sci-biology/trinityrnaseq: version bump but dropping KEYWORDS because we relocate *.pm file into vendor_perl and all 'use blah' calls to trinity-provided perl modules need to be changed to 'use trinityrnaseq::blah', or PERL5INC modified?

Package-Manager: portage-2.2.18

4 files changed, 105 insertions, 0 deletions

diff --git a/sci-biology/trinityrnaseq/ChangeLog b/sci-biology/trinityrnaseq/ChangeLog
index 0376bce0e..405ac839c 100644
--- a/sci-biology/trinityrnaseq/ChangeLog
+++ b/sci-biology/trinityrnaseq/ChangeLog
@@ -2,6 +2,15 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+*trinityrnaseq-2.1.1 (20 Nov 2015)
+
+  20 Nov 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +files/disable_some_plugins.patch, +trinityrnaseq-2.1.1.ebuild:
+  sci-biology/trinityrnaseq: version bump but dropping KEYWORDS because we
+  relocate *.pm file into vendor_perl and all 'use blah' calls to trinity-
+  provided perl modules need to be changed to 'use trinityrnaseq::blah', or
+  PERL5INC modified?
+
   06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
   sci-biology/trinityrnaseq: Add github to remote-id in metadata.xml
 
diff --git a/sci-biology/trinityrnaseq/Manifest b/sci-biology/trinityrnaseq/Manifest
index 654ee86b6..c6e18e680 100644
--- a/sci-biology/trinityrnaseq/Manifest
+++ b/sci-biology/trinityrnaseq/Manifest
@@ -1 +1,2 @@
 DIST trinityrnaseq-2.0.6.tar.gz 158619106 SHA256 e0c3ec885fdcfe3422ea492372518ddf5d1aed3daa187c69c4254516b0845de1 SHA512 459461db38e42d0b77b9cb84b1ecc4ccb03bbe0fe6e970915d5df58e8c98368a07fab7a157679b0d4247b729b49966b1f3927abee11059e5e3a3406e8e598d45 WHIRLPOOL 040926ab4d1a157c340cf5886bc4cf2846e8756d84c39a1f8673b5ba59dd57b39f075b0fc915deff05dd50655b0e8f0c1b8fe3b6ceb0e0a4b2aec618bef58470
+DIST trinityrnaseq-2.1.1.tar.gz 137541420 SHA256 012ccb42e1eab8a5b14c4e78becf3e7e69964d76c17fcca8110db6ffe63d3e0b SHA512 36b67211902871c6dbba31a074c4e92d2e925c57fe54bf59418874282e283693d2d9b4e14333385a7adcef3edbf928bc1001df105b56412841662c45a9a74f3f WHIRLPOOL 73869a3f2dbc72011723429d6ac3acb3fde8c7ccfe4122510afbea9fdfc732a457c8f5d16573190448c4e0d2c5dcc437e2f9cfe96f4239368c95b2da79fd52bd
diff --git a/sci-biology/trinityrnaseq/files/disable_some_plugins.patch b/sci-biology/trinityrnaseq/files/disable_some_plugins.patch
new file mode 100644
index 000000000..43a06ae53
--- /dev/null
+++ b/sci-biology/trinityrnaseq/files/disable_some_plugins.patch
@@ -0,0 +1,20 @@
+--- trinityrnaseq-2.1.1/trinity-plugins/Makefile.ori	2015-11-21 00:34:52.310075544 +0100
++++ trinityrnaseq-2.1.1/trinity-plugins/Makefile	2015-11-21 00:37:16.260075920 +0100
+@@ -10,7 +10,7 @@
+ PARAFLY_CODE=parafly-code
+ TRIMMOMATIC_CODE=Trimmomatic-0.32
+ 
+-trinity_essentials: jellyfish scaffold_iworm_contigs_target fastool_target parafly_target trimmomatic_target samtools
++trinity_essentials: scaffold_iworm_contigs_target fastool_target parafly_target
+ 
+ trimmomatic_target:
+ 	ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
+@@ -31,7 +31,7 @@
+ #	cd htslib-1.2.1 && ./configure && $(MAKE)
+ 	tar xvf ${HTSLIB_CODE} && cd htslib && $(MAKE)
+ 
+-scaffold_iworm_contigs_target: htslib_target
++scaffold_iworm_contigs_target:
+ 	cd scaffold_iworm_contigs && $(MAKE)
+ 
+ fastool_target:
diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
new file mode 100644
index 000000000..0d5ba5346
--- /dev/null
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.1.1.ebuild
@@ -0,0 +1,75 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+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/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD-BroadInstitute"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	sci-biology/parafly
+	=sci-biology/jellyfish-2.1.4
+	>=sci-libs/htslib-1.2.1
+	<=sci-biology/samtools-1.1
+	>=sci-biology/trimmomatic-0.32
+	dev-perl/IO-All"
+# ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed
+# version of bundled jellyfish is 2.1.4
+# version of bundled samtools is 0.1.19
+# version of bundled htslib is 1.2.1
+# version of bundled GAL is 0.2.1
+# version of bundled trimmomatic is 0.32
+
+# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases
+
+src_prepare(){
+	epatch "${FILESDIR}"/disable_some_plugins.patch
+}
+
+#src_compile(){
+#	emake all
+#	emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly
+#}
+
+src_install(){
+	perl_set_version
+	dobin Trinity util/*.pl trinity-plugins/GAL_0.2.1/fasta_tool
+	# should become a new package depending on dev-perl/IO-All
+	dobin trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool
+	dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md
+	#
+	insinto /usr/share/"${PN}"/util
+	rm -f util/fasta_tool
+	doins -r util/*
+	#
+	dobin Inchworm/bin/*
+	cd Chrysalis
+	dobin MakeDepend checkLock BreakTransByPairs Chrysalis GraphFromFasta IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts RunButterfly TranscriptomeFromVaryK analysis/ReadsToComponents.pl
+	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}/${PN}"/HPC
+	doins PerlLib/HPC/*.pm
+	insinto "${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}"
+}