trinity: Remove following successful test of trinity-devel

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: trinity: Remove following successful test of trinity-devel
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Sat, 22 Sep 2018 14:50:03 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat Sep 22 09:50:03 2018 -0500
Changeset:	1445c6cef9c7cd28e3b6a8e4e6243a15d1797e4b

Modified Files:
	Makefile
Removed Files:
	trinity/DESCR
	trinity/Makefile
	trinity/PLIST
	trinity/TODO
	trinity/distinfo
	trinity/patches/patch-Makefile
	trinity/patches/patch-PerlLib_HPC_SLURM__handler.pm
	trinity/patches/patch-trinity-plugins_Makefile
	trinity/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile

Log Message:
trinity: Remove following successful test of trinity-devel

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=1445c6cef9c7cd28e3b6a8e4e6243a15d1797e4b

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                                           |   1 -
 trinity/DESCR                                      |   4 -
 trinity/Makefile                                   | 202 --------
 trinity/PLIST                                      | 577 ---------------------
 trinity/TODO                                       |   1 -
 trinity/distinfo                                   |  10 -
 trinity/patches/patch-Makefile                     |  14 -
 .../patches/patch-PerlLib_HPC_SLURM__handler.pm    |  28 -
 trinity/patches/patch-trinity-plugins_Makefile     |  42 --
 ...inity-plugins_scaffold__iworm__contigs_Makefile |  18 -
 10 files changed, 897 deletions(-)

diffs:
diff --git a/Makefile b/Makefile
index b4aa1bb924..10abcc4949 100644
--- a/Makefile
+++ b/Makefile
@@ -4541,7 +4541,6 @@ SUBDIR+=	triangle
 SUBDIR+=	triforce-afl
 SUBDIR+=	trimadap
 SUBDIR+=	trimmomatic
-SUBDIR+=	trinity
 SUBDIR+=	trinity-devel
 SUBDIR+=	tripwire2
 SUBDIR+=	truecrypt
diff --git a/trinity/DESCR b/trinity/DESCR
deleted file mode 100644
index 7752b73aa7..0000000000
--- a/trinity/DESCR
+++ /dev/null
@@ -1,4 +0,0 @@
-Trinity represents a novel method for the efficient and robust de novo
-reconstruction of transcriptomes from RNA-seq data.  Trinity combines three
-independent software modules: Inchworm, Chrysalis, and Butterfly, applied
-sequentially to process large volumes of RNA-seq reads.
diff --git a/trinity/Makefile b/trinity/Makefile
deleted file mode 100644
index 4ec9e0cafb..0000000000
--- a/trinity/Makefile
+++ /dev/null
@@ -1,202 +0,0 @@
-# $NetBSD$
-#
-###########################################################
-#               Generated by fbsd2pkg                     #
-###########################################################
-
-# To-do:
-#	Unbundle collectl (low priority)
-
-# Trinity core programs: Inchworm, Chrysalis, Butterfly
-# Bundled plugins: Trinity is very sensitive to having the correct versions
-# of some of these.  Test thoroughly if you change any of them.
-# collectl 3.7.4
-# samtools 0.1.19 (must use this version: 1.x does not work well)
-# jellyfish 2.1.4 (2.2.0 seems OK)
-# parafly 0.1 (determined from config.h)
-# fastool 7c3e034f05 Nov 18 2013 commit on Github
-# htslib 1.2.1
-# slclust unknown (last version on SF is 02022010)
-# Trimmomatic 0.32
-
-###########################################################
-# Unconverted and partially converted FreeBSD port syntax:
-
-#USE_JAVA=	yes
-#JAVA_VERSION=	1.7 1.6
-#		slclust:/usr/wip/biology/slclust
-
-DEPENDS+=	coreutils>=0:../../sysutils/coreutils
-DEPENDS+=	bowtie<2:../../wip/bowtie
-DEPENDS+=	bowtie2>=2:../../wip/bowtie2
-DEPENDS+=	jellyfish>=2.1.4:../../wip/jellyfish2
-DEPENDS+=	parafly>=0:../../wip/parafly
-DEPENDS+=	fastool>=0:../../wip/fastool
-DEPENDS+=	p5-transdecoder>=0:../../wip/p5-transdecoder
-DEPENDS+=	Trimmomatic>=0.32:../../wip/trimmomatic
-DEPENDS+=	rsem>=1.2.30:../../wip/rsem
-DEPENDS+=	slclust>=0:../../wip/slclust
-DEPENDS+=	samtools>=1.3:../../wip/samtools
-
-DISTNAME=	trinity-${PORTVERSION}
-CATEGORIES=	biology
-MASTER_SITES=	${MASTER_SITE_GITHUB:=trinityrnaseq/}
-GITHUB_PROJECT=	trinityrnaseq
-GITHUB_TAG=	v${PORTVERSION}
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	http://trinityrnaseq.github.io/
-COMMENT=	Trinity assembles transcript sequences from Illumina RNA-Seq data
-
-DEPENDS+=	dos2unix>=0:../../converters/dos2unix
-
-# Check this
-LICENSE=	modified-bsd
-
-# Test and change if necessary.
-# MAKE_JOBS_SAFE=	no
-
-ONLY_FOR_PLATFORM=	*-*-x86_64
-
-SUBST_CLASSES+=		env
-SUBST_STAGE.env=	post-patch
-SUBST_SED.env+=		-e "s|gcc|${CC}|g"
-SUBST_SED.env+=		-e "s|g++|${CXX}|g"
-SUBST_FILES.env+=	${WRKSRC}/Chrysalis/Makefile*
-SUBST_FILES.env+=	${WRKSRC}/trinity-plugins/fstrozzi-Fastool-7c3e034f05/Makefile
-SUBST_FILES.env+=	${WRKSRC}/trinity-plugins/slclust/src/Makefile
-
-SUBST_CLASSES+=		collectl
-SUBST_STAGE.collectl=	post-patch
-SUBST_SED.collectl+=	-e 's|make |${MAKE} |g'
-SUBST_FILES.collectl+=	${WRKSRC}/trinity-plugins/collectl/build_collectl.sh
-
-SUBST_CLASSES+=		path
-SUBST_STAGE.path=	post-patch
-SUBST_SED.path+=	-e 's|$$FindBin::Bin|$$FindBin::Bin/../libexec/trinity|g'
-SUBST_SED.path+=	-e 's|$$FindBin::RealBin|$$FindBin::RealBin/../libexec/trinity|g'
-SUBST_SED.path+=	-e 's|$$ROOTDIR/trinity-plugins/BIN|&:$$JELLYFISH_DIR/bin:$$FASTOOL_DIR|g'
-SUBST_SED.path+=	-e 's|$$JELLYFISH_DIR/bin/jellyfish|jellyfish|g'
-SUBST_SED.path+=	-e 's|$$FASTOOL_DIR/fastool|fastool|g'
-SUBST_SED.path+=	-e 's|$$ROOTDIR/trinity-plugins/parafly/bin/ParaFly|ParaFly|g'
-SUBST_SED.path+=	-e 's|$$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar|${PREFIX}/lib/java/trimmomatic.jar|g'
-SUBST_SED.path+=	-e 's|$$ROOTDIR/trinity-plugins/Trimmomatic|${PREFIX}/share/Trimmomatic|g'
-SUBST_FILES.path+=	${WRKSRC}/Trinity
-
-SUBST_CLASSES+=		upath
-SUBST_STAGE.upath=	post-patch
-SUBST_SED.upath+=	-e 's|$$JELLYFISH_DIR/bin/jellyfish|jellyfish|g'
-SUBST_SED.upath+=	-e 's|$$FASTOOL_DIR/fastool|fastool|g'
-SUBST_FILES.upath+=	${WRKSRC}/util/insilico_read_normalization.pl
-
-SUBST_CLASSES+=		rjpath
-SUBST_STAGE.rjpath=	post-patch
-SUBST_SED.rjpath+=	-e 's|$$JELLYFISH_DIR/bin/jellyfish|jellyfish|g'
-SUBST_FILES.rjpath+=	${WRKSRC}/util/misc/run_jellyfish.pl
-
-SUBST_CLASSES+=		trim
-SUBST_STAGE.trim=	post-patch
-SUBST_SED.trim+=	-e 's|$$FindBin::Bin/../../trinity-plugins/Trimmomatic/trimmomatic.jar|${PREFIX}/lib/java/trimmomatic.jar|g'
-SUBST_SED.trim+=	-e 's|/seq/regev_genome_portal/SOFTWARE/BIN/trimmomatic.jar|${PREFIX}/lib/java/trimmomatic.jar|g'
-SUBST_FILES.trim+=	${WRKSRC}/util/misc/run_trimmomatic_qual_trimming.pl
-
-SUBST_CLASSES+=		chrys
-SUBST_STAGE.chrys=	post-patch
-SUBST_SED.chrys+=	-e "s|-lm -pthread|-lm -pthread -Wl,-rpath=${_GCC_RUNTIME}|g"
-SUBST_FILES.chrys+=	${WRKSRC}/Chrysalis/Makefile
-
-SUBST_CLASSES+=		trinpath
-SUBST_STAGE.trinpath=	post-patch
-SUBST_SED.trinpath+=	-e 's|$$BASEDIR/Trinity|Trinity|g'
-SUBST_FILES.trinpath+=	${WRKSRC}/util/run_Trinity_edgeR_pipeline.pl
-
-SUBST_CLASSES+=		trinpath2
-SUBST_STAGE.trinpath2=	post-patch
-SUBST_SED.trinpath2+=	-e 's|$$FindBin::Bin/../../Trinity|Trinity|g'
-SUBST_FILES.trinpath2+=	${WRKSRC}/util/support_scripts/write_partitioned_trinity_cmds.pl
-
-SUBST_CLASSES+=		perl
-SUBST_STAGE.perl=	post-patch
-SUBST_SED.perl+=	-e "s|/usr/bin/perl|${PREFIX}/bin/perl|g"
-SUBST_FILES.perl+=	${WRKSRC}/trinity-plugins/collectl/bin/collectl
-SUBST_FILES.perl+=	${WRKSRC}/trinity-plugins/collectl/bin/*.pl
-
-USE_LANGUAGES=	c c++
-USE_TOOLS+=	bash gmake pax perl
-REPLACE_BASH=	util/*/*.sh trinity-plugins/collectl/build_collectl.sh
-REPLACE_PERL=	Trinity util/*.pl util/fasta_tool util/misc/Monarch \
-		util/*/*.pl util/*/*/*.pl util/*/*/*/*.pl \
-		Chrysalis/*.pl PerlLib/*.p* PerlLib/*/*.pm \
-		trinity-plugins/GAL_0.2.1/fasta_tool
-REPLACE_PYTHON=	trinity-plugins/collectl/collectl2html \
-		util/deprecated/eXpress_util/*.py
-
-WRKSRC=		${WRKDIR}/trinityrnaseq-${PORTVERSION}
-
-CFLAGS+=	-fopenmp
-CXXFLAGS=	-fopenmp
-
-PORTVERSION=	2.1.1
-EXAMPLESDIR=	${PREFIX}/share/examples/trinity
-LIBEXEC_DIR=	${PREFIX}/libexec/trinity
-PLUGINS_DIR=	${LIBEXEC_DIR}/trinity-plugins
-
-INSTALLATION_DIRS= \
-	bin \
-	libexec/trinity/Chrysalis \
-	libexec/trinity/Inchworm/bin \
-	libexec/trinity/Butterfly \
-	libexec/trinity/trinity-plugins/collectl \
-	libexec/trinity/trinity-plugins/scaffold_iworm_contigs
-
-pre-patch:
-	dos2unix \
-		${WRKSRC}/PerlLib/HPC/GridRunner.pm \
-		${WRKSRC}/PerlLib/HPC/SLURM_handler.pm
-
-.if ${CXX} != g++
-post-patch:
-	${MV} -n ${WRKSRC}/Chrysalis/Makefile_g++ \
-		${WRKSRC}/Chrysalis/Makefile_${CXX}
-	${MV} -n ${WRKSRC}/Chrysalis/Makefile_g++_x86_64 \
-		${WRKSRC}/Chrysalis/Makefile_${CXX}_x86_64
-	${MV} -n ${WRKSRC}/Chrysalis/Makefile_g++_i386 \
-		${WRKSRC}/Chrysalis/Makefile_${CXX}_i386
-.endif
-
-# FIXME: More may need to be installed
-do-install:
-	${INSTALL_SCRIPT} ${WRKSRC}/Trinity ${DESTDIR}${PREFIX}/bin
-	cd ${WRKSRC}/Chrysalis && \
-		${INSTALL_PROGRAM} BreakTransByPairs Chrysalis \
-			CreateIwormFastaBundle \
-			GraphFromFasta GraphFromFasta_MPI \
-			IsoformAugment JoinTransByPairs QuantifyGraph \
-			ReadsToTranscripts ReadsToTranscripts_MPI \
-			ReadsToTranscripts_MPI_chang RunButterfly \
-			TranscriptomeFromVaryK checkLock \
-			${DESTDIR}${LIBEXEC_DIR}/Chrysalis
-	${INSTALL_SCRIPT} ${WRKSRC}/Chrysalis/ReadsToComponents.pl \
-		${DESTDIR}${LIBEXEC_DIR}/Chrysalis
-	${INSTALL_PROGRAM} ${WRKSRC}/Inchworm/bin/* \
-		${DESTDIR}${LIBEXEC_DIR}/Inchworm/bin
-	${INSTALL_SCRIPT} ${WRKSRC}/Butterfly/Butterfly.jar \
-		${DESTDIR}${LIBEXEC_DIR}/Butterfly
-	cd ${WRKSRC} && pax -rw PerlLib -s ',.*.orig$$,,' \
-		${DESTDIR}${LIBEXEC_DIR}
-	cd ${WRKSRC} && pax -rw util ${DESTDIR}${LIBEXEC_DIR}
-	cd ${WRKSRC}/trinity-plugins/collectl && \
-		pax -rw bin ${DESTDIR}${PLUGINS_DIR}/collectl
-	cd ${WRKSRC}/trinity-plugins && \
-		pax -rw GAL_0.2.1 ${DESTDIR}${PLUGINS_DIR}
-	${INSTALL_PROGRAM} ${WRKSRC}/trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs \
-		${DESTDIR}${PLUGINS_DIR}/scaffold_iworm_contigs
-	cd ${WRKSRC}/sample_data && pax -rw * \
-		${DESTDIR}${EXAMPLESDIR}
-
-.include "../../wip/htslib/buildlink3.mk"
-.include "../../devel/libexecinfo/buildlink3.mk"
-.include "../../devel/zlib/buildlink3.mk"
-.include "../../lang/python/application.mk"
-.include "../../mk/curses.buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/trinity/PLIST b/trinity/PLIST
deleted file mode 100644
index 2494e2479f..0000000000
--- a/trinity/PLIST
+++ /dev/null
@@ -1,577 +0,0 @@
-@comment $NetBSD$
-bin/Trinity
-libexec/trinity/Butterfly/Butterfly.jar
-libexec/trinity/Chrysalis/BreakTransByPairs
-libexec/trinity/Chrysalis/Chrysalis
-libexec/trinity/Chrysalis/CreateIwormFastaBundle
-libexec/trinity/Chrysalis/GraphFromFasta
-libexec/trinity/Chrysalis/GraphFromFasta_MPI
-libexec/trinity/Chrysalis/IsoformAugment
-libexec/trinity/Chrysalis/JoinTransByPairs
-libexec/trinity/Chrysalis/QuantifyGraph
-libexec/trinity/Chrysalis/ReadsToComponents.pl
-libexec/trinity/Chrysalis/ReadsToTranscripts
-libexec/trinity/Chrysalis/ReadsToTranscripts_MPI
-libexec/trinity/Chrysalis/ReadsToTranscripts_MPI_chang
-libexec/trinity/Chrysalis/RunButterfly
-libexec/trinity/Chrysalis/TranscriptomeFromVaryK
-libexec/trinity/Chrysalis/checkLock
-libexec/trinity/Inchworm/bin/FastaToDeBruijn
-libexec/trinity/Inchworm/bin/cigar_tweaker
-libexec/trinity/Inchworm/bin/fastaToKmerCoverageStats
-libexec/trinity/Inchworm/bin/inchworm
-libexec/trinity/Inchworm/bin/pull_reads_with_kmers
-libexec/trinity/PerlLib/Ascii_genome_illustrator.pm
-libexec/trinity/PerlLib/BED_utils.pm
-libexec/trinity/PerlLib/BHStats.pm
-libexec/trinity/PerlLib/CDNA/Alignment_segment.pm
-libexec/trinity/PerlLib/CDNA/Alternative_splice_comparer.pm
-libexec/trinity/PerlLib/CDNA/CDNA_alignment.pm
-libexec/trinity/PerlLib/CDNA/CDNA_stitcher.pm
-libexec/trinity/PerlLib/CDNA/Gene_obj_alignment_assembler.pm
-libexec/trinity/PerlLib/CDNA/Genome_based_cDNA_assembler.pm
-libexec/trinity/PerlLib/CDNA/Genome_based_cDNA_graph_assembler.pm
-libexec/trinity/PerlLib/CDNA/Overlap_assembler.pm
-libexec/trinity/PerlLib/CDNA/PASA_alignment_assembler.pm
-libexec/trinity/PerlLib/CDNA/Splice_graph_assembler.pm
-libexec/trinity/PerlLib/CIGAR.pm
-libexec/trinity/PerlLib/CMD_processor.pm
-libexec/trinity/PerlLib/COMMON.pm
-libexec/trinity/PerlLib/CanvasXpress/Heatmap.pm
-libexec/trinity/PerlLib/ColorGradient.pm
-libexec/trinity/PerlLib/EM.pm
-libexec/trinity/PerlLib/Exons_to_geneobj.pm
-libexec/trinity/PerlLib/Fasta_reader.pm
-libexec/trinity/PerlLib/Fasta_retriever.pm
-libexec/trinity/PerlLib/Fastq_reader.pm
-libexec/trinity/PerlLib/GFF3_alignment_utils.pm
-libexec/trinity/PerlLib/GFF3_utils.pm
-libexec/trinity/PerlLib/GFF_maker.pm
-libexec/trinity/PerlLib/GTF.pm
-libexec/trinity/PerlLib/GTF_utils.pm
-libexec/trinity/PerlLib/Gene_obj.pm
-libexec/trinity/PerlLib/Gene_obj_indexer.pm
-libexec/trinity/PerlLib/HPC/Base_handler.pm
-libexec/trinity/PerlLib/HPC/FarmIt.pm
-libexec/trinity/PerlLib/HPC/GridRunner.pm
-libexec/trinity/PerlLib/HPC/LSF_handler.pm
-libexec/trinity/PerlLib/HPC/PBS_handler.pm
-libexec/trinity/PerlLib/HPC/SGE_handler.pm
-libexec/trinity/PerlLib/HPC/SLURM_handler.pm
-libexec/trinity/PerlLib/KmerGraphLib/AlignGraph.pm
-libexec/trinity/PerlLib/KmerGraphLib/AlignNode.pm
-libexec/trinity/PerlLib/KmerGraphLib/GenericGraph.pm
-libexec/trinity/PerlLib/KmerGraphLib/GenericNode.pm
-libexec/trinity/PerlLib/KmerGraphLib/KmerGraph.pm
-libexec/trinity/PerlLib/KmerGraphLib/KmerNode.pm
-libexec/trinity/PerlLib/KmerGraphLib/ReadCoverageGraph.pm
-libexec/trinity/PerlLib/KmerGraphLib/ReadCoverageNode.pm
-libexec/trinity/PerlLib/KmerGraphLib/ReadManager.pm
-libexec/trinity/PerlLib/KmerGraphLib/ReadTracker.pm
-libexec/trinity/PerlLib/KmerGraphLib/SAM_entry.pm
-libexec/trinity/PerlLib/KmerGraphLib/SAM_reader.pm
-libexec/trinity/PerlLib/KmerGraphLib/SAM_to_AlignGraph.pm
-libexec/trinity/PerlLib/KmerGraphLib/StringGraph.pm
-libexec/trinity/PerlLib/KmerGraphLib/StringNode.pm
-libexec/trinity/PerlLib/Ktree.pm
-libexec/trinity/PerlLib/Longest_orf.pm
-libexec/trinity/PerlLib/Nuc_translator.pm
-libexec/trinity/PerlLib/Overlap_info.pm
-libexec/trinity/PerlLib/Overlap_piler.pm
-libexec/trinity/PerlLib/PSL_parser.pm
-libexec/trinity/PerlLib/Pipeliner.pm
-libexec/trinity/PerlLib/Process_cmd.pm
-libexec/trinity/PerlLib/SAM_entry.pm
-libexec/trinity/PerlLib/SAM_reader.pm
-libexec/trinity/PerlLib/Simulate/Uniform_Read_Generator.pm
-libexec/trinity/PerlLib/SingleLinkageClusterer.pm
-libexec/trinity/PerlLib/Thread_helper.pm
-libexec/trinity/PerlLib/TiedHash.pm
-libexec/trinity/PerlLib/VCF_parser.pm
-libexec/trinity/PerlLib/WigParser.pm
-libexec/trinity/PerlLib/overlapping_nucs.ph
-libexec/trinity/PerlLib/test_Fasta_retriever.pl
-libexec/trinity/PerlLib/test_htc_gridrunner_LSF.pl
-libexec/trinity/PerlLib/test_htc_gridrunner_SGE.pl
-libexec/trinity/trinity-plugins/GAL_0.2.1/README
-libexec/trinity/trinity-plugins/GAL_0.2.1/fasta_tool
-libexec/trinity/trinity-plugins/collectl/bin/UNINSTALL
-libexec/trinity/trinity-plugins/collectl/bin/client.pl
-libexec/trinity/trinity-plugins/collectl/bin/col2tlviz.pl
-libexec/trinity/trinity-plugins/collectl/bin/collectl
-libexec/trinity/trinity-plugins/collectl/bin/collectl.conf
-libexec/trinity/trinity-plugins/collectl/bin/collectl2html
-libexec/trinity/trinity-plugins/collectl/bin/envrules.std
-libexec/trinity/trinity-plugins/collectl/bin/formatit.ph
-libexec/trinity/trinity-plugins/collectl/bin/gexpr.ph
-libexec/trinity/trinity-plugins/collectl/bin/graphite.ph
-libexec/trinity/trinity-plugins/collectl/bin/hello.ph
-libexec/trinity/trinity-plugins/collectl/bin/lexpr.ph
-libexec/trinity/trinity-plugins/collectl/bin/make_data_files.py
-libexec/trinity/trinity-plugins/collectl/bin/misc.ph
-libexec/trinity/trinity-plugins/collectl/bin/plot.py
-libexec/trinity/trinity-plugins/collectl/bin/proctree.ph
-libexec/trinity/trinity-plugins/collectl/bin/timetable.py
-libexec/trinity/trinity-plugins/collectl/bin/vmstat.ph
-libexec/trinity/trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs
-libexec/trinity/util/PBS/N50stats.pl
-libexec/trinity/util/PBS/README
-libexec/trinity/util/PBS/TRINITY.CONFIG.template
-libexec/trinity/util/PBS/pbs_check.pl
-libexec/trinity/util/PBS/trinity_kill.pl
-libexec/trinity/util/PBS/trinity_kill.sh
-libexec/trinity/util/PBS/trinity_pbs.cont
-libexec/trinity/util/PBS/trinity_pbs.header
-libexec/trinity/util/PBS/trinity_pbs.p1
-libexec/trinity/util/PBS/trinity_pbs.p2
-libexec/trinity/util/PBS/trinity_pbs.p3
-libexec/trinity/util/PBS/trinity_pbs.p4a
-libexec/trinity/util/PBS/trinity_pbs.p4b
-libexec/trinity/util/PBS/trinity_pbs.p5b
-libexec/trinity/util/PBS/trinity_pbs.sh
-libexec/trinity/util/R/expression_analysis_lib.R
-libexec/trinity/util/R/get_Poisson_conf_intervals.R
-libexec/trinity/util/R/noiseq.r
-libexec/trinity/util/SAM_nameSorted_to_uniq_count_stats.pl
-libexec/trinity/util/TrinityStats.pl
-libexec/trinity/util/abundance_estimates_to_matrix.pl
-libexec/trinity/util/align_and_estimate_abundance.pl
-libexec/trinity/util/analyze_blastPlus_topHit_coverage.pl
-libexec/trinity/util/bowtie_PE_separate_then_join.pl
-libexec/trinity/util/deprecated/PairPathsToGraphDot.pl
-libexec/trinity/util/deprecated/RSEM_util/Nx_rsem_to_table.pl
-libexec/trinity/util/deprecated/RSEM_util/merge_RSEM_counts_and_labels_single_table.pl
-libexec/trinity/util/deprecated/RSEM_util/merge_RSEM_frag_counts_single_table.pl
-libexec/trinity/util/deprecated/RSEM_util/merge_RSEM_output_to_matrix.pl
-libexec/trinity/util/deprecated/RSEM_util/run_RSEM_align_n_estimate.pl
-libexec/trinity/util/deprecated/alignReads.pl
-libexec/trinity/util/deprecated/annot_genome_SAM_to_transcript_FPKM_simple.pl
-libexec/trinity/util/deprecated/annot_genome_SAM_to_transcriptome_SAM.pl
-libexec/trinity/util/deprecated/blastn_illumina_to_SAM.pl
-libexec/trinity/util/deprecated/cigar_tweaker.pl
-libexec/trinity/util/deprecated/cmd_process_forker.pl
-libexec/trinity/util/deprecated/csfastX_to_defastA.pl
-libexec/trinity/util/deprecated/distribute_sam_aligned_reads.pl
-libexec/trinity/util/deprecated/eXpress_util/filter_contigs.py
-libexec/trinity/util/deprecated/eXpress_util/merge_eXpress_frag_counts_single_table.pl
-libexec/trinity/util/deprecated/eXpress_util/run_eXpress_align_n_estimate.pl
-libexec/trinity/util/deprecated/eXpress_util/usage.txt
-libexec/trinity/util/deprecated/eXpress_util/use_express.py
-libexec/trinity/util/deprecated/fasta_to_deBruijn_graph.pl
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-share/examples/trinity/test_GenomeGuidedTrinity/old/run_Schizo_TrinityGG.SE.sh
-share/examples/trinity/test_GenomeGuidedTrinity/old/run_Schizo_TrinityGG.sh
-share/examples/trinity/test_GenomeGuidedTrinity/old/run_genome-guided_Trinity.sh
-share/examples/trinity/test_GenomeGuidedTrinity/old/run_mouse_TrinityGG.sh
-share/examples/trinity/test_GenomeGuidedTrinity/run_Schizo_TrinityGG_jaccard_clip.sh
-share/examples/trinity/test_GenomeGuidedTrinity/run_genome-guided_Trinity_use_existing_bam.sh
-share/examples/trinity/test_GenomeGuidedTrinity/top100k.Left.fq.gz
-share/examples/trinity/test_GenomeGuidedTrinity/top100k.Right.fq.gz
-share/examples/trinity/test_GenomeGuidedTrinity/top100k.genome.gz
-share/examples/trinity/test_InSilicoReadNormalization/Makefile
-share/examples/trinity/test_InSilicoReadNormalization/cleanme.pl
-share/examples/trinity/test_InSilicoReadNormalization/test_PE_normalization.sh
-share/examples/trinity/test_InSilicoReadNormalization/test_PE_normalization.w_base_cov_stats.sh
-share/examples/trinity/test_InSilicoReadNormalization/test_SE_normalization.sh
-share/examples/trinity/test_Inchworm/jellyfish.kmers.fa.gz
-share/examples/trinity/test_Inchworm/runMe_MPI.sh
-share/examples/trinity/test_Trinity_Assembly/Makefile
-share/examples/trinity/test_Trinity_Assembly/README
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/align_reads_via_bowtie.sh
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/bowtie2.sam.aligned.bam
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex01/ex01.IGV.png
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex01/ex01.reads.left.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex01/ex01.reads.right.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex01/ex01.refSeq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex02/ex02.refSeq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex02/ex2.reads.left.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex02/ex2.reads.right.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex02/example2.png
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex02/region2.sam
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex02/region2.sam.adj
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex03/ex03.refSeq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex03/ex3.reads.left.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex03/ex3.reads.right.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex03/example3.png
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex03/region3.sam
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex03/region3.sam.adj
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex04/ex04.refSeq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex04/ex4.reads.left.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex04/ex4.reads.right.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex04/example4.png
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex04/region4.sam
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex04/region4.sam.adj
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/clean.left.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/clean.right.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/ex05.refSeq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/ex5.reads.left.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/ex5.reads.right.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/example5.png
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/isoform_pair.fasta
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/isoform_pair.fasta.Bfly.dot
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/isoform_pair.fasta.gmap.bed
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/isoform_pair.fasta.gmap.gff
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/region5.sam
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/region5.sam.adj
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.clean.sh
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex05/runMe.sh
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex06/ex06.refSeq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex06/ex6.reads.left.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex06/ex6.reads.right.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex06/example6.png
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex06/region6.sam
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex06/region6.sam.adj
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex07/ex07.refSeq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex07/ex7.reads.left.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex07/ex7.reads.right.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex07/example7.png
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex07/region7.sam
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex07/region7.sam.adj
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex08/ex08.refSeq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex08/ex8.reads.left.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex08/ex8.reads.right.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex08/example8.png
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex08/region8.sam
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex08/region8.sam.adj
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/ex09.refSeq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/ex9.reads.left.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/ex9.reads.right.fq
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/example9.png
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/region9.sam
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/region9.sam.adj
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/ex09/runMe.sh
-share/examples/trinity/test_Trinity_Assembly/__indiv_ex_sample_derived/refSeqs.fa
-share/examples/trinity/test_Trinity_Assembly/cleanme.pl
-share/examples/trinity/test_Trinity_Assembly/longReads.fa
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe.diff_kmer_length.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_CuffFly.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_PasaFly.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_as_DS.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_bowtie_components.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_include_long_reads.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_no_cleanup.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_parallel_iworm_assembly.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_using_Grid_LSF.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_using_Grid_SGE.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_w_monitoring.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__run_abundance_estimation_include_antisense.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__test_runMe.singleFQ.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__test_runMe_include_normalization.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__test_runMe_with_jaccard_clip.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/runMe_no_qualTrim.sh
-share/examples/trinity/test_Trinity_Assembly/reads.left.fq.gz
-share/examples/trinity/test_Trinity_Assembly/reads.right.fq.gz
-share/examples/trinity/test_Trinity_Assembly/reads2.left.fq.gz
-share/examples/trinity/test_Trinity_Assembly/reads2.right.fq.gz
-share/examples/trinity/test_Trinity_Assembly/runMe.sh
-share/examples/trinity/test_Trinity_Assembly/test_FL.sh
-share/examples/trinity/test_align_and_estimate_abundance/Makefile
-share/examples/trinity/test_align_and_estimate_abundance/align_and_estimate_tester.pl
-share/examples/trinity/test_align_and_estimate_abundance/cleanme.pl
-share/examples/trinity/test_align_and_estimate_abundance/plot_paired_comparisons.Rscript
-share/examples/trinity/test_align_and_estimate_abundance/samples.txt
-share/examples/trinity/test_full_edgeR_pipeline/Makefile
-share/examples/trinity/test_full_edgeR_pipeline/cleanme.pl
-share/examples/trinity/test_full_edgeR_pipeline/runMe.sh
-share/examples/trinity/test_full_edgeR_pipeline/samples_n_reads_decribed.txt
diff --git a/trinity/TODO b/trinity/TODO
deleted file mode 100644
index b2e3b56f25..0000000000
--- a/trinity/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test.
diff --git a/trinity/distinfo b/trinity/distinfo
deleted file mode 100644
index b1218cd2ac..0000000000
--- a/trinity/distinfo
+++ /dev/null
@@ -1,10 +0,0 @@
-$NetBSD$
-
-SHA1 (trinity-2.1.1.tar.gz) = 5b537b8f8c35c6dd2853c9d82c761e6efd35c228
-RMD160 (trinity-2.1.1.tar.gz) = 8dd567d9f9a737a4efdd62dcb447a7275be3a10e
-SHA512 (trinity-2.1.1.tar.gz) = 36b67211902871c6dbba31a074c4e92d2e925c57fe54bf59418874282e283693d2d9b4e14333385a7adcef3edbf928bc1001df105b56412841662c45a9a74f3f
-Size (trinity-2.1.1.tar.gz) = 137541420 bytes
-SHA1 (patch-Makefile) = 1a7a185ad8252b74fdc2398049966acf21bc250c
-SHA1 (patch-PerlLib_HPC_SLURM__handler.pm) = c2bb0872340389f043b540ff457ebcabbdf48116
-SHA1 (patch-trinity-plugins_Makefile) = 0cb5fe8664eb3f2b80bd9873207d958c21a2f76f
-SHA1 (patch-trinity-plugins_scaffold__iworm__contigs_Makefile) = fb0abe2a37d7cd99190ad4f851bd695a014ec4f0
diff --git a/trinity/patches/patch-Makefile b/trinity/patches/patch-Makefile
deleted file mode 100644
index 5d71ae72fc..0000000000
--- a/trinity/patches/patch-Makefile
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD$
-
-# Makefile patch for plugins install
---- Makefile.orig	2015-10-15 12:07:11.000000000 +0000
-+++ Makefile
-@@ -14,7 +14,7 @@ else
- endif
- 
- 
--all: inchworm_target chrysalis_target trinity_essentials
-+all: inchworm_target chrysalis_target trinity_essentials plugins
- 	sh ./util/support_scripts/trinity_install_tests.sh
- 
- inchworm_target:
diff --git a/trinity/patches/patch-PerlLib_HPC_SLURM__handler.pm b/trinity/patches/patch-PerlLib_HPC_SLURM__handler.pm
deleted file mode 100644
index c3e0dfc35e..0000000000
--- a/trinity/patches/patch-PerlLib_HPC_SLURM__handler.pm
+++ /dev/null
@@ -1,28 +0,0 @@
-$NetBSD$
-
-# Patch for SLURM plugin
---- PerlLib/HPC/SLURM_handler.pm.orig	2016-01-28 15:46:19.663726750 +0000
-+++ PerlLib/HPC/SLURM_handler.pm
-@@ -41,11 +41,12 @@ sub submit_job_to_grid {
-      ##with SLURM max expected running time should preferably be specified, otherwise the scheduler will assume default value for the partition; structure is days-hours:minutes:seconds like so 1-02:30:00  
-     
-     $cmd .= " $shell_script 2>&1 ";
-+    print STDERR "\nExecuting $cmd\n";
-         
- 
-     my $job_id_text = `$cmd`;
-     
--    # print STDERR "\n$job_id_text\n";
-+    print STDERR "\n$job_id_text\n";
-     
-     my $ret = $?;
-     
-@@ -82,7 +83,7 @@ sub job_running_or_pending_on_grid {
-         confess "Error, need job ID as parameter";
-     }
-     
--    # print STDERR "Polling grid to check status of job: $job_id\n";
-+    print STDERR "Polling grid to check status of job: $job_id\n";
-     
-     my $response = `sacct -j $job_id`;
-     #print STDERR "Response:\n$response\n";
diff --git a/trinity/patches/patch-trinity-plugins_Makefile b/trinity/patches/patch-trinity-plugins_Makefile
deleted file mode 100644
index 680d1a9ac8..0000000000
--- a/trinity/patches/patch-trinity-plugins_Makefile
+++ /dev/null
@@ -1,42 +0,0 @@
-$NetBSD$
-
-# Split plugins patch
---- trinity-plugins/Makefile.orig	2015-10-15 12:07:11.000000000 +0000
-+++ trinity-plugins/Makefile
-@@ -10,7 +10,8 @@ FASTOOL_CODE=fstrozzi-Fastool-7c3e034f05
- 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: jellyfish scaffold_iworm_contigs_target fastool_target parafly_target trimmomatic_target samtools
-+trinity_essentials: scaffold_iworm_contigs_target fastool_target
- 
- trimmomatic_target:
- 	ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
-@@ -27,11 +28,12 @@ jellyfish:
- 	mv tmp.jellyfish jellyfish
- 
- htslib_target:
--#	tar xjvf htslib-1.2.1.tar.bz2
--#	cd htslib-1.2.1 && ./configure && $(MAKE)
-+	tar xjvf htslib-1.2.1.tar.bz2
-+	cd htslib-1.2.1 && ./configure && $(MAKE)
- 	tar xvf ${HTSLIB_CODE} && cd htslib && $(MAKE)
- 
--scaffold_iworm_contigs_target: htslib_target
-+# scaffold_iworm_contigs_target: htslib_target
-+scaffold_iworm_contigs_target:
- 	cd scaffold_iworm_contigs && $(MAKE)
- 
- fastool_target:
-@@ -48,7 +50,9 @@ parafly_target:
- ### Needed for downstream analyses
- ##################################
- 
--plugins: slclust_target collectl_target
-+# All plugins except collectl are installed as dependency ports
-+# plugins: slclust_target collectl_target
-+plugins: collectl_target
- 	@echo "\n\n** Done building plugins **\n\n"
- 
- 
diff --git a/trinity/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile b/trinity/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile
deleted file mode 100644
index edb507580e..0000000000
--- a/trinity/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-$NetBSD$
-
-# Proper rpath patch
---- trinity-plugins/scaffold_iworm_contigs/Makefile.orig	2015-10-15 12:07:11.000000000 +0000
-+++ trinity-plugins/scaffold_iworm_contigs/Makefile
-@@ -1,10 +1,8 @@
--CXX    = g++
-+CXX    ?= g++
- prefix = ../htslib
- 
- ScaffoldIwormContigs:
--	$(CXX) -I$(prefix) -L$(prefix) ScaffoldIwormContigs.cpp error_checker.cpp -lhts -lz -o scaffold_iworm_contigs
-+	$(CXX) $(CXXFLAGS) $(LDFLAGS) ScaffoldIwormContigs.cpp error_checker.cpp -L${LOCALBASE}/lib -lhts -lz -o scaffold_iworm_contigs
- 
- clean:
- 	rm scaffold_iworm_contigs
--
--
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