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author | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2018-04-21 20:53:23 +0200 |
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committer | Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> | 2018-04-21 20:53:23 +0200 |
commit | 2dffd7378f16086d11d32432d30d0325d40d3238 (patch) | |
tree | 2370b7c4ff1903c9b978cbcb7cb0959c4445504a | |
parent | sci-biology/salmon: document install procedure issues (diff) | |
download | sci-2dffd7378f16086d11d32432d30d0325d40d3238.tar.gz sci-2dffd7378f16086d11d32432d30d0325d40d3238.tar.bz2 sci-2dffd7378f16086d11d32432d30d0325d40d3238.zip |
sci-biology/trinityrnaseq: version bump (no KEYWORDS set)
The perl include paths are not matching the paths in *.pm files
all *.pm need to be patched so that they could be placed into
site_perl subdirectory.
In brief, the package still does not support installation into
a site-wide directory. users are supposed to executed off the
unpacked tarball directly.
Package-Manager: Portage-2.3.28, Repoman-2.3.9
-rw-r--r-- | sci-biology/trinityrnaseq/Manifest | 1 | ||||
-rw-r--r-- | sci-biology/trinityrnaseq/files/trinityrnaseq-2.1.1-disable_some_plugins.patch (renamed from sci-biology/trinityrnaseq/files/disable_some_plugins.patch) | 0 | ||||
-rw-r--r-- | sci-biology/trinityrnaseq/files/trinityrnaseq-2.6.6-disable_some_plugins.patch | 23 | ||||
-rw-r--r-- | sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild | 4 | ||||
-rw-r--r-- | sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild | 4 | ||||
-rw-r--r-- | sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild | 4 | ||||
-rw-r--r-- | sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild | 76 |
7 files changed, 106 insertions, 6 deletions
diff --git a/sci-biology/trinityrnaseq/Manifest b/sci-biology/trinityrnaseq/Manifest index 3dab0eef6..c8bda9d39 100644 --- a/sci-biology/trinityrnaseq/Manifest +++ b/sci-biology/trinityrnaseq/Manifest @@ -1,3 +1,4 @@ DIST trinityrnaseq-2.0.6.tar.gz 158619106 BLAKE2B 9be82099f8c563ac6520462feffcdcb1d0cec7fde4b5d3a430abde987bc419f6011642c1a2548de27734493ac8728e9c24d8a67bd8201108a9b1e26020aca2d6 SHA512 459461db38e42d0b77b9cb84b1ecc4ccb03bbe0fe6e970915d5df58e8c98368a07fab7a157679b0d4247b729b49966b1f3927abee11059e5e3a3406e8e598d45 DIST trinityrnaseq-2.1.1.tar.gz 137541420 SHA256 012ccb42e1eab8a5b14c4e78becf3e7e69964d76c17fcca8110db6ffe63d3e0b SHA512 36b67211902871c6dbba31a074c4e92d2e925c57fe54bf59418874282e283693d2d9b4e14333385a7adcef3edbf928bc1001df105b56412841662c45a9a74f3f WHIRLPOOL 73869a3f2dbc72011723429d6ac3acb3fde8c7ccfe4122510afbea9fdfc732a457c8f5d16573190448c4e0d2c5dcc437e2f9cfe96f4239368c95b2da79fd52bd DIST trinityrnaseq-2.2.0.tar.gz 174159736 SHA256 f34603e56ac76a81447dd230b31248d5890ecffee8ef264104d4f1fa7fe46c9e SHA512 87ba299df990d066ae6aa8a870c3a27647da0d78cf0a48c5084967865d4e278ce383b3f6e54541d4626654f0638f12c739aaed04ed770bc99ed84b94c2e6e5c3 WHIRLPOOL 027ccd958288991c4871cfa6b370d14bc2bf586bc1ffc3247795aaf305368caac373343682f11cde6d72a65422c95718b89fee65ac77c04a21c7c3aaa4c8112d +DIST trinityrnaseq-2.6.6.tar.gz 21796945 BLAKE2B 0d5ff2d7e2ba11d231695c19e0125d507a5f510a944fc3ab68c3e5073b6bb4ef0973bc02b207b79ea6adbc58a469eeb894610bd765c11ccf3963deaeebe3ff00 SHA512 2e4438010cc987706b8f7dd343cdd84024318f2e7370bce40be6d54b07b17bfd6a4a28c27400250384e4ffd560386fde3b9c51987f86b376e11c4daa10d6b7cb diff --git a/sci-biology/trinityrnaseq/files/disable_some_plugins.patch b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.1.1-disable_some_plugins.patch index 43a06ae53..43a06ae53 100644 --- a/sci-biology/trinityrnaseq/files/disable_some_plugins.patch +++ b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.1.1-disable_some_plugins.patch diff --git a/sci-biology/trinityrnaseq/files/trinityrnaseq-2.6.6-disable_some_plugins.patch b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.6.6-disable_some_plugins.patch new file mode 100644 index 000000000..02f4d5d8a --- /dev/null +++ b/sci-biology/trinityrnaseq/files/trinityrnaseq-2.6.6-disable_some_plugins.patch @@ -0,0 +1,23 @@ +--- trinity-plugins/Makefile 2018-04-21 20:01:58.389880915 +0200 ++++ trinity-plugins/Makefile 2018-04-21 20:03:31.752684954 +0200 +@@ -7,7 +7,7 @@ + + + +-trinity_essentials: seqtk_target parafly_target trimmomatic_target ++trinity_essentials: parafly_target + + trimmomatic_target: + ln -sf ${TRIMMOMATIC_CODE} Trimmomatic +@@ -39,11 +39,9 @@ + cd COLLECTL && tar xvf ${COLLECTL_CODE}.src.tar.gz && ln -sf ${COLLECTL_CODE} collectl + + clean: +- rm -rf ./seqtk-trinity-0.0.2 + cd scaffold_iworm_contigs && $(MAKE) clean + cd parafly-code && $(MAKE) clean + rm -f ./parafly # rm symlink +- rm -f ./Trimmomatic # rm symlink + cd slclust && $(MAKE) clean + cd COLLECTL && rm -rf ${COLLECTL_CODE} && rm -f collectl + @echo "\n\n** Done cleaning plugins area **" diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild index 95a9ae58d..1941db22a 100644 --- a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild +++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2018 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -21,7 +21,7 @@ IUSE="" DEPEND="" RDEPEND="${DEPEND} sci-biology/parafly - >=sci-biology/jellyfish-2.1.4 + >=sci-biology/jellyfish-2.1.4:2 sci-biology/samtools:0.1-legacy >=sci-biology/GAL-0.2.1 dev-perl/IO-All" diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild index 952d3a41a..8f131cb17 100644 --- a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild +++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2018 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -20,7 +20,7 @@ IUSE="" DEPEND="" RDEPEND="${DEPEND} sci-biology/parafly - >=sci-biology/jellyfish-2.1.4 + >=sci-biology/jellyfish-2.1.4:2 >=sci-libs/htslib-1.2.1 sci-biology/samtools:0.1-legacy >=sci-biology/trimmomatic-0.32 diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild index a6692a0ec..19085d752 100644 --- a/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild +++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2018 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -20,7 +20,7 @@ IUSE="" DEPEND="" RDEPEND="${DEPEND} sci-biology/parafly - >=sci-biology/jellyfish-2.1.4 + >=sci-biology/jellyfish-2.1.4:2 >=sci-libs/htslib-1.2.1 sci-biology/samtools:0.1-legacy >=sci-biology/trimmomatic-0.32 diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild new file mode 100644 index 000000000..238766eed --- /dev/null +++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild @@ -0,0 +1,76 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +# Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software ... + +DESCRIPTION="Transcriptome assembler for RNA-seq reads" +HOMEPAGE="http://trinityrnaseq.github.io/" +SRC_URI="https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD-BroadInstitute" +SLOT="0" +KEYWORDS="" # PERL5INC path is wrong when /usr/bin/Trinity is executed +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + sci-biology/parafly + >=sci-biology/jellyfish-2.2.6:2 + >=sci-libs/htslib-1.2.1 + >=sci-biology/samtools-1.3:0 + >=sci-biology/trimmomatic-0.36 + >=sci-biology/GAL-0.2.1 + dev-perl/IO-All + sci-biology/seqtools" +# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases +# has the following "plugins" (aka bundled 3rd-party code) +# slclust +# DEXseq_util +# COLLECTL +# ParaFly-0.1.0 + +S="${WORKDIR}"/trinityrnaseq-Trinity-v"${PV}" + +src_prepare(){ + epatch "${FILESDIR}"/"${P}"-disable_some_plugins.patch +} + +#src_compile(){ +# emake all +# emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly +#} + +src_install(){ + dodoc Chrysalis/chrysalis.notes + dodoc Changelog.txt + perl_set_version + dobin Trinity util/*.pl + dobin Inchworm/bin/* + cd Chrysalis || die + dobin MakeDepend checkLock BreakTransByPairs BubbleUpClustering Chrysalis CreateIwormFastaBundle GraphFromFasta GraphFromFasta_MPI IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts ReadsToTranscripts_MPI ReadsToTranscripts_MPI_chang RunButterfly TranscriptomeFromVaryK analysis/ReadsToComponents.pl + cd ../util/R || die + insinto /usr/share/"${PN}"/R + doins *.R + cd ../PBS || die + insinto /usr/share/"${PN}"/PBS + doins * + cd .. || die + cp -rp support_scripts misc "${ED}"/usr/share/"${PN}"/ || die + cd "${S}" || die + insinto "${VENDOR_LIB}/${PN}" + doins util/misc/PerlLib/*.pm PerlLib/*.pm + insinto "${VENDOR_LIB}/${PN}"/KmerGraphLib + doins PerlLib/KmerGraphLib/*.pm + insinto "${VENDOR_LIB}/${PN}"/CDNA + doins PerlLib/CDNA/*.pm + insinto "${VENDOR_LIB}/${PN}"/Simulate + doins PerlLib/Simulate/*.pm + insinto "${VENDOR_LIB}/${PN}"/CanvasXpress + doins PerlLib/CanvasXpress/*.pm + chmod a+rx -R "${ED}/${VENDOR_LIB}/${PN}" +} |