commit: 7f5edd6bb6505ec292bf540e7ad1b34fbe9ec59a Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> AuthorDate: Tue Jan 25 10:19:22 2022 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org> CommitDate: Tue Jan 25 10:19:22 2022 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7f5edd6b
sci-biology/trinityrnaseq: bump to 2.1.3.2 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org> .../trinityrnaseq/trinityrnaseq-2.11.0.ebuild | 70 ---------------------- .../trinityrnaseq/trinityrnaseq-2.13.2.ebuild | 45 ++++++++++++++ 2 files changed, 45 insertions(+), 70 deletions(-) diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild deleted file mode 100644 index 9ecaf24f2..000000000 --- a/sci-biology/trinityrnaseq/trinityrnaseq-2.11.0.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit perl-module - -# 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="https://github.com/Trinotate/Trinotate.github.io/wiki"; -SRC_URI="https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v${PV}/${PN}-v${PV}.FULL_with_extendedTestData.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD-BroadInstitute" -SLOT="0" -KEYWORDS="" # PERL5INC path is wrong when /usr/bin/Trinity is executed - -DEPEND="" -RDEPEND="${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="${WORKDIR}/${PN}-v${PV}" - -PATCHES=( - "${FILESDIR}/${PN}-2.11.0-fix-compilation.patch" -) - -src_compile(){ - emake all - emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly -} - -src_install(){ - dodoc Chrysalis/chrysalis.notes - dodoc Changelog.txt - perl_set_version - dobin Trinity - perl_domodule util/*.pl - dobin Inchworm/bin/* - cd Chrysalis/bin || die - dobin BubbleUpClustering Chrysalis CreateIwormFastaBundle GraphFromFasta QuantifyGraph ReadsToTranscripts - cd ../../util/R || die - insinto /usr/share/"${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 - perl_domodule util/misc/PerlLib/*.pm PerlLib/*.pm - perl_domodule PerlLib/KmerGraphLib/*.pm - perl_domodule PerlLib/CDNA/*.pm - perl_domodule PerlLib/Simulate/*.pm - perl_domodule PerlLib/CanvasXpress/*.pm - chmod a+rx -R "${ED}/${VENDOR_LIB}/${PN}" -} diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild new file mode 100644 index 000000000..3b94d9713 --- /dev/null +++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.13.2.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit perl-module + +DESCRIPTION="Transcriptome assembler for RNA-seq reads" +HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki"; +SRC_URI="https://github.com/${PN}/${PN}/releases/download/Trinity-v${PV}/${PN}-v${PV}.FULL_with_extendedTestData.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${PN}-v${PV}" + +LICENSE="BSD-BroadInstitute" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND="" +RDEPEND="${DEPEND} + sci-biology/parafly + >=sci-biology/jellyfish-2.2.6:2 + >=sci-libs/htslib-1.2.1 + >=sci-biology/samtools-1.3:0 + >=sci-biology/trimmomatic-0.36 + >=sci-biology/GAL-0.2.1 + dev-perl/IO-All + sci-biology/seqtools +" + +PATCHES=( + "${FILESDIR}/${PN}-2.11.0-fix-compilation.patch" +) + +src_compile(){ + # missing submodule for bamsifter + emake no_bamsifter + emake plugins +} + +src_install(){ + # fix the install path + sed -e "s:/usr/local/bin:${ED}/usr/bin:g" \ + -i util/support_scripts/trinity_installer.py || die + dodir /usr/bin + default +}
