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authorMartin Mokrejs <mmokrejs@fold.natur.cuni.cz>2018-04-21 20:53:23 +0200
committerMartin Mokrejs <mmokrejs@fold.natur.cuni.cz>2018-04-21 20:53:23 +0200
commit2dffd7378f16086d11d32432d30d0325d40d3238 (patch)
tree2370b7c4ff1903c9b978cbcb7cb0959c4445504a
parentsci-biology/salmon: document install procedure issues (diff)
downloadsci-2dffd7378f16086d11d32432d30d0325d40d3238.tar.gz
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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/Manifest1
-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.patch23
-rw-r--r--sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild4
-rw-r--r--sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild4
-rw-r--r--sci-biology/trinityrnaseq/trinityrnaseq-2.2.0.ebuild4
-rw-r--r--sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild76
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}"
+}