jdk-1.8" RDEPEND="${DEPEND} >=virtual/jre-1.8" +# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar +# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not sci-biology/samtools either +# replacing picard.jar with a symlink to picard.jar from sci-biology.picard does not help either S="${WORKDIR}" @@ -73,8 +76,13 @@ src_install() { # make sure we force java to point a to $HOME which is inside our sanbox # directory area. We force -Duser.home . It seems also -Dinstall4j.userHome # could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/ - sed \ - -e 's#"$app_java_home/bin/java" -Dinstall4j.jvmDir# '"${EPREFIX}""/usr/bin/java -Duser.home=${TMPDIR} -Dinstall4j.jvmDir -Djava.util.prefs.systemRoot=${TMPDIR}#" -i "${WORKDIR}"/${P}.sh || die + if [ -z "${EPREFIX}" ]; then + sed \ + -e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home=${TMPDIR} -Dinstall4j.jvmDir -Djava.util.prefs.systemRoot=${TMPDIR}#" -i "${WORKDIR}"/${P}.sh || die + else + sed \ + -e 's#"$app_java_home/bin/java" -Dinstall4j.jvmDir# '"${EPREFIX}""/usr/bin/java -Duser.home=${TMPDIR} -Dinstall4j.jvmDir -Djava.util.prefs.systemRoot=${TMPDIR}#" -i "${WORKDIR}"/${P}.sh || die + fi sh \ "${WORKDIR}"/${P}.sh \ -q -overwrite \ @@ -82,7 +90,16 @@ src_install() { --destination="${ED}"/opt/Tablet \ -dir "${ED}"/opt/Tablet || die - rm -rf "${ED}"/opt/Tablet/jre || die + rm -rf "${ED}"/opt/Tablet/jre "${ED}"/opt/Tablet/.install4j || die + + # zap bundled jars + # do not zap even picard.jar because tablet does not start then with an error: + # java.lang.NoClassDefFoundError: net/sf/samtools/SAMReadGroupRecord + # not even a symlink to "${EPREFIX}"/usr/share/picard/lib/picard.jar helps + # + # for f in picard.jar; do + # rm -f "${ED}"/opt/Tablet/lib/"$f" || die + # done # this dies with tablet-bin-1.14.04.10 with # * python2_7: running python_doscript /mnt/1TB/var/tmp/portage/sci-biology/tablet-bin-1.14.04.10/work/coveragestats.py @@ -96,6 +113,7 @@ src_install() { insinto /opt/Tablet/utils doins coveragestats.py - echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet - doenvd 99Tablet + # do not use 99Tablet to avoid file collision with sci-biology/tablet + echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet-bin + doenvd 99Tablet-bin } diff --git a/sci-biology/tablet/tablet-1.15.09.01.ebuild b/sci-biology/tablet/tablet-1.15.09.01.ebuild index 2d30b71bb..17f7a5365 100644 --- a/sci-biology/tablet/tablet-1.15.09.01.ebuild +++ b/sci-biology/tablet/tablet-1.15.09.01.ebuild @@ -30,21 +30,22 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}" DEPEND="${PYTHON_DEPS} >=virtual/jdk-1.8:*" RDEPEND="${PYTHON_DEPS} - >=virtual/jre-1.8:* - sci-biology/samtools - sci-biology/picard - dev-db/sqlite:3" + >=virtual/jre-1.8:*" +# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar +# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not sci-biology/samtools either +# replacing picard.jar with a symlink to picard.jar from sci-biology.picard does not help either S="${WORKDIR}" src_install() { - cd lib || die - java-pkg_dojar tablet.jar + java-pkg_dojar lib/tablet.jar java-pkg_dolauncher ${PN} - java-pkg_dojar tablet-resources.jar - java-pkg_dojar flamingo.jar - java-pkg_dojar scri-commons.jar - java-pkg_dojar samtools*.jar + java-pkg_dojar lib/tablet-resources.jar + java-pkg_dojar lib/flamingo.jar + java-pkg_dojar lib/scri-commons.jar + java-pkg_dojar lib/samtools*.jar + java-pkg_dojar lib/picard*.jar + java-pkg_dojar lib/sqlite-jdbc*.jar echo "PATH=${EPREFIX}/usr/share/${PN}/" > 99Tablet doenvd 99Tablet diff --git a/sci-biology/tablet/tablet-1.16.09.06.ebuild b/sci-biology/tablet/tablet-1.16.09.06.ebuild index c4be1406f..f90f09bfb 100644 --- a/sci-biology/tablet/tablet-1.16.09.06.ebuild +++ b/sci-biology/tablet/tablet-1.16.09.06.ebuild @@ -18,7 +18,7 @@ if [ "$PV" == "9999" ]; then KEYWORDS="" else ESVN_REPO_URI="http://ics.hutton.ac.uk/svn/tablet/tags/${PV}" - KEYWORDS="" + KEYWORDS="~amd64 ~x86" fi LICENSE="Tablet" @@ -30,19 +30,22 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}" DEPEND="${PYTHON_DEPS} >=virtual/jdk-1.8:*" RDEPEND="${PYTHON_DEPS} - >=virtual/jre-1.8:* - sci-biology/samtools - sci-biology/picard - dev-db/sqlite:3" + >=virtual/jre-1.8:*" +# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar +# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not sci-biology/samtools either +# replacing picard.jar with a symlink to picard.jar from sci-biology.picard does not help either S="${WORKDIR}" src_install() { - java-pkg_dojar lib/tablet-resources.jar java-pkg_dojar lib/tablet.jar + java-pkg_dolauncher ${PN} + java-pkg_dojar lib/tablet-resources.jar java-pkg_dojar lib/flamingo.jar java-pkg_dojar lib/scri-commons.jar java-pkg_dojar lib/samtools*.jar + java-pkg_dojar lib/picard*.jar # is picard-1.113 in tablet-1.16.09.06 + java-pkg_dojar lib/sqlite-jdbc*.jar echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet doenvd 99Tablet diff --git a/sci-biology/tablet/tablet-9999.ebuild b/sci-biology/tablet/tablet-9999.ebuild index f5846c8ef..f137ea9ad 100644 --- a/sci-biology/tablet/tablet-9999.ebuild +++ b/sci-biology/tablet/tablet-9999.ebuild @@ -30,19 +30,22 @@ REQUIRED_USE="${PYTHON_REQUIRED_USE}" DEPEND="${PYTHON_DEPS} >=virtual/jdk-1.8:*" RDEPEND="${PYTHON_DEPS} - >=virtual/jre-1.8:* - sci-biology/samtools - sci-biology/picard - dev-db/sqlite:3" + >=virtual/jre-1.8:*" +# contains bundled sqlite-jdbc-3.8.6.jar, samtools-linux64.jar, picard.jar +# sqlite-jdbc-3.8.6.jar is not dev-db/sqlite:3 and samtools-linux64.jar is not sci-biology/samtools either +# replacing picard.jar with a symlink to picard.jar from sci-biology.picard does not help either S="${WORKDIR}" src_install() { - java-pkg_dojar lib/tablet-resources.jar java-pkg_dojar lib/tablet.jar + java-pkg_dolauncher ${PN} + java-pkg_dojar lib/tablet-resources.jar java-pkg_dojar lib/flamingo.jar java-pkg_dojar lib/scri-commons.jar java-pkg_dojar lib/samtools*.jar + java-pkg_dojar lib/picard*.jar + java-pkg_dojar lib/sqlite-jdbc*.jar echo "PATH=${EPREFIX}/usr/share/${PN}" > 99Tablet doenvd 99Tablet |