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Update trinity from jb-wip
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By: outpaddling
Date: Wed May 11 09:49:05 2016 -0500
Changeset: 72fcf941bed18f9b18dfc961b5d4cb4ae9544fbc
Modified Files:
trinity/DESCR
trinity/Makefile
trinity/PLIST
trinity/TODO
trinity/distinfo
Added Files:
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
Removed Files:
trinity/buildlink3.mk
trinity/patches/patch-PerlLib-HTC-SLURM_handler.pm
trinity/patches/patch-PerlLib_HTC_FarmIt.pm
trinity/patches/patch-Trinity
Log Message:
Update trinity from jb-wip
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=72fcf941bed18f9b18dfc961b5d4cb4ae9544fbc
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
trinity/DESCR | 7 +-
trinity/Makefile | 304 ++++++++++---------
trinity/PLIST | 321 +++++++++++++++++----
trinity/TODO | 7 +-
trinity/buildlink3.mk | 22 --
trinity/distinfo | 16 +-
trinity/patches/patch-Makefile | 14 +
trinity/patches/patch-PerlLib-HTC-SLURM_handler.pm | 12 -
.../patches/patch-PerlLib_HPC_SLURM__handler.pm | 28 ++
trinity/patches/patch-PerlLib_HTC_FarmIt.pm | 15 -
trinity/patches/patch-Trinity | 41 ---
trinity/patches/patch-trinity-plugins_Makefile | 42 +++
...inity-plugins_scaffold__iworm__contigs_Makefile | 18 ++
13 files changed, 551 insertions(+), 296 deletions(-)
diffs:
diff --git a/trinity/DESCR b/trinity/DESCR
index 4a95382..7752b73 100644
--- a/trinity/DESCR
+++ b/trinity/DESCR
@@ -1,3 +1,4 @@
-[description of the port]
-
-WWW: http://port.home.page/
+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
index 14bc1df..e46e5a5 100644
--- a/trinity/Makefile
+++ b/trinity/Makefile
@@ -1,170 +1,204 @@
-# $NetBSD: Makefile,v 1.2 2015/01/28 22:10:06 outpaddling Exp $
-
+# $NetBSD$
+#
###########################################################
# 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:
-# # Requires OpenMP. Use newer GCC for better optimizer.
-# USE_GCC= yes
-# USE_JAVA= yes
-# JAVA_VERSION= 1.7 1.6
-# MAKE_FLAGS+= FORCE_UNSAFE_CONFIGURE=1
-# post-patch:
-# ${MV} ${WRKSRC}/Chrysalis/Makefile_g++ \
-# ${WRKSRC}/Chrysalis/Makefile_${CXX}
-# ${MV} ${WRKSRC}/Chrysalis/Makefile_g++_x86_64 \
-# ${WRKSRC}/Chrysalis/Makefile_${CXX}_x86_64
-# ${MV} ${WRKSRC}/Chrysalis/Makefile_g++_i386 \
-# ${WRKSRC}/Chrysalis/Makefile_${CXX}_i386
-
-PKGNAME= trinity-2014.04.13
-DISTNAME= trinityrnaseq_r20140413p1
+#USE_JAVA= yes
+#JAVA_VERSION= 1.7 1.6
+# slclust:/usr/wip/biology/slclust
+
+DEPENDS+= coreutils>=0:../../sysutils/coreutils \
+ bowtie<2:../../wip/bowtie \
+ bowtie2>=2:../../wip/bowtie2 \
+ jellyfish>=2.1.4:../../wip/jellyfish2 \
+ parafly>=0:../../wip/parafly \
+ fastool>=0:../../wip/fastool \
+ p5-transdecoder>=0:../../wip/p5-transdecoder \
+ Trimmomatic>=0.32:../../wip/trimmomatic \
+ rsem>=1.2.30:../../wip/rsem \
+ slclust>=0:../../wip/slclust \
+ samtools>=1.3:../../wip/samtools
+
+DISTNAME= trinity-${PORTVERSION}
CATEGORIES= biology
-MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=trinityrnaseq/PREV_CONTENTS/previous_releases/}
-
-MAINTAINER= jwbacon%tds.net@localhost
-
-COMMENT= RNA sequence assembly
-# LICENSE=
-
-ONLY_FOR_PLATFORM= *-*-x86_64
+MASTER_SITES= ${MASTER_SITE_GITHUB:=trinityrnaseq/}
+GITHUB_PROJECT= trinityrnaseq
+GITHUB_TAG= v${PORTVERSION}
+
+MAINTAINER= bacon4000%gmail.com@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
-MAKE_JOBS_SAFE= no
-
-# Just assuming C and C++: Adjust this!
USE_LANGUAGES= c c++
-USE_TOOLS+= gmake pax perl bash:run
-REPLACE_SH= trinity-plugins/collectl/make_data_files.sh \
- trinity-plugins/collectl/plot.sh \
- trinity-plugins/collectl/timetable.sh \
- util/*/*.sh
-REPLACE_PERL= util/*/*.pl \
- Chrysalis/*.pl
-# FIXME: Coreutils doesn't build, but we should use the pkg anyway
-REPLACE_BASH= trinity-plugins/coreutils/build_parallel_sort.sh
-
-DEPENDS+= p5-PerlIO-gzip>=0:../../devel/p5-PerlIO-gzip
-
-# Some scripts are not available during patch stage
-SUBST_CLASSES+= shebang
-SUBST_STAGE.shebang= post-build
-SUBST_FILES.shebang= ${WRKSRC}/trinity-plugins/collectl/bin/collectl \
- ${WRKSRC}/trinity-plugins/collectl/bin/*.pl
-SUBST_SED.shebang= -e "s|/usr/bin/perl|${PREFIX}/bin/perl|g"
-
-SUBST_CLASSES+= targets
-SUBST_STAGE.targets= post-patch
-SUBST_FILES.targets= ${WRKSRC}/Makefile
-SUBST_SED.targets= -e "s|chrysalis_target jellyfish|chrysalis_target|g"
-
-SUBST_CLASSES+= compiler
-SUBST_STAGE.compiler= post-patch
-SUBST_FILES.compiler= ${WRKSRC}/Makefile \
- ${WRKSRC}/Chrysalis/Makefile* \
- ${WRKSRC}/trinity-plugins/fastool/Makefile \
- ${WRKSRC}/trinity-plugins/slclust/src/Makefile
-SUBST_SED.compiler= -e "s|gcc|${CC}|g" -e "s|g++|${CXX}|g"
-
-# FIXME: SUBST following patch file makes using pkgvi difficult
-# Work around by doing this in pre-build stage instead of post-patch
-SUBST_CLASSES+= plugins
-SUBST_STAGE.plugins= pre-build
-SUBST_FILES.plugins= ${WRKSRC}/Trinity
-SUBST_SED.plugins= -e 's|$$ROOTDIR/trinity-plugins/jellyfish|${PREFIX}|g' \
- -e 's|$$ROOTDIR/trinity-plugins/parafly|${PREFIX}|g'
-
-SUBST_CLASSES+= util
-SUBST_STAGE.util= post-patch
-SUBST_FILES.util= ${WRKSRC}/util/insilico_read_normalization.pl
-SUBST_SED.util= \
- -e 's|$$ROOTDIR/trinity-plugins/jellyfish|${LOCALBASE}|g' \
- -e 's|$$ROOTDIR/trinity-plugins/fastool|${LOCALBASE}/bin|g'
-
-SUBST_CLASSES+= make
-SUBST_STAGE.make= post-patch
-SUBST_FILES.make= ${WRKSRC}/trinity-plugins/collectl/build_collectl.sh
-SUBST_SED.make= -e 's|/bin/bash|/usr/bin/env bash|g' \
- -e 's|make |${GMAKE} |g'
-
-# GridRunner: ParaFly is intalled separately, so remove absolute path
-SUBST_CLASSES+= parafly
-SUBST_STAGE.parafly= post-patch
-SUBST_FILES.parafly= ${WRKSRC}/PerlLib/HTC/GridRunner.pm
-SUBST_SED.parafly= -e 's|$$trin_home/trinity-plugins/parafly/bin/||g'
-
-# Remove absolute paths to Trinity command
-SUBST_CLASSES+= pipeline
-SUBST_STAGE.pipeline= post-patch
-SUBST_FILES.pipeline= ${WRKSRC}/util/run_Trinity_edgeR_pipeline.pl
-SUBST_SED.pipeline= -e 's|$$BASEDIR/Trinity|Trinity|g'
-
-SUBST_CLASSES+= gc_write
-SUBST_STAGE.gc_write= post-patch
-SUBST_FILES.gc_write= ${WRKSRC}/util/support_scripts/GG_write_trinity_cmds.pl
-SUBST_SED.gc_write= -e 's|$$FindBin::Bin/../../Trinity|Trinity|g'
+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
-DATADIR= ${PREFIX}/share/trinity
-DOCSDIR= ${PREFIX}/share/doc/trinity
+CXXFLAGS= -fopenmp
-# Add p4-sys-cpu for CPU_MAX?
+FETCH_USING= curl
+PORTVERSION= 2.1.1
+EXAMPLESDIR= ${PREFIX}/share/examples/trinity
LIBEXEC_DIR= ${PREFIX}/libexec/trinity
PLUGINS_DIR= ${LIBEXEC_DIR}/trinity-plugins
-# FIXME: Much more needs to be installed
-# FIXME: Some of the 'plugins' should really be separate ports
-# Just dumping them to libexec/trinity for now
+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:
- ${MKDIR} ${DESTDIR}${PREFIX}/bin
${INSTALL_SCRIPT} ${WRKSRC}/Trinity ${DESTDIR}${PREFIX}/bin
- ${MKDIR} ${DESTDIR}${LIBEXEC_DIR}/Chrysalis
cd ${WRKSRC}/Chrysalis && \
${INSTALL_PROGRAM} BreakTransByPairs Chrysalis \
- GraphFromFasta IsoformAugment JoinTransByPairs \
- QuantifyGraph ReadsToTranscripts RunButterfly \
+ 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
- ${MKDIR} ${DESTDIR}${LIBEXEC_DIR}/Inchworm/bin
${INSTALL_PROGRAM} ${WRKSRC}/Inchworm/bin/* \
${DESTDIR}${LIBEXEC_DIR}/Inchworm/bin
- ${MKDIR} ${DESTDIR}${LIBEXEC_DIR}/Butterfly
${INSTALL_SCRIPT} ${WRKSRC}/Butterfly/Butterfly.jar \
${DESTDIR}${LIBEXEC_DIR}/Butterfly
- cd ${WRKSRC} && pax -rw PerlLib \
+ cd ${WRKSRC} && pax -rw PerlLib -s ',.*.orig$$,,' \
${DESTDIR}${LIBEXEC_DIR}
- cd ${WRKSRC} && pax -rw util \
- ${DESTDIR}${LIBEXEC_DIR}
- ${MKDIR} ${DESTDIR}${PLUGINS_DIR}/fastool
- ${INSTALL_PROGRAM} ${WRKSRC}/trinity-plugins/fastool/fastool \
- ${DESTDIR}${PLUGINS_DIR}/fastool
- ${MKDIR} ${DESTDIR}${PLUGINS_DIR}/collectl
+ cd ${WRKSRC} && pax -rw util ${DESTDIR}${LIBEXEC_DIR}
cd ${WRKSRC}/trinity-plugins/collectl && \
pax -rw bin ${DESTDIR}${PLUGINS_DIR}/collectl
- ${MKDIR} ${DESTDIR}${PLUGINS_DIR}/coreutils
- cd ${WRKSRC}/trinity-plugins/coreutils && \
- pax -rw bin ${DESTDIR}${PLUGINS_DIR}/coreutils
- ${MKDIR} ${DESTDIR}${PLUGINS_DIR}/parafly/bin
- ${INSTALL_PROGRAM} ${WRKSRC}/trinity-plugins/parafly/bin/ParaFly \
- ${DESTDIR}${PLUGINS_DIR}/parafly/bin
- ${MKDIR} ${DESTDIR}${PLUGINS_DIR}/Trimmomatic
- cd ${WRKSRC}/trinity-plugins/Trimmomatic && \
- pax -rw adapters trimmomatic*.jar \
- ${DESTDIR}${PLUGINS_DIR}/Trimmomatic
+ 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/bowtie/buildlink3.mk"
-.include "../../wip/samtools/buildlink3.mk"
-.include "../../wip/jellyfish/buildlink3.mk"
-.include "../../wip/parafly/buildlink3.mk"
-# Causes configure failure on Avi, but not on centosdev, where -lexecinfo
-# is not added for some reason. Limit to non-Linux platforms?
-#.include "../../devel/libexecinfo/buildlink3.mk"
+ ${DESTDIR}${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
index 540c986..4775fad 100644
--- a/trinity/PLIST
+++ b/trinity/PLIST
@@ -1,15 +1,19 @@
-@comment $NetBSD: PLIST,v 1.1 2015/01/28 16:44:31 outpaddling Exp $
+@comment $NetBSD$
bin/Trinity
libexec/trinity/Butterfly/Butterfly.jar
libexec/trinity/Chrysalis/BreakTransByPairs
libexec/trinity/Chrysalis/checkLock
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/Inchworm/bin/cigar_tweaker
@@ -20,8 +24,6 @@ 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/cache_completed_LSF_cmds
-libexec/trinity/PerlLib/cache_completed_SGE_cmds
libexec/trinity/PerlLib/CanvasXpress/Heatmap.pm
libexec/trinity/PerlLib/CDNA/Alignment_segment.pm
libexec/trinity/PerlLib/CDNA/Alternative_splice_comparer.pm
@@ -35,12 +37,10 @@ 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/cmds_for_parafly.txt
-libexec/trinity/PerlLib/cmds_for_parafly.txt.completed
libexec/trinity/PerlLib/ColorGradient.pm
+libexec/trinity/PerlLib/COMMON.pm
libexec/trinity/PerlLib/EM.pm
libexec/trinity/PerlLib/Exons_to_geneobj.pm
-libexec/trinity/PerlLib/FailedCommands
libexec/trinity/PerlLib/Fasta_reader.pm
libexec/trinity/PerlLib/Fasta_retriever.pm
libexec/trinity/PerlLib/Fastq_reader.pm
@@ -51,34 +51,13 @@ 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/HTC/Base_handler.pm
-libexec/trinity/PerlLib/HTC/FarmIt.pm
-libexec/trinity/PerlLib/HTC/GridRunner.pm
-libexec/trinity/PerlLib/HTC/LSF_handler.pm
-libexec/trinity/PerlLib/HTC/SGE_handler.pm
-libexec/trinity/PerlLib/HTC/SLURM_handler.pm
-libexec/trinity/PerlLib/J14349.S0.sh.e7297570
-libexec/trinity/PerlLib/J14349.S0.sh.o7297570
-libexec/trinity/PerlLib/J14349.S10.sh.e7297580
-libexec/trinity/PerlLib/J14349.S10.sh.o7297580
-libexec/trinity/PerlLib/J14349.S1.sh.e7297571
-libexec/trinity/PerlLib/J14349.S1.sh.o7297571
-libexec/trinity/PerlLib/J14349.S2.sh.e7297572
-libexec/trinity/PerlLib/J14349.S2.sh.o7297572
-libexec/trinity/PerlLib/J14349.S3.sh.e7297573
-libexec/trinity/PerlLib/J14349.S3.sh.o7297573
-libexec/trinity/PerlLib/J14349.S4.sh.e7297574
-libexec/trinity/PerlLib/J14349.S4.sh.o7297574
-libexec/trinity/PerlLib/J14349.S5.sh.e7297575
-libexec/trinity/PerlLib/J14349.S5.sh.o7297575
-libexec/trinity/PerlLib/J14349.S6.sh.e7297576
-libexec/trinity/PerlLib/J14349.S6.sh.o7297576
-libexec/trinity/PerlLib/J14349.S7.sh.e7297577
-libexec/trinity/PerlLib/J14349.S7.sh.o7297577
-libexec/trinity/PerlLib/J14349.S8.sh.e7297578
-libexec/trinity/PerlLib/J14349.S8.sh.o7297578
-libexec/trinity/PerlLib/J14349.S9.sh.e7297579
-libexec/trinity/PerlLib/J14349.S9.sh.o7297579
+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
@@ -100,6 +79,8 @@ libexec/trinity/PerlLib/Nuc_translator.pm
libexec/trinity/PerlLib/Overlap_info.pm
libexec/trinity/PerlLib/Overlap_piler.pm
libexec/trinity/PerlLib/overlapping_nucs.ph
+libexec/trinity/PerlLib/Pipeliner.pm
+libexec/trinity/PerlLib/Process_cmd.pm
libexec/trinity/PerlLib/PSL_parser.pm
libexec/trinity/PerlLib/SAM_entry.pm
libexec/trinity/PerlLib/SAM_reader.pm
@@ -115,6 +96,7 @@ libexec/trinity/PerlLib/WigParser.pm
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/collectl2html
libexec/trinity/trinity-plugins/collectl/bin/collectl.conf
libexec/trinity/trinity-plugins/collectl/bin/envrules.std
libexec/trinity/trinity-plugins/collectl/bin/formatit.ph
@@ -122,24 +104,16 @@ 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.sh
+libexec/trinity/trinity-plugins/collectl/bin/make_data_files.py
libexec/trinity/trinity-plugins/collectl/bin/misc.ph
-libexec/trinity/trinity-plugins/collectl/bin/nvidia.ph
-libexec/trinity/trinity-plugins/collectl/bin/plot.sh
+libexec/trinity/trinity-plugins/collectl/bin/plot.py
libexec/trinity/trinity-plugins/collectl/bin/proctree.ph
-libexec/trinity/trinity-plugins/collectl/bin/sexpr.ph
-libexec/trinity/trinity-plugins/collectl/bin/timetable.sh
+libexec/trinity/trinity-plugins/collectl/bin/timetable.py
libexec/trinity/trinity-plugins/collectl/bin/UNINSTALL
libexec/trinity/trinity-plugins/collectl/bin/vmstat.ph
-libexec/trinity/trinity-plugins/coreutils/bin/sort
-libexec/trinity/trinity-plugins/fastool/fastool
-libexec/trinity/trinity-plugins/parafly/bin/ParaFly
-libexec/trinity/trinity-plugins/Trimmomatic/adapters/TruSeq2-PE.fa
-libexec/trinity/trinity-plugins/Trimmomatic/adapters/TruSeq2-SE.fa
-libexec/trinity/trinity-plugins/Trimmomatic/adapters/TruSeq3-PE.fa
-libexec/trinity/trinity-plugins/Trimmomatic/adapters/TruSeq3-SE.fa
-libexec/trinity/trinity-plugins/Trimmomatic/trimmomatic-0.30.jar
-libexec/trinity/trinity-plugins/Trimmomatic/trimmomatic.jar
+libexec/trinity/trinity-plugins/GAL_0.2.1/fasta_tool
+libexec/trinity/trinity-plugins/GAL_0.2.1/README
+libexec/trinity/trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs
libexec/trinity/util/abundance_estimates_to_matrix.pl
libexec/trinity/util/align_and_estimate_abundance.pl
libexec/trinity/util/analyze_blastPlus_topHit_coverage.pl
@@ -170,21 +144,25 @@ libexec/trinity/util/deprecated/sort_fasta.sh
libexec/trinity/util/deprecated/write_inchworm_cmds.pl
libexec/trinity/util/fasta_tool
libexec/trinity/util/filter_fasta_by_rsem_values.pl
-libexec/trinity/util/HTC_helpers/bsub_fasta_bin_cmd_processor.pl
-libexec/trinity/util/HTC_helpers/htc_bin_blastPlus.pl
-libexec/trinity/util/HTC_helpers/run_cmds_on_grid.pl
libexec/trinity/util/insilico_read_normalization.pl
-libexec/trinity/util/ladeda.pl
libexec/trinity/util/misc/acc_list_to_fasta_entries.pl
libexec/trinity/util/misc/alexie_analyze_blast.pl
libexec/trinity/util/misc/allele_simulator.pl
+libexec/trinity/util/misc/altsplice_simulation_toolkit/sim_single_bubble.pl
libexec/trinity/util/misc/analyze_blastPlus_topHit_coverage.annotate_details_w_FL_info.pl
libexec/trinity/util/misc/analyze_blastPlus_topHit_coverage.by_prioritized_compreh_category.pl
libexec/trinity/util/misc/analyze_blastPlus_topHit_coverage.extract_OS.pl
libexec/trinity/util/misc/analyze_blastPlus_topHit_coverage.org_matrix.pl
libexec/trinity/util/misc/Artemis/join_multi_wig_to_graph_plot.pl
libexec/trinity/util/misc/average.pl
+libexec/trinity/util/misc/bam_gene_tests/extract_bam_reads_per_target_gene.pl
+libexec/trinity/util/misc/bam_gene_tests/extract_bam_reads_per_target_transcript.pl
+libexec/trinity/util/misc/bam_gene_tests/harvest_transcripts.pl
+libexec/trinity/util/misc/bam_gene_tests/write_trin_cmds.pl
libexec/trinity/util/misc/blastn_wrapper.pl
+libexec/trinity/util/misc/blast_outfmt6_group_segments.pl
+libexec/trinity/util/misc/blast_outfmt6_group_segments.to_Markov_Clustering.pl
+libexec/trinity/util/misc/blast_outfmt6_group_segments.tophit_coverage.pl
libexec/trinity/util/misc/BLAT_to_SAM.pl
libexec/trinity/util/misc/blat_util/blat_sam_add_reads2.pl
libexec/trinity/util/misc/blat_util/blat_top_hit_extractor.pl
@@ -202,8 +180,11 @@ libexec/trinity/util/misc/chrys_graph_to_dot.pl
libexec/trinity/util/misc/combined_nameSorted_to_dup_pairs_removed.pl
libexec/trinity/util/misc/compare_bflies.pl
libexec/trinity/util/misc/component_to_graph_dot.pl
+libexec/trinity/util/misc/contig_ExN50_statistic.pl
libexec/trinity/util/misc/convert_fasta_identifiers_for_FL_analysis.pl
libexec/trinity/util/misc/count_features_given_MIN_FPKM_threshold.pl
+libexec/trinity/util/misc/count_iso_per_gene_dist.pl
+libexec/trinity/util/misc/count_matrix_features_given_MIN_TPM_threshold.pl
libexec/trinity/util/misc/count_N50_given_MIN_FPKM_threshold.pl
libexec/trinity/util/misc/count_number_fasta_seqs.pl
libexec/trinity/util/misc/count_trans_per_component.pl
@@ -212,6 +193,7 @@ libexec/trinity/util/misc/describe_SAM_read_flag_info.pl
libexec/trinity/util/misc/examine_iworm_FL_across_threads.pl
libexec/trinity/util/misc/examine_weldmer_halves.pl
libexec/trinity/util/misc/extract_fastQ_pairings.pl
+libexec/trinity/util/misc/fan_out_fasta_seqs_to_indiv_files.pl
libexec/trinity/util/misc/fasta_file_reformatter.pl
libexec/trinity/util/misc/fasta_filter_by_min_length.pl
libexec/trinity/util/misc/fasta_remove_duplicates.pl
@@ -222,13 +204,18 @@ libexec/trinity/util/misc/fastq_cleaner.pl
libexec/trinity/util/misc/fastq_interleave_pairs.pl
libexec/trinity/util/misc/fastq_merge_sorted_tab_lists.pl
libexec/trinity/util/misc/fastQ_rand_subset.pl
+libexec/trinity/util/misc/fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl
libexec/trinity/util/misc/fastq_stats.pl
libexec/trinity/util/misc/fastQ_top_N_records.pl
libexec/trinity/util/misc/fastq_unweave_pairs.pl
libexec/trinity/util/misc/frag_boundary_to_wig.pl
libexec/trinity/util/misc/frag_to_bed.pl
libexec/trinity/util/misc/gene_gff3_to_introns.pl
+libexec/trinity/util/misc/gene_to_shared_transcript_content.pl
+libexec/trinity/util/misc/genome_gff3_to_gene_gff3_partitions.pl
+libexec/trinity/util/misc/get_longest_isoform_seq_per_trinity_gene.pl
libexec/trinity/util/misc/get_path_nodes_from_fasta.pl
+libexec/trinity/util/misc/get_welds_from_chrysals_graphFromFasta_out.pl
libexec/trinity/util/misc/gff3_file_to_cdna.pl
libexec/trinity/util/misc/gff3_file_utr_coverage_trimmer.pl
libexec/trinity/util/misc/gff3_to_genome_feature_base_encoding.parse_SAM.pl
@@ -242,10 +229,20 @@ libexec/trinity/util/misc/gtf_to_introns.pl
libexec/trinity/util/misc/HiCpipe_nameSortedSam_to_raw.pl
libexec/trinity/util/misc/hicpipe_raw_converter.pl
libexec/trinity/util/misc/identify_distal_isoform_variations.pl
+libexec/trinity/util/misc/illustrate_ref_comparison.pl
libexec/trinity/util/misc/insilico_norm_kmer_hists/kmer_histo.all.txt
libexec/trinity/util/misc/insilico_norm_kmer_hists/kmer_histo.NormMaxKCov50.txt
libexec/trinity/util/misc/insilico_norm_kmer_hists/plot_me.R
libexec/trinity/util/misc/insilico_norm_kmer_hists/result.pdf
+libexec/trinity/util/misc/iso_reco_analysis/bam_to_cuff.pl
+libexec/trinity/util/misc/iso_reco_analysis/cuff_gtf_to_bed.pl
+libexec/trinity/util/misc/iso_reco_analysis/gene_gff3_to_bed_cmds.pl
+libexec/trinity/util/misc/iso_reco_analysis/gmap_to_ref.pl
+libexec/trinity/util/misc/iso_reco_analysis/notes
+libexec/trinity/util/misc/iso_reco_analysis/run_trinity_no_LR.pl
+libexec/trinity/util/misc/iso_reco_analysis/run_trinity_WITH_LR.pl
+libexec/trinity/util/misc/iso_reco_analysis/sim_reads.pl
+libexec/trinity/util/misc/iso_reco_analysis/trans_gff3_to_bed_cmds.pl
libexec/trinity/util/misc/jaccard_sam_pair_refiner.pl
libexec/trinity/util/misc/join_any.pl
libexec/trinity/util/misc/join_by_left_col.pl
@@ -255,27 +252,41 @@ libexec/trinity/util/misc/m8_blastclust.pl
libexec/trinity/util/misc/map_gtf_transcripts_to_genome_annots.pl
libexec/trinity/util/misc/merge_blast_n_rsem_results.pl
libexec/trinity/util/misc/merge_rsem_n_express_for_compare.pl
+libexec/trinity/util/misc/merge_RSEM_output_to_matrix.pl
libexec/trinity/util/misc/Monarch
+libexec/trinity/util/misc/Monarch_util/generate_gene_alt_splicing_graphs.pl
+libexec/trinity/util/misc/Monarch_util/generate_trans_graphs.pl
+libexec/trinity/util/misc/mpi_iworm_proc_contigs_to_fa.pl
libexec/trinity/util/misc/N50.pl
libexec/trinity/util/misc/nameSorted_SAM_to_FastQ.pl
+libexec/trinity/util/misc/omp_iworm_thread_contigs_to_fa.pl
libexec/trinity/util/misc/organize_data_table_by_trinity_component.pl
+libexec/trinity/util/misc/pair_up_fastq_files_1_2.pl
+libexec/trinity/util/misc/pair_up_fastq_files_LeftRight.pl
+libexec/trinity/util/misc/pair_up_fastq_files_R1_R2.pl
libexec/trinity/util/misc/pairwise_kmer_content_comparer.pl
libexec/trinity/util/misc/PerlLib/SegmentGraph.pm
libexec/trinity/util/misc/plot_expressed_gene_dist.pl
libexec/trinity/util/misc/print_kmers.pl
libexec/trinity/util/misc/print.pl
+libexec/trinity/util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl
libexec/trinity/util/misc/prop_pair_sam_refiner.pl
libexec/trinity/util/misc/remove_cntrl_chars.pl
libexec/trinity/util/misc/row_to_column.pl
+libexec/trinity/util/misc/run_bwa.pl
libexec/trinity/util/misc/run_bwasw_trinity.pl
+libexec/trinity/util/misc/run_GSNAP.pl
libexec/trinity/util/misc/run_HiCpipe_bowtie.pl
+libexec/trinity/util/misc/run_HISAT.pl
libexec/trinity/util/misc/run_jellyfish.pl
libexec/trinity/util/misc/run_read_simulator_per_fasta_entry.pl
libexec/trinity/util/misc/run_read_simulator_per_gene.pl
+libexec/trinity/util/misc/run_STAR.pl
libexec/trinity/util/misc/run_TOPHAT.pl
libexec/trinity/util/misc/run_trimmomatic_qual_trimming.pl
libexec/trinity/util/misc/SAM_coordsorted_max_reads_per_position.pl
libexec/trinity/util/misc/SAM_intron_extractor.pl
+libexec/trinity/util/misc/SAM_pair_to_bed.pl
libexec/trinity/util/misc/SAM_show_alignment.pl
libexec/trinity/util/misc/SAM_show_alignment.summarize_stats.pl
libexec/trinity/util/misc/SAM_sortAny_to_count_stats.pl
@@ -284,6 +295,8 @@ libexec/trinity/util/misc/SAM_to_fasta.pl
libexec/trinity/util/misc/SAM_toString.pl
libexec/trinity/util/misc/shuffle.pl
libexec/trinity/util/misc/simulate_illuminaPE_from_transcripts.pl
+libexec/trinity/util/misc/simulate_reads_sam_and_fa.pl
+libexec/trinity/util/misc/sixFrameTranslation.pl
libexec/trinity/util/misc/sort_fastq.pl
libexec/trinity/util/misc/splice_path_analysis/assess_intron_path_sensitivity.pl
libexec/trinity/util/misc/splice_path_analysis/assess_intron_path_sensitivity.summarizer.pl
@@ -295,6 +308,7 @@ libexec/trinity/util/misc/strip_fasta_header.pl
libexec/trinity/util/misc/tab_to_fasta.pl
libexec/trinity/util/misc/tab_to_fastQ.pl
libexec/trinity/util/misc/tblastn_wrapper.pl
+libexec/trinity/util/misc/TEST_SUPPORT/BFLY_TESTING/graph_out_to_bfly_cmd.pl
libexec/trinity/util/misc/testUnlimitStacksize.pl
libexec/trinity/util/misc/TophatCufflinksWrapper.pl
libexec/trinity/util/misc/transcript_coverage_UTR_trimmer.pl
@@ -321,7 +335,10 @@ libexec/trinity/util/retrieve_sequences_from_fasta.pl
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/run_DE_analysis_from_samples_file.pl
+libexec/trinity/util/run_RSEM_from_samples_file.pl
libexec/trinity/util/run_Trinity_edgeR_pipeline.pl
+libexec/trinity/util/run_Trinity_from_samples_file.pl
libexec/trinity/util/SAM_nameSorted_to_uniq_count_stats.pl
libexec/trinity/util/support_scripts/define_coverage_partitions.pl
libexec/trinity/util/support_scripts/define_SAM_coverage_partitions2.pl
@@ -333,18 +350,19 @@ libexec/trinity/util/support_scripts/fastQ_to_fastA.pl
libexec/trinity/util/support_scripts/fastQ_to_tab.pl
libexec/trinity/util/support_scripts/fragment_coverage_writer.pl
libexec/trinity/util/support_scripts/get_Trinity_gene_to_trans_map.pl
-libexec/trinity/util/support_scripts/GG_trinity_accession_incrementer.pl
-libexec/trinity/util/support_scripts/GG_write_trinity_cmds.pl
+libexec/trinity/util/support_scripts/GG_partitioned_trinity_aggregator.pl
libexec/trinity/util/support_scripts/inchworm_transcript_splitter.pl
-libexec/trinity/util/support_scripts/install_tests.sh
libexec/trinity/util/support_scripts/jaccard_fasta_clipper.pl
libexec/trinity/util/support_scripts/jaccard_wig_clipper.pl
libexec/trinity/util/support_scripts/join_partitions_within_range.pl
+libexec/trinity/util/support_scripts/kallisto_trans_to_gene_results.pl
libexec/trinity/util/support_scripts/merge_left_right_nameSorted_SAMs.pl
libexec/trinity/util/support_scripts/nbkc_merge_left_right_stats.pl
libexec/trinity/util/support_scripts/nbkc_normalize.pl
libexec/trinity/util/support_scripts/ordered_fragment_coords_to_jaccard.pl
libexec/trinity/util/support_scripts/partition_chrysalis_graphs_n_reads.pl
+libexec/trinity/util/support_scripts/partitioned_trinity_aggregator.pl
+libexec/trinity/util/support_scripts/plugin_install_tests.sh
libexec/trinity/util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl
libexec/trinity/util/support_scripts/print_butterfly_assemblies.pl
libexec/trinity/util/support_scripts/process_GMAP_alignments_gff3_chimeras_ok.pl
@@ -362,5 +380,198 @@ libexec/trinity/util/support_scripts/SAM_strand_separator.pl
libexec/trinity/util/support_scripts/SAM_to_frag_coords.pl
libexec/trinity/util/support_scripts/scaffold_iworm_contigs.pl
libexec/trinity/util/support_scripts/segment_GFF_partitions.pl
+libexec/trinity/util/support_scripts/tests/test_prep.py
+libexec/trinity/util/support_scripts/tests/test.py
+libexec/trinity/util/support_scripts/tests/tests.py
+libexec/trinity/util/support_scripts/trinity_install_tests.sh
libexec/trinity/util/support_scripts/wig_clip_to_bed.pl
+libexec/trinity/util/support_scripts/write_partitioned_trinity_cmds.pl
libexec/trinity/util/TrinityStats.pl
+share/examples/trinity/Makefile
+share/examples/trinity/__regression_tests/test_GraphFromFasta/both.fa.gz
+share/examples/trinity/__regression_tests/test_GraphFromFasta/inchworm.K25.L25.fa.gz
+share/examples/trinity/__regression_tests/test_GraphFromFasta/iworm_scaffolds.txt.gz
+share/examples/trinity/__regression_tests/test_GraphFromFasta/runMe.sh
+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/Makefile
+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_DATA/Sp_ds.10k.left.fq.gz
+share/examples/trinity/test_DATA/Sp_ds.10k.right.fq.gz
+share/examples/trinity/test_DATA/Sp_hs.10k.left.fq.gz
+share/examples/trinity/test_DATA/Sp_hs.10k.right.fq.gz
+share/examples/trinity/test_DATA/Sp_log.10k.left.fq.gz
+share/examples/trinity/test_DATA/Sp_log.10k.right.fq.gz
+share/examples/trinity/test_DATA/Sp_plat.10k.left.fq.gz
+share/examples/trinity/test_DATA/Sp_plat.10k.right.fq.gz
+share/examples/trinity/test_DATA/Trinity.fasta
+share/examples/trinity/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/cleanme.pl
+share/examples/trinity/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/counts.matrix
+share/examples/trinity/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/Makefile
+share/examples/trinity/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/run_DESeq2.sh
+share/examples/trinity/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/samples.txt
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/cleanMe.sh
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/all_data_files.list
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/cysts.dat
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/example.matrix.normalized.FPKM
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc.dat
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc_vs_cysts.eps
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc_vs_cysts.results.txt
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/TMM_info.txt
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_run_edgeR.1820.R
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_runTMM.R
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_targets.1820.dat
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/example.matrix
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/Makefile
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/runMe.sh
+share/examples/trinity/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/Trinity.fa.seqLens
+share/examples/trinity/test_DE_analysis/deprecated/testEdgeRfuncs/cleanMe.sh
+share/examples/trinity/test_DE_analysis/deprecated/testEdgeRfuncs/dataA.dat
+share/examples/trinity/test_DE_analysis/deprecated/testEdgeRfuncs/dataB.dat
+share/examples/trinity/test_DE_analysis/deprecated/testEdgeRfuncs/Makefile
+share/examples/trinity/test_DE_analysis/deprecated/testEdgeRfuncs/run_edgeR_on_sample_data.R
+share/examples/trinity/test_DE_analysis/deprecated/testEdgeRfuncs/runMe.sh
+share/examples/trinity/test_DE_analysis/deprecated/testEdgeRfuncs/targets.dat
+share/examples/trinity/test_DE_analysis/Makefile
+share/examples/trinity/test_DE_analysis/notes
+share/examples/trinity/test_DE_analysis/samples.txt
+share/examples/trinity/test_DE_analysis/Trinity_trans.counts.matrix
+share/examples/trinity/test_DE_analysis/Trinity_trans.TMM.EXPR.matrix
+share/examples/trinity/test_DE_analysis/Trinity_trans.TPM.not_cross_norm
+share/examples/trinity/test_full_edgeR_pipeline/cleanme.pl
+share/examples/trinity/test_full_edgeR_pipeline/Makefile
+share/examples/trinity/test_full_edgeR_pipeline/runMe.sh
+share/examples/trinity/test_full_edgeR_pipeline/samples_n_reads_decribed.txt
+share/examples/trinity/test_GenomeGuidedTrinity/cleanme.pl
+share/examples/trinity/test_GenomeGuidedTrinity/Makefile
+share/examples/trinity/test_GenomeGuidedTrinity/mm9chr17.annotation.bed.gz
+share/examples/trinity/test_GenomeGuidedTrinity/mm9chr17.fasta.gz
+share/examples/trinity/test_GenomeGuidedTrinity/mm9chr17.tophat.bam
+share/examples/trinity/test_GenomeGuidedTrinity/old/run_genome-guided_Trinity.sh
+share/examples/trinity/test_GenomeGuidedTrinity/old/__run_genome-guided_Trinity_use_existing_bam.use_LSF.sh
+share/examples/trinity/test_GenomeGuidedTrinity/old/__run_genome-guided_Trinity_use_existing_bam.use_PBS.sh
+share/examples/trinity/test_GenomeGuidedTrinity/old/__run_genome-guided_Trinity_use_existing_bam.use_SGE.sh
+share/examples/trinity/test_GenomeGuidedTrinity/old/run_mouse_TrinityGG.sh
+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/run_genome-guided_Trinity_use_existing_bam.sh
+share/examples/trinity/test_GenomeGuidedTrinity/run_Schizo_TrinityGG_jaccard_clip.sh
+share/examples/trinity/test_GenomeGuidedTrinity/SP2.annot.bed.gz
+share/examples/trinity/test_GenomeGuidedTrinity/SP2.chr.bam
+share/examples/trinity/test_GenomeGuidedTrinity/SP2.chr.fa.gz
+share/examples/trinity/test_GenomeGuidedTrinity/SP2.chr.SE.sam.gz
+share/examples/trinity/test_GenomeGuidedTrinity/top100k.genome.gz
+share/examples/trinity/test_GenomeGuidedTrinity/top100k.Left.fq.gz
+share/examples/trinity/test_GenomeGuidedTrinity/top100k.Right.fq.gz
+share/examples/trinity/test_GOSeq_trinotate_pipe/from_enrichnet.org/Cancer_genes_Futreal2004.ids
+share/examples/trinity/test_GOSeq_trinotate_pipe/from_enrichnet.org/Parkinsons_disease_Phenopedia2011.ids
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/cleanme.pl
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/ds_induced_vs_log.accs.lab
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/ds_induced_vs_log.factors
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/hs_induced_vs_log.accs.lab
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/hs_induced_vs_log.factors
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/runMe.sh
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/Trinity.seq_lengths
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/Trinotate_report.xls
+share/examples/trinity/test_GOSeq_trinotate_pipe/Spombe/Trinotate_report.xls.trans.gene_ontology
+share/examples/trinity/test_Inchworm/jellyfish.kmers.fa.gz
+share/examples/trinity/test_Inchworm/runMe_MPI.sh
+share/examples/trinity/test_InSilicoReadNormalization/cleanme.pl
+share/examples/trinity/test_InSilicoReadNormalization/Makefile
+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_Trinity_Assembly/cleanme.pl
+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/longReads.fa
+share/examples/trinity/test_Trinity_Assembly/Makefile
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__run_abundance_estimation_include_antisense.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_CuffFly.sh
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe.diff_kmer_length.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_no_qualTrim.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_PasaFly.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_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/__runMe_with_qual_trimming.sh
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_w_monitoring.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.singleFQ.sh
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__test_runMe_with_jaccard_clip.sh
+share/examples/trinity/test_Trinity_Assembly/README
+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/reads.left.fq.gz
+share/examples/trinity/test_Trinity_Assembly/reads.right.fq.gz
+share/examples/trinity/test_Trinity_Assembly/runMe.sh
+share/examples/trinity/test_Trinity_Assembly/test_FL.sh
diff --git a/trinity/TODO b/trinity/TODO
index 835201f..b2e3b56 100644
--- a/trinity/TODO
+++ b/trinity/TODO
@@ -1,6 +1 @@
-
-Clean up jellyfish script - contains paths in pkg work dir
-
-Patch TRINITY_HOME in Trinity script
-
-Make sure separate ParaFly is used by GridRunner
+Clean up and test.
diff --git a/trinity/buildlink3.mk b/trinity/buildlink3.mk
deleted file mode 100644
index 49cdd8f..0000000
--- a/trinity/buildlink3.mk
+++ /dev/null
@@ -1,22 +0,0 @@
-# $NetBSD: buildlink3.mk,v 1.1 2015/01/28 16:44:31 outpaddling Exp $
-# XXX
-# XXX This file was created automatically using createbuildlink-3.16.
-# XXX After this file has been verified as correct, the comment lines
-# XXX beginning with "XXX" should be removed. Please do not commit
-# XXX unverified buildlink3.mk files.
-# XXX
-# XXX Packages that only install static libraries or headers should
-# XXX include the following line:
-# XXX
-# XXX BUILDLINK_DEPMETHOD.trinity?= build
-
-BUILDLINK_TREE+= trinity
-
-.if !defined(TRINITY_BUILDLINK3_MK)
-TRINITY_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.trinity+= trinity>=2014.04.13
-BUILDLINK_PKGSRCDIR.trinity?= ../../wip/trinity
-.endif # TRINITY_BUILDLINK3_MK
-
-BUILDLINK_TREE+= -trinity
diff --git a/trinity/distinfo b/trinity/distinfo
index 6ef27f2..b1218cd 100644
--- a/trinity/distinfo
+++ b/trinity/distinfo
@@ -1,8 +1,10 @@
-$NetBSD: distinfo,v 1.1 2015/01/28 16:44:31 outpaddling Exp $
+$NetBSD$
-SHA1 (trinityrnaseq_r20140413p1.tar.gz) = d916cc7099a6a45de923e20bba85bb7949420395
-RMD160 (trinityrnaseq_r20140413p1.tar.gz) = f62a9830fef47d0ad3b85b65c365994e8e684447
-Size (trinityrnaseq_r20140413p1.tar.gz) = 156313571 bytes
-SHA1 (patch-PerlLib-HTC-SLURM_handler.pm) = fc978425c6c9a2894e8a08e3914bf85b4916c707
-SHA1 (patch-PerlLib_HTC_FarmIt.pm) = a3a1b8542ad11c609d89fccce6a65b7e843544f5
-SHA1 (patch-Trinity) = bfba1122d8bbae8bc533b4a7e2abd95ee37caa32
+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
new file mode 100644
index 0000000..5d71ae7
--- /dev/null
+++ b/trinity/patches/patch-Makefile
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# 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-HTC-SLURM_handler.pm b/trinity/patches/patch-PerlLib-HTC-SLURM_handler.pm
deleted file mode 100644
index ae6a360..0000000
--- a/trinity/patches/patch-PerlLib-HTC-SLURM_handler.pm
+++ /dev/null
@@ -1,12 +0,0 @@
---- PerlLib/HTC/SLURM_handler.pm.orig 2014-08-15 08:34:45.000000000 -0500
-+++ PerlLib/HTC/SLURM_handler.pm 2014-08-15 08:35:47.000000000 -0500
---- PerlLib/HTC/SLURM_handler.pm.orig 2014-04-23 15:59:17.000000000 +0000
-+++ PerlLib/HTC/SLURM_handler.pm
-@@ -42,6 +42,7 @@ sub submit_job_to_grid {
-
- $cmd .= " $shell_script 2>&1 ";
-
-+ print STDERR "\nExecuting $cmd\n";
-
- my $job_id_text = `$cmd`;
-
diff --git a/trinity/patches/patch-PerlLib_HPC_SLURM__handler.pm b/trinity/patches/patch-PerlLib_HPC_SLURM__handler.pm
new file mode 100644
index 0000000..c3e0dfc
--- /dev/null
+++ b/trinity/patches/patch-PerlLib_HPC_SLURM__handler.pm
@@ -0,0 +1,28 @@
+$NetBSD$
+
+# 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-PerlLib_HTC_FarmIt.pm b/trinity/patches/patch-PerlLib_HTC_FarmIt.pm
deleted file mode 100644
index b6a6d5d..0000000
--- a/trinity/patches/patch-PerlLib_HTC_FarmIt.pm
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD: patch-PerlLib_HTC_FarmIt.pm,v 1.1 2015/01/28 16:44:31 outpaddling Exp $
-
---- PerlLib/HTC/FarmIt.pm.orig 2014-04-23 15:59:17.000000000 +0000
-+++ PerlLib/HTC/FarmIt.pm
-@@ -447,8 +447,8 @@ sub _wait_for_completions {
-
- if ($all_OK) {
- # lets not retain the shell script and stderr and stdout. Only retain them for failures.
-- unlink($shell_script);
-- unlink("$shell_script.stderr", "$shell_script.stdout");
-+ # unlink($shell_script);
-+ # unlink("$shell_script.stderr", "$shell_script.stdout");
- delete $self->{job_id_to_shell_script}->{$job_id};
-
- print "OK. Trying to delete $shell_script and .stderr and .stdout.\n" if $SEE;
diff --git a/trinity/patches/patch-Trinity b/trinity/patches/patch-Trinity
deleted file mode 100644
index dc2240a..0000000
--- a/trinity/patches/patch-Trinity
+++ /dev/null
@@ -1,41 +0,0 @@
---- Trinity.orig 2014-04-23 11:04:48.000000000 -0500
-+++ Trinity 2014-05-23 16:54:38.000000000 -0500
---- Trinity.orig 2014-04-23 16:04:48.000000000 +0000
-+++ Trinity
-@@ -6,7 +6,7 @@ use threads;
- no strict qw(subs refs);
-
- use FindBin;
--use lib ("$FindBin::Bin/PerlLib");
-+use lib ("$FindBin::Bin/../libexec/trinity/PerlLib");
- use File::Basename;
- use Time::localtime;
- use Cwd;
-@@ -15,7 +15,7 @@ use Getopt::Long qw(:config no_ignore_ca
-
- BEGIN {
-
-- $ENV{TRINITY_HOME} = "$FindBin::Bin";
-+ $ENV{TRINITY_HOME} = "$FindBin::Bin/../libexec/trinity";
-
- }
-
-@@ -26,7 +26,8 @@ open (STDERR, ">&STDOUT"); ## capturing
-
- # Site specific setup
-
--my $CPU_MAX = 64; # set higher at your own risk. Definitely don't set it higher than the number of cores available on your machine.
-+# FIXME: Linux-specific. Use a Perl module or something else portable.
-+my $CPU_MAX = `nproc`;
-
- my $IWORM_KMER_SIZE = 25;
- my $MIN_IWORM_LEN = 25;
-@@ -476,7 +477,7 @@ _ADVANCEDUSAGE_
- ;
-
-
--my $ROOTDIR = "$FindBin::RealBin";
-+my $ROOTDIR = "$FindBin::RealBin/../libexec/trinity";
- my $UTILDIR = "$ROOTDIR/util";
- my $INCHWORM_DIR = "$ROOTDIR/Inchworm";
- my $CHRYSALIS_DIR = "$ROOTDIR/Chrysalis";
diff --git a/trinity/patches/patch-trinity-plugins_Makefile b/trinity/patches/patch-trinity-plugins_Makefile
new file mode 100644
index 0000000..680d1a9
--- /dev/null
+++ b/trinity/patches/patch-trinity-plugins_Makefile
@@ -0,0 +1,42 @@
+$NetBSD$
+
+# 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 && $(MAKE)
+
+ fastool_target:
+@@ -48,7 +50,9 @@ parafly_target:
+ ### Needed for downstream analyses
+ ##################################
+
+-plugins: slclust_target collectl_target
++# All plugins except collectl are installed as dependency ports
++# plugins: slclust_target collectl_target
++plugins: collectl_target
+ @echo "\n\n** Done building plugins **\n\n"
+
+
diff --git a/trinity/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile b/trinity/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile
new file mode 100644
index 0000000..edb5075
--- /dev/null
+++ b/trinity/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile
@@ -0,0 +1,18 @@
+$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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