156 lines
6.2 KiB
Makefile
156 lines
6.2 KiB
Makefile
# $NetBSD$
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#
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###########################################################
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# Generated by fbsd2pkg #
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# Fri Sep 14 20:48:17 CDT 2018 #
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###########################################################
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###########################################################
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# Unconverted and partially converted FreeBSD port syntax:
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# Trinity core programs: Inchworm, Chrysalis, Butterfly
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# Bundled plugins: Trinity is very sensitive to having the correct versions
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# of some of these. Test thoroughly if you change any of them.
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# To-do:
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# Unbundle collectl (low priority)
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## Should work on other 64-bit archs, but untested
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#ONLY_FOR_ARCH= amd64
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# Should salmon use bl3?
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# bowtie should not have bl3
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DEPENDS= coreutils>=0:../../sysutils/coreutils
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DEPENDS+= slclust>=0.0.0.20100202:../../wip/slclust
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DEPENDS+= salmon>=0.11.3:../../wip/salmon
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DEPENDS+= bowtie>=1.1.2:../../wip/bowtie
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DEPENDS+= bowtie2>=2.3.4.2:../../wip/bowtie2
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DEPENDS+= samtools>=1.9:../../wip/samtools
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DEPENDS+= jellyfish>=2.2.10:../../wip/jellyfish2
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DEPENDS+= parafly>=2013.01.21:../../wip/parafly
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DEPENDS+= fastool>=0.1.4:../../wip/fastool
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DEPENDS+= p5-transdecoder>=5.3.0:../../wip/p5-transdecoder
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DEPENDS+= Trimmomatic>=0.38:../../wip/trimmomatic
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DEPENDS+= rsem>=1.2.30:../../wip/rsem
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DEPENDS+= ncbi-blast+>=2.7.1:../../biology/ncbi-blast+
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DISTNAME= trinity-${PV}
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CATEGORIES= biology
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MASTER_SITES= ${MASTER_SITE_GITHUB:=trinityrnaseq/}
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GITHUB_PROJECT= trinityrnaseq
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GITHUB_TAG= Trinity-v${PV}
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MAINTAINER= bacon@NetBSD.org
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HOMEPAGE= https://trinityrnaseq.github.io/
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COMMENT= Assembles transcript sequences from Illumina RNA-Seq data
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LICENSE= modified-bsd
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USE_LANGUAGES= c c++
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USE_JAVA= run
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USE_TOOLS+= bash cmake gmake pax perl
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REPLACE_BASH= util/*/*.sh
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REPLACE_BASH+= util/*/*/*.sh
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REPLACE_BASH+= Analysis/*/*/*.sh
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REPLACE_PERL= Trinity util/misc/Monarch
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REPLACE_PERL+= util/*.pl util/*/*.pl util/*/*/*.pl util/*/*/*/*.pl
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REPLACE_PERL+= Chrysalis/analysis/*.pl
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REPLACE_PERL+= Analysis/*/*.pl Analysis/*/*/*.pl Analysis/*/*/*/*.pl
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REPLACE_PERL+= Analysis/*/*.cgi Analysis/*/PtR
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REPLACE_PERL+= PerlLib/*.pm PerlLib/*/*.pm PerlLib/*.ph PerlLib/*.pl
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REPLACE_PYTHON= util/support_scripts/trinity_installer.py
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REPLACE_PYTHON+= util/misc/alt_GG_read_partitioning_JCornish/genwig2.py
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REPLACE_PYTHON+= util/misc/sim_test_framework/run_Trinity_eval.sh
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REPLACE_PYTHON+= util/misc/TPM_weighted_gene_length.py
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REPLACE_PYTHON+= Analysis/SuperTranscripts/*.py
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REPLACE_PYTHON+= Analysis/SuperTranscripts/*/*.py
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REPLACE_RSCRIPT+= Analysis/*/*.Rscript
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REPLACE_RSCRIPT+= util/misc/*.Rscript
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SUBST_CLASSES+= paths
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SUBST_STAGE.paths= post-patch
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SUBST_SED.paths+= -e 's|$$FindBin::Bin|$$FindBin::Bin/../libexec/trinity|g'
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SUBST_SED.paths+= -e 's|$$FindBin::RealBin|$$FindBin::RealBin/../libexec/trinity|g'
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SUBST_SED.paths+= -e 's|$$ROOTDIR/trinity-plugins/BIN/ParaFly|ParaFly|g'
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SUBST_SED.paths+= -e 's|$$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar|${JAVAJARDIR}/trimmomatic.jar|g'
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SUBST_SED.paths+= -e 's|$$ROOTDIR/trinity-plugins/Trimmomatic|${PREFIX}/share/Trimmomatic|g'
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SUBST_FILES.paths+= ${WRKSRC}/Trinity
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SUBST_CLASSES+= jelly
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SUBST_STAGE.jelly= post-patch
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SUBST_SED.jelly+= -e 's|$$JELLYFISH_DIR/bin/jellyfish|jellyfish|g'
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SUBST_FILES.jelly+= ${WRKSRC}/util/misc/run_jellyfish.pl
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SUBST_CLASSES+= trimmo
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SUBST_STAGE.trimmo= post-patch
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SUBST_SED.trimmo+= -e 's|$$FindBin::RealBin/../../trinity-plugins/Trimmomatic/trimmomatic.jar|${JAVAJARDIR}/trimmomatic.jar|g'
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SUBST_SED.trimmo+= -e 's|/seq/regev_genome_portal/SOFTWARE/BIN/trimmomatic.jar|${JAVAJARDIR}/trimmomatic.jar|g'
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SUBST_FILES.trimmo+= ${WRKSRC}/util/misc/run_trimmomatic_qual_trimming.pl
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SUBST_CLASSES+= rpath
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SUBST_STAGE.rpath= post-patch
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SUBST_SED.rpath+= -e "s|-lm -pthread|-lm -pthread -Wl,-rpath=${_GCC_RUNTIME}|g"
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SUBST_FILES.rpath+= ${WRKSRC}/Chrysalis/Makefile
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SUBST_CLASSES+= trinity
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SUBST_STAGE.trinity= post-patch
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SUBST_SED.trinity+= -e 's|$$FindBin::Bin/../../Trinity|Trinity|g'
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SUBST_FILES.trinity+= ${WRKSRC}/util/support_scripts/write_partitioned_trinity_cmds.pl
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SUBST_CLASSES+= build
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SUBST_STAGE.build= post-build
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SUBST_SED.build+= -e "s|/usr/bin/perl|${PREFIX}/bin/perl|g"
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SUBST_FILES.build+= ${WRKSRC}/trinity-plugins/COLLECTL/collectl/collectl
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SUBST_FILES.build+= ${WRKSRC}/trinity-plugins/COLLECTL/collectl/*.pl
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CFLAGS+= -fopenmp
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CXXFLAGS= -fopenmp
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PV= 2.8.3
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EXAMPLESDIR= ${PREFIX}/share/examples/trinity
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LIBEXEC_DIR= ${PREFIX}/libexec/trinity
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PLUGINS_DIR= ${LIBEXEC_DIR}/trinity-plugins
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REPLACE_INTERPRETER+= Rscript
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REPLACE.Rscript.old= .*Rscript
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REPLACE.Rscript.new= ${PREFIX}/bin/Rscript
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REPLACE_FILES.Rscript= ${REPLACE_RSCRIPT}
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# Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
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# .include "../../mk/bsd.prefs.mk"
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INSTALLATION_DIRS= bin libexec/trinity/Chrysalis/bin libexec/trinity/Inchworm/bin libexec/trinity/Butterfly libexec/trinity/trinity-plugins/scaffold_iworm_contigs libexec/trinity/trinity-plugins/BIN share/examples
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post-extract:
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${CHMOD} -R g-w ${WRKSRC}
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# FIXME: More may need to be installed
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do-install:
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${INSTALL_SCRIPT} ${WRKSRC}/Trinity ${DESTDIR}${PREFIX}/bin
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${INSTALL_PROGRAM} ${WRKSRC}/Chrysalis/bin/* \
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${DESTDIR}${LIBEXEC_DIR}/Chrysalis/bin
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${INSTALL_SCRIPT} ${WRKSRC}/Chrysalis/analysis/ReadsToComponents.pl \
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${DESTDIR}${LIBEXEC_DIR}/Chrysalis/bin
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${INSTALL_PROGRAM} ${WRKSRC}/Inchworm/bin/* \
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${DESTDIR}${LIBEXEC_DIR}/Inchworm/bin
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${INSTALL_SCRIPT} ${WRKSRC}/Butterfly/Butterfly.jar \
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${DESTDIR}${LIBEXEC_DIR}/Butterfly
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cd ${WRKSRC} && pax -rw PerlLib \
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${DESTDIR}${LIBEXEC_DIR}
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cd ${WRKSRC} && pax -rw util \
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${DESTDIR}${LIBEXEC_DIR}
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cd ${WRKSRC} && pax -rw Analysis \
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${DESTDIR}${LIBEXEC_DIR}
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${INSTALL_PROGRAM} ${WRKSRC}/trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs \
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${DESTDIR}${PLUGINS_DIR}/scaffold_iworm_contigs
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${INSTALL_PROGRAM} ${WRKSRC}/trinity-plugins/BIN/seqtk-trinity \
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${DESTDIR}${PLUGINS_DIR}/BIN
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cd ${WRKSRC}/sample_data && pax -rw * \
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${DESTDIR}${EXAMPLESDIR}
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${LN} -fs ${PREFIX}/bin/Trinity \
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${DESTDIR}${PREFIX}/libexec/trinity/Trinity
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${RM} ${DESTDIR}${PREFIX}/libexec/trinity/util/support_scripts/plugin_install_tests.sh.orig
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.include "../../lang/python/application.mk"
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.include "../../wip/htslib/buildlink3.mk"
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.include "../../devel/zlib/buildlink3.mk"
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.include "../../mk/bsd.pkg.mk"
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