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trinity-devel: Rename to trinity, now mainstream
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Sat Sep 22 09:51:16 2018 -0500
Changeset: d775f1776ba31890b863352126a4fcdbd22e1d60
Modified Files:
Makefile
Added Files:
trinity/DESCR
trinity/Makefile
trinity/PLIST
trinity/distinfo
trinity/patches/patch-Chrysalis_CMakeLists.txt
trinity/patches/patch-Chrysalis_Makefile
trinity/patches/patch-Inchworm_CMakeLists.txt
trinity/patches/patch-Inchworm_Makefile
trinity/patches/patch-Makefile
trinity/patches/patch-trinity-plugins_Makefile
trinity/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile
trinity/patches/patch-trinity-plugins_seqtk-trinity-0.0.2_Makefile
trinity/patches/patch-util_support__scripts_plugin__install__tests.sh
Removed Files:
trinity-devel/DESCR
trinity-devel/Makefile
trinity-devel/PLIST
trinity-devel/distinfo
trinity-devel/patches/patch-Chrysalis_CMakeLists.txt
trinity-devel/patches/patch-Chrysalis_Makefile
trinity-devel/patches/patch-Inchworm_CMakeLists.txt
trinity-devel/patches/patch-Inchworm_Makefile
trinity-devel/patches/patch-Makefile
trinity-devel/patches/patch-trinity-plugins_Makefile
trinity-devel/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile
trinity-devel/patches/patch-trinity-plugins_seqtk-trinity-0.0.2_Makefile
trinity-devel/patches/patch-util_support__scripts_plugin__install__tests.sh
Log Message:
trinity-devel: Rename to trinity, now mainstream
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=d775f1776ba31890b863352126a4fcdbd22e1d60
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 2 +-
trinity-devel/DESCR | 4 -
trinity-devel/Makefile | 154 ------
trinity-devel/PLIST | 615 ---------------------
trinity-devel/distinfo | 15 -
.../patches/patch-Chrysalis_CMakeLists.txt | 14 -
trinity-devel/patches/patch-Chrysalis_Makefile | 22 -
.../patches/patch-Inchworm_CMakeLists.txt | 14 -
trinity-devel/patches/patch-Inchworm_Makefile | 16 -
trinity-devel/patches/patch-Makefile | 14 -
.../patches/patch-trinity-plugins_Makefile | 35 --
...inity-plugins_scaffold__iworm__contigs_Makefile | 16 -
...ch-trinity-plugins_seqtk-trinity-0.0.2_Makefile | 14 -
...util_support__scripts_plugin__install__tests.sh | 14 -
trinity/DESCR | 4 +
trinity/Makefile | 154 ++++++
trinity/PLIST | 615 +++++++++++++++++++++
trinity/distinfo | 15 +
trinity/patches/patch-Chrysalis_CMakeLists.txt | 14 +
trinity/patches/patch-Chrysalis_Makefile | 22 +
trinity/patches/patch-Inchworm_CMakeLists.txt | 14 +
trinity/patches/patch-Inchworm_Makefile | 16 +
trinity/patches/patch-Makefile | 14 +
trinity/patches/patch-trinity-plugins_Makefile | 35 ++
...inity-plugins_scaffold__iworm__contigs_Makefile | 16 +
...ch-trinity-plugins_seqtk-trinity-0.0.2_Makefile | 14 +
...util_support__scripts_plugin__install__tests.sh | 14 +
27 files changed, 948 insertions(+), 948 deletions(-)
diffs:
diff --git a/Makefile b/Makefile
index 10abcc4949..83a94ada72 100644
--- a/Makefile
+++ b/Makefile
@@ -4541,7 +4541,7 @@ SUBDIR+= triangle
SUBDIR+= triforce-afl
SUBDIR+= trimadap
SUBDIR+= trimmomatic
-SUBDIR+= trinity-devel
+SUBDIR+= trinity
SUBDIR+= tripwire2
SUBDIR+= truecrypt
SUBDIR+= tsh
diff --git a/trinity-devel/DESCR b/trinity-devel/DESCR
deleted file mode 100644
index 7752b73aa7..0000000000
--- a/trinity-devel/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-devel/Makefile b/trinity-devel/Makefile
deleted file mode 100644
index 3ef0276936..0000000000
--- a/trinity-devel/Makefile
+++ /dev/null
@@ -1,154 +0,0 @@
-# $NetBSD$
-#
-###########################################################
-# Generated by fbsd2pkg #
-# Fri Sep 14 20:48:17 CDT 2018 #
-###########################################################
-
-###########################################################
-# Unconverted and partially converted FreeBSD port syntax:
-
-# 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.
-# To-do:
-# Unbundle collectl (low priority)
-## Should work on other 64-bit archs, but untested
-#ONLY_FOR_ARCH= amd64
-
-# Should salmon use bl3?
-# bowtie should not have bl3
-DEPENDS= coreutils>=0:../../sysutils/coreutils
-DEPENDS+= slclust>=0.0.0.20100202:../../wip/slclust
-DEPENDS+= salmon>=0.11.3:../../wip/salmon
-DEPENDS+= bowtie>=1.1.2:../../wip/bowtie
-DEPENDS+= bowtie2>=2.3.4.2:../../wip/bowtie2
-DEPENDS+= samtools>=1.9:../../wip/samtools
-DEPENDS+= jellyfish>=2.2.10:../../wip/jellyfish2
-DEPENDS+= parafly>=2013.01.21:../../wip/parafly
-DEPENDS+= fastool>=0.1.4:../../wip/fastool
-DEPENDS+= p5-transdecoder>=5.3.0:../../wip/p5-transdecoder
-DEPENDS+= Trimmomatic>=0.38:../../wip/trimmomatic
-DEPENDS+= rsem>=1.2.30:../../wip/rsem
-
-DISTNAME= trinity-${PV}
-CATEGORIES= biology
-MASTER_SITES= ${MASTER_SITE_GITHUB:=trinityrnaseq/}
-GITHUB_PROJECT= trinityrnaseq
-GITHUB_TAG= Trinity-v${PV}
-
-MAINTAINER= bacon%NetBSD.org@localhost
-HOMEPAGE= http://trinityrnaseq.github.io/
-COMMENT= Assembles transcript sequences from Illumina RNA-Seq data
-LICENSE= modified-bsd
-
-USE_LANGUAGES= c c++
-USE_JAVA= run
-USE_TOOLS+= bash cmake gmake pax perl
-
-REPLACE_BASH= util/*/*.sh
-REPLACE_BASH+= util/*/*/*.sh
-REPLACE_BASH+= Analysis/*/*/*.sh
-REPLACE_PERL= Trinity util/misc/Monarch
-REPLACE_PERL+= util/*.pl util/*/*.pl util/*/*/*.pl util/*/*/*/*.pl
-REPLACE_PERL+= Chrysalis/analysis/*.pl
-REPLACE_PERL+= Analysis/*/*.pl Analysis/*/*/*.pl Analysis/*/*/*/*.pl
-REPLACE_PERL+= Analysis/*/*.cgi Analysis/*/PtR
-REPLACE_PERL+= PerlLib/*.pm PerlLib/*/*.pm PerlLib/*.ph PerlLib/*.pl
-REPLACE_PYTHON= util/support_scripts/trinity_installer.py
-REPLACE_PYTHON+=util/misc/alt_GG_read_partitioning_JCornish/genwig2.py
-REPLACE_PYTHON+=util/misc/sim_test_framework/run_Trinity_eval.sh
-REPLACE_PYTHON+=util/misc/TPM_weighted_gene_length.py
-REPLACE_PYTHON+=Analysis/SuperTranscripts/*.py
-REPLACE_PYTHON+=Analysis/SuperTranscripts/*/*.py
-REPLACE_RSCRIPT+= Analysis/*/*.Rscript
-REPLACE_RSCRIPT+= util/misc/*.Rscript
-
-SUBST_CLASSES+= paths
-SUBST_STAGE.paths= post-patch
-SUBST_SED.paths+= -e 's|$$FindBin::Bin|$$FindBin::Bin/../libexec/trinity|g'
-SUBST_SED.paths+= -e 's|$$FindBin::RealBin|$$FindBin::RealBin/../libexec/trinity|g'
-SUBST_SED.paths+= -e 's|$$ROOTDIR/trinity-plugins/BIN/ParaFly|ParaFly|g'
-SUBST_SED.paths+= -e 's|$$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar|${JAVAJARDIR}/trimmomatic.jar|g'
-SUBST_SED.paths+= -e 's|$$ROOTDIR/trinity-plugins/Trimmomatic|${PREFIX}/share/Trimmomatic|g'
-SUBST_FILES.paths+= ${WRKSRC}/Trinity
-
-SUBST_CLASSES+= jelly
-SUBST_STAGE.jelly= post-patch
-SUBST_SED.jelly+= -e 's|$$JELLYFISH_DIR/bin/jellyfish|jellyfish|g'
-SUBST_FILES.jelly+= ${WRKSRC}/util/misc/run_jellyfish.pl
-
-SUBST_CLASSES+= trimmo
-SUBST_STAGE.trimmo= post-patch
-SUBST_SED.trimmo+= -e 's|$$FindBin::RealBin/../../trinity-plugins/Trimmomatic/trimmomatic.jar|${JAVAJARDIR}/trimmomatic.jar|g'
-SUBST_SED.trimmo+= -e 's|/seq/regev_genome_portal/SOFTWARE/BIN/trimmomatic.jar|${JAVAJARDIR}/trimmomatic.jar|g'
-SUBST_FILES.trimmo+= ${WRKSRC}/util/misc/run_trimmomatic_qual_trimming.pl
-
-SUBST_CLASSES+= rpath
-SUBST_STAGE.rpath= post-patch
-SUBST_SED.rpath+= -e "s|-lm -pthread|-lm -pthread -Wl,-rpath=${_GCC_RUNTIME}|g"
-SUBST_FILES.rpath+= ${WRKSRC}/Chrysalis/Makefile
-
-SUBST_CLASSES+= trinity
-SUBST_STAGE.trinity= post-patch
-SUBST_SED.trinity+= -e 's|$$FindBin::Bin/../../Trinity|Trinity|g'
-SUBST_FILES.trinity+= ${WRKSRC}/util/support_scripts/write_partitioned_trinity_cmds.pl
-
-SUBST_CLASSES+= build
-SUBST_STAGE.build= post-build
-SUBST_SED.build+= -e "s|/usr/bin/perl|${PREFIX}/bin/perl|g"
-SUBST_FILES.build+= ${WRKSRC}/trinity-plugins/COLLECTL/collectl/collectl
-SUBST_FILES.build+= ${WRKSRC}/trinity-plugins/COLLECTL/collectl/*.pl
-
-CFLAGS+= -fopenmp
-CXXFLAGS= -fopenmp
-
-PV= 2.8.3
-EXAMPLESDIR= ${PREFIX}/share/examples/trinity
-LIBEXEC_DIR= ${PREFIX}/libexec/trinity
-PLUGINS_DIR= ${LIBEXEC_DIR}/trinity-plugins
-
-REPLACE_INTERPRETER+= Rscript
-REPLACE.Rscript.old= .*Rscript
-REPLACE.Rscript.new= ${PREFIX}/bin/Rscript
-REPLACE_FILES.Rscript= ${REPLACE_RSCRIPT}
-
-# Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
-# .include "../../mk/bsd.prefs.mk"
-
-INSTALLATION_DIRS= bin libexec/trinity/Chrysalis/bin libexec/trinity/Inchworm/bin libexec/trinity/Butterfly libexec/trinity/trinity-plugins/scaffold_iworm_contigs libexec/trinity/trinity-plugins/BIN share/examples
-
-post-extract:
- ${CHMOD} -R g-w ${WRKSRC}
-
-# FIXME: More may need to be installed
-do-install:
- ${INSTALL_SCRIPT} ${WRKSRC}/Trinity ${DESTDIR}${PREFIX}/bin
- ${INSTALL_PROGRAM} ${WRKSRC}/Chrysalis/bin/* \
- ${DESTDIR}${LIBEXEC_DIR}/Chrysalis/bin
- ${INSTALL_SCRIPT} ${WRKSRC}/Chrysalis/analysis/ReadsToComponents.pl \
- ${DESTDIR}${LIBEXEC_DIR}/Chrysalis/bin
- ${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 \
- ${DESTDIR}${LIBEXEC_DIR}
- cd ${WRKSRC} && pax -rw util \
- ${DESTDIR}${LIBEXEC_DIR}
- cd ${WRKSRC} && pax -rw Analysis \
- ${DESTDIR}${LIBEXEC_DIR}
- ${INSTALL_PROGRAM} ${WRKSRC}/trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs \
- ${DESTDIR}${PLUGINS_DIR}/scaffold_iworm_contigs
- ${INSTALL_PROGRAM} ${WRKSRC}/trinity-plugins/BIN/seqtk-trinity \
- ${DESTDIR}${PLUGINS_DIR}/BIN
- cd ${WRKSRC}/sample_data && pax -rw * \
- ${DESTDIR}${EXAMPLESDIR}
- ${LN} -fs ${PREFIX}/bin/Trinity \
- ${DESTDIR}${PREFIX}/libexec/trinity/Trinity
- ${RM} ${DESTDIR}${PREFIX}/libexec/trinity/util/support_scripts/plugin_install_tests.sh.orig
-
-.include "../../lang/python/application.mk"
-.include "../../wip/htslib/buildlink3.mk"
-.include "../../devel/zlib/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff --git a/trinity-devel/PLIST b/trinity-devel/PLIST
deleted file mode 100644
index d04d0ed9af..0000000000
--- a/trinity-devel/PLIST
+++ /dev/null
@@ -1,615 +0,0 @@
-@comment $NetBSD$
-bin/Trinity
-libexec/trinity/Analysis/DifferentialExpression/DE_graph_to_dot.pl
-libexec/trinity/Analysis/DifferentialExpression/DTE_to_DTU.pl
-libexec/trinity/Analysis/DifferentialExpression/GOplot.Rscript
-libexec/trinity/Analysis/DifferentialExpression/Glimma.Trinity.Rscript
-libexec/trinity/Analysis/DifferentialExpression/PtR
-libexec/trinity/Analysis/DifferentialExpression/R/edgeR_funcs.R
-libexec/trinity/Analysis/DifferentialExpression/R/get_cluster_info.R
-libexec/trinity/Analysis/DifferentialExpression/R/heatmap.3.R
-libexec/trinity/Analysis/DifferentialExpression/R/jaccard_distance.R
-libexec/trinity/Analysis/DifferentialExpression/R/manually_define_clusters.R
-libexec/trinity/Analysis/DifferentialExpression/R/misc_rnaseq_funcs.R
-libexec/trinity/Analysis/DifferentialExpression/R/pairs3.R
-libexec/trinity/Analysis/DifferentialExpression/R/rnaseq_plot_funcs.R
-libexec/trinity/Analysis/DifferentialExpression/R/test.heatmap.3.R
-libexec/trinity/Analysis/DifferentialExpression/R/tests/test_heatmap_w_pca.R
-libexec/trinity/Analysis/DifferentialExpression/R/vioplot2.R
-libexec/trinity/Analysis/DifferentialExpression/ROKU.pl
-libexec/trinity/Analysis/DifferentialExpression/TissueEnrichment/DE_graph_to_dot.pl
-libexec/trinity/Analysis/DifferentialExpression/TissueEnrichment/DE_results_to_pairwise_summary.pl
-libexec/trinity/Analysis/DifferentialExpression/TissueEnrichment/README.md
-libexec/trinity/Analysis/DifferentialExpression/TissueEnrichment/group_isoforms_by_tissue_enrichment.pl
-libexec/trinity/Analysis/DifferentialExpression/TissueEnrichment/pairwise_DE_summary_to_DE_classification.pl
-libexec/trinity/Analysis/DifferentialExpression/add_annot_to_trans_id.pl
-libexec/trinity/Analysis/DifferentialExpression/add_annotations_to_GO_and_lengths_file.R
-libexec/trinity/Analysis/DifferentialExpression/add_blastx_hit_to_trinity_id.pl
-libexec/trinity/Analysis/DifferentialExpression/analyze_diff_expr.pl
-libexec/trinity/Analysis/DifferentialExpression/assign_tissue_specific.pl
-libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/Islam_scde_data/es.mef.fpkm.matrix
-libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/MLF_ESC_NPC.cuff.genes.fpkm.matrix.gz
-libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/cleanme.pl
-libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/orig.samples.txt
-libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/runMe.sh
-libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/samples.txt
-libexec/trinity/Analysis/DifferentialExpression/compare_gene_trans_DE_ranks.pl
-libexec/trinity/Analysis/DifferentialExpression/cut_tree_into_clusters.pl
-libexec/trinity/Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl
-libexec/trinity/Analysis/DifferentialExpression/diff_expr_analysis_to_heatmap_html.pl
-libexec/trinity/Analysis/DifferentialExpression/diff_express.cgi
-libexec/trinity/Analysis/DifferentialExpression/downsample_count_matrix.pl
-libexec/trinity/Analysis/DifferentialExpression/extract_GO_enriched_genes.pl
-libexec/trinity/Analysis/DifferentialExpression/filter_diff_expr.pl
-libexec/trinity/Analysis/DifferentialExpression/filter_matrix_min_sum_rowcounts.pl
-libexec/trinity/Analysis/DifferentialExpression/get_tissue_enriched_DE_one_vs_all.pl
-libexec/trinity/Analysis/DifferentialExpression/get_transcript_lengths.pl
-libexec/trinity/Analysis/DifferentialExpression/identify_diff_isoform_splicing.pl
-libexec/trinity/Analysis/DifferentialExpression/log2_transform_matrix.pl
-libexec/trinity/Analysis/DifferentialExpression/log2_transform_median_center_fpkm_matrix.pl
-libexec/trinity/Analysis/DifferentialExpression/matrix_to_gene_plots.pl
-libexec/trinity/Analysis/DifferentialExpression/merge_matrices.pl
-libexec/trinity/Analysis/DifferentialExpression/merge_subclusters.pl
-libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/DE_pair_counts_to_matrix.pl
-libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/EBSeq_to_pairwise_summary.pl
-libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/add_counts_to_classes.pl
-libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/class_to_separate_fpkm_matrices.pl
-libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/edgeR_to_pairwise_summary.pl
-libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/examine_rank_correlation.pl
-libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/extract_venn_agree_from_summaries.pl
-libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/mmdiff_to_pairwise_summary.pl
-libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/notes
-libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/pairwise_DE_summary_to_DE_classification.pl
-libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/venn_pairwise_summaries.pair_stats.pl
-libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/venn_pairwise_summaries.pl
-libexec/trinity/Analysis/DifferentialExpression/plot_all_DE_MAplots.Rscript
-libexec/trinity/Analysis/DifferentialExpression/plot_all_DE_volcanos.Rscript
-libexec/trinity/Analysis/DifferentialExpression/plot_expression_patterns.pl
-libexec/trinity/Analysis/DifferentialExpression/plot_log2FC_hist.Rscript
-libexec/trinity/Analysis/DifferentialExpression/prep_n_run_GOplot.pl
-libexec/trinity/Analysis/DifferentialExpression/prune_isoforms_fasta.pl
-libexec/trinity/Analysis/DifferentialExpression/prune_isoforms_gtf.pl
-libexec/trinity/Analysis/DifferentialExpression/rank_roku_by_expr.pl
-libexec/trinity/Analysis/DifferentialExpression/remove_batch_effects_from_count_matrix.pl
-libexec/trinity/Analysis/DifferentialExpression/rename_matrix_column_labels.pl
-libexec/trinity/Analysis/DifferentialExpression/rename_matrix_feature_identifiers.pl
-libexec/trinity/Analysis/DifferentialExpression/replicates_to_sample_averages_matrix.pl
-libexec/trinity/Analysis/DifferentialExpression/run_DE_analysis.pl
-libexec/trinity/Analysis/DifferentialExpression/run_GOseq.pl
-libexec/trinity/Analysis/DifferentialExpression/run_TMM_normalization_write_FPKM_matrix.pl
-libexec/trinity/Analysis/DifferentialExpression/stratify_diff_expression.pl
-libexec/trinity/Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.make_index_html.pl
-libexec/trinity/Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.pl
-libexec/trinity/Analysis/DifferentialExpression/summarize_diff_expr_across_min_threshold_ranges.pl
-libexec/trinity/Analysis/DifferentialExpression/validate_UP_subset.Rscript
-libexec/trinity/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
-libexec/trinity/Analysis/FL_reconstruction_analysis/R/boot.tree.R
-libexec/trinity/Analysis/FL_reconstruction_analysis/compute_oracle.pl
-libexec/trinity/Analysis/FL_reconstruction_analysis/count_by_expression_quintile.pl
-libexec/trinity/Analysis/FL_reconstruction_analysis/fusion_comparisons_via_maps_files.pl
-libexec/trinity/Analysis/FL_reconstruction_analysis/get_genes_from_maps_file.pl
-libexec/trinity/Analysis/FL_reconstruction_analysis/maps_file_to_paralog_representation.pl
-libexec/trinity/Analysis/FL_reconstruction_analysis/oracle_counter.pl
-libexec/trinity/Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.pl
-libexec/trinity/Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.tiers_to_boxplot.pl
-libexec/trinity/Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl
-libexec/trinity/Analysis/FL_reconstruction_analysis/util/blat_map_filter_with_isoforms.pl
-libexec/trinity/Analysis/FL_reconstruction_analysis/util/blat_psl_to_align_summary_stats.pl
-libexec/trinity/Analysis/FL_reconstruction_analysis/util/blat_query_top_hit_extractor.pl
-libexec/trinity/Analysis/FL_reconstruction_analysis/util/blat_top_tier_genes.pl
-libexec/trinity/Analysis/GenomeViewPlugin/test.html
-libexec/trinity/Analysis/GenomeViewPlugin/test_session.html
-libexec/trinity/Analysis/GenomeViewPlugin/trinity_to_genomeview_html.pl
-libexec/trinity/Analysis/SuperTranscripts/AllelicVariants/VCF_to_annotated_SNP_report.pl
-libexec/trinity/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
-libexec/trinity/Analysis/SuperTranscripts/AllelicVariants/util/clean_bam.pl
-libexec/trinity/Analysis/SuperTranscripts/DTU/README.md
-libexec/trinity/Analysis/SuperTranscripts/DTU/dexseq_wrapper.pl
-libexec/trinity/Analysis/SuperTranscripts/DTU/util/reformat_featureCounts.pl
-libexec/trinity/Analysis/SuperTranscripts/README.md
-libexec/trinity/Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py
-libexec/trinity/Analysis/SuperTranscripts/_misc/aln_before_after.pl
-libexec/trinity/Analysis/SuperTranscripts/extract_supertranscript_from_reference.py
-libexec/trinity/Analysis/SuperTranscripts/pylib/Compact_graph_partial.py
-libexec/trinity/Analysis/SuperTranscripts/pylib/Compact_graph_pruner.py
-libexec/trinity/Analysis/SuperTranscripts/pylib/Compact_graph_whole.py
-libexec/trinity/Analysis/SuperTranscripts/pylib/DP_matrix.py
-libexec/trinity/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.py
-libexec/trinity/Analysis/SuperTranscripts/pylib/GraphCycleException.py
-libexec/trinity/Analysis/SuperTranscripts/pylib/Node_alignment.py
-libexec/trinity/Analysis/SuperTranscripts/pylib/Node_path.py
-libexec/trinity/Analysis/SuperTranscripts/pylib/Splice_model_refiner.py
-libexec/trinity/Analysis/SuperTranscripts/pylib/TGLOBALS.py
-libexec/trinity/Analysis/SuperTranscripts/pylib/TGraph.py
-libexec/trinity/Analysis/SuperTranscripts/pylib/TNode.py
-libexec/trinity/Analysis/SuperTranscripts/pylib/Topological_sort.py
-libexec/trinity/Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.py
-libexec/trinity/Analysis/SuperTranscripts/pylib/Trinity_util.py
-libexec/trinity/Analysis/SuperTranscripts/pylib/__init__.py
-libexec/trinity/Butterfly/Butterfly.jar
-libexec/trinity/Chrysalis/bin/BubbleUpClustering
-libexec/trinity/Chrysalis/bin/Chrysalis
-libexec/trinity/Chrysalis/bin/CreateIwormFastaBundle
-libexec/trinity/Chrysalis/bin/GraphFromFasta
-libexec/trinity/Chrysalis/bin/QuantifyGraph
-libexec/trinity/Chrysalis/bin/ReadsToComponents.pl
-libexec/trinity/Chrysalis/bin/ReadsToTranscripts
-libexec/trinity/Inchworm/bin/FastaToDeBruijn
-libexec/trinity/Inchworm/bin/fastaToKmerCoverageStats
-libexec/trinity/Inchworm/bin/inchworm
-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
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-libexec/trinity/util/support_scripts/merge_pair_and_LR_scaff_links.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/outfmt6_add_percent_match_length.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
-libexec/trinity/util/support_scripts/revcomp_fasta.pl
-libexec/trinity/util/support_scripts/run_TMM_scale_matrix.pl
-libexec/trinity/util/support_scripts/run_UpperQuartileNormalization_matrix.pl
-libexec/trinity/util/support_scripts/salmon_runner.pl
-libexec/trinity/util/support_scripts/salmon_trans_to_gene_results.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/sample_data_tests.py
-libexec/trinity/util/support_scripts/tests/test_prep.py
-libexec/trinity/util/support_scripts/tests/tests.py
-libexec/trinity/util/support_scripts/trinity_install_tests.sh
-libexec/trinity/util/support_scripts/trinity_installer.py
-libexec/trinity/util/support_scripts/wig_clip_to_bed.pl
-libexec/trinity/util/support_scripts/write_partitioned_trinity_cmds.pl
-share/examples/trinity/Makefile
-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/__indiv_ex_sample_derived/refSeqs.fa.gene_trans_map
-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_full_cleanup.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_include_supertranscripts.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_piecemeal.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_trin_complete.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_use_bowtie2.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_use_my_ramdisk.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_use_workdir.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_PE_samples_file.min_kmer_cov_3.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__run_PE_samples_file.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__run_SE_samples_file.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_NO_normalization.sh
-share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__test_runMe_docker.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_lenient_path_extension.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.fa.gz
-share/examples/trinity/test_Trinity_Assembly/reads.left.fq.gz
-share/examples/trinity/test_Trinity_Assembly/reads.right.fa.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/samples.PE.txt
-share/examples/trinity/test_Trinity_Assembly/samples.SE.txt
-share/examples/trinity/test_Trinity_Assembly/test_FL.sh
diff --git a/trinity-devel/distinfo b/trinity-devel/distinfo
deleted file mode 100644
index 1a18fb467e..0000000000
--- a/trinity-devel/distinfo
+++ /dev/null
@@ -1,15 +0,0 @@
-$NetBSD$
-
-SHA1 (trinity-2.8.3.tar.gz) = e9553095eb526bb478eac8237fae2bab7d143126
-RMD160 (trinity-2.8.3.tar.gz) = 92a7a81b15a220ff70f3ff5cb3fb80617d041c9d
-SHA512 (trinity-2.8.3.tar.gz) = 45f0712b2732591688697d3b4726e3c2f64a507d97f080b1cfeaf2d16647b196b2a3b45aac45640877bb0c4eced8578ca16fc57cd778b7a1c84908c76cee299f
-Size (trinity-2.8.3.tar.gz) = 21707766 bytes
-SHA1 (patch-Chrysalis_CMakeLists.txt) = cc637a1b8dbbd95e49c94ac3c1bd361612bc01ee
-SHA1 (patch-Chrysalis_Makefile) = 151e0c2838db9822858879fa15c47a76f75f33bb
-SHA1 (patch-Inchworm_CMakeLists.txt) = 0a00585801893b2ebac759ecf5db91b76218238f
-SHA1 (patch-Inchworm_Makefile) = 43279c6a1d6c2d1a00d5f993c734122b351ff517
-SHA1 (patch-Makefile) = a428497a9d0a674d210ab5dde97d18ac9b0adba2
-SHA1 (patch-trinity-plugins_Makefile) = a7f6526429ed3007d0336fc765fd61161f9a3ed5
-SHA1 (patch-trinity-plugins_scaffold__iworm__contigs_Makefile) = 65b8d5c5bb46448080515968f6bb49df463567be
-SHA1 (patch-trinity-plugins_seqtk-trinity-0.0.2_Makefile) = 30946c32223ae06311e7315a467af5c5de626f0c
-SHA1 (patch-util_support__scripts_plugin__install__tests.sh) = ecfe2717a827a16df01834fba8e73a8fc09ed6d7
diff --git a/trinity-devel/patches/patch-Chrysalis_CMakeLists.txt b/trinity-devel/patches/patch-Chrysalis_CMakeLists.txt
deleted file mode 100644
index 49a7dbae42..0000000000
--- a/trinity-devel/patches/patch-Chrysalis_CMakeLists.txt
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD$
-
-# Portability
---- Chrysalis/CMakeLists.txt.orig 2018-09-01 15:19:53 UTC
-+++ Chrysalis/CMakeLists.txt
-@@ -18,7 +18,7 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}
- set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O2 -march=native -DNDEBUG ")
- set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g -O0")
-
--set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lm -ldl ")
-+set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lm ")
-
- MESSAGE(STATUS "system: ${CMAKE_SYSTEM_NAME}")
- if (${CMAKE_SYSTEM_NAME} STREQUAL "Linux")
diff --git a/trinity-devel/patches/patch-Chrysalis_Makefile b/trinity-devel/patches/patch-Chrysalis_Makefile
deleted file mode 100644
index b77ae5f267..0000000000
--- a/trinity-devel/patches/patch-Chrysalis_Makefile
+++ /dev/null
@@ -1,22 +0,0 @@
-$NetBSD$
-
-# Must use gmake
---- Chrysalis/Makefile.orig 2018-09-01 15:20:04 UTC
-+++ Chrysalis/Makefile
-@@ -1,13 +1,13 @@
- all:
- mkdir -p build
-- cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && make DESTDIR=../ install
-+ cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && ${MAKE} DESTDIR=../ install
-
- debug:
- mkdir -p build
-- cd build && cmake -DCMAKE_INSTALL_PREFIX="" -DCMAKE_BUILD_TYPE=Debug ../ && make DESTDIR=../ install
-+ cd build && cmake -DCMAKE_INSTALL_PREFIX="" -DCMAKE_BUILD_TYPE=Debug ../ && ${MAKE} DESTDIR=../ install
-
-
- clean:
- @echo cleaning
-- (cd build && make clean) || :
-+ (cd build && ${MAKE} clean) || :
- rm -rf ./build ./bin
diff --git a/trinity-devel/patches/patch-Inchworm_CMakeLists.txt b/trinity-devel/patches/patch-Inchworm_CMakeLists.txt
deleted file mode 100644
index 784afd9776..0000000000
--- a/trinity-devel/patches/patch-Inchworm_CMakeLists.txt
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD$
-
-# Portability
---- Inchworm/CMakeLists.txt.orig 2018-09-01 15:19:04 UTC
-+++ Inchworm/CMakeLists.txt
-@@ -18,7 +18,7 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}
- set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O2 -march=native -DNDEBUG ")
- set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g -O0")
-
--set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lm -ldl ")
-+set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lm ")
-
- MESSAGE(STATUS "system: ${CMAKE_SYSTEM_NAME}")
- if (${CMAKE_SYSTEM_NAME} STREQUAL "Linux")
diff --git a/trinity-devel/patches/patch-Inchworm_Makefile b/trinity-devel/patches/patch-Inchworm_Makefile
deleted file mode 100644
index fe44c2675f..0000000000
--- a/trinity-devel/patches/patch-Inchworm_Makefile
+++ /dev/null
@@ -1,16 +0,0 @@
-$NetBSD$
-
-# Must use gmake
---- Inchworm/Makefile.orig 2018-09-01 15:18:14 UTC
-+++ Inchworm/Makefile
-@@ -1,8 +1,8 @@
- all:
- mkdir -p build
-- cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && make DESTDIR=../ install
-+ cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && ${MAKE} DESTDIR=../ install
-
- clean:
- @echo cleaning
-- (cd build && make clean) || :
-+ (cd build && ${MAKE} clean) || :
- rm -rf ./build ./bin
diff --git a/trinity-devel/patches/patch-Makefile b/trinity-devel/patches/patch-Makefile
deleted file mode 100644
index 28d726fc08..0000000000
--- a/trinity-devel/patches/patch-Makefile
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD$
-
-# Build plugins
---- Makefile.orig 2018-09-01 14:38:58 UTC
-+++ Makefile
-@@ -17,7 +17,7 @@ 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
-
-
diff --git a/trinity-devel/patches/patch-trinity-plugins_Makefile b/trinity-devel/patches/patch-trinity-plugins_Makefile
deleted file mode 100644
index 95677e3641..0000000000
--- a/trinity-devel/patches/patch-trinity-plugins_Makefile
+++ /dev/null
@@ -1,35 +0,0 @@
-$NetBSD$
-
-# Unbundle deps, build scaffold_iworm_contigs
---- trinity-plugins/Makefile.orig 2018-08-22 01:25:08 UTC
-+++ trinity-plugins/Makefile
-@@ -9,12 +9,11 @@ TRIMMOMATIC_CODE=Trimmomatic-0.36
-
-
-
--trinity_essentials: seqtk_target parafly_target trimmomatic_target
-+trinity_essentials: scaffold_iworm_contigs_target seqtk_target
-
- trimmomatic_target:
- ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
-
--
- seqtk_target:
- cd seqtk-trinity-0.0.2 && $(MAKE) CXX=$(CXX) CC=$(CC)
- mv seqtk-trinity-0.0.2/seqtk-trinity ./BIN/.
-@@ -24,12 +23,14 @@ parafly_target:
- cd ${PARAFLY_CODE} && sh ./configure --prefix=`pwd` CXX=$(CXX) CC=$(CC) CFLAGS="-fopenmp" CXXFLAGS="-fopenmp" && $(MAKE) install && \
- cp bin/ParaFly ../BIN/
-
-+scaffold_iworm_contigs_target:
-+ cd scaffold_iworm_contigs && $(MAKE)
-
- ##################################
- ### Needed for downstream analyses
- ##################################
-
--plugins: slclust_target collectl_target
-+plugins: collectl_target
- @echo "\n\n** Done building plugins **\n\n"
-
-
diff --git a/trinity-devel/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile b/trinity-devel/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile
deleted file mode 100644
index 40007968f5..0000000000
--- a/trinity-devel/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile
+++ /dev/null
@@ -1,16 +0,0 @@
-$NetBSD$
-
-# Respect pkgsrc env
---- trinity-plugins/scaffold_iworm_contigs/Makefile.orig 2018-08-22 01:25:08 UTC
-+++ trinity-plugins/scaffold_iworm_contigs/Makefile
-@@ -1,8 +1,8 @@
--CXX = g++
-+CXX ?= g++
- prefix = ../htslib
-
- ScaffoldIwormContigs:
-- $(CXX) $(LDFLAGS) -I$(prefix) -L$(prefix) ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs
-+ $(CXX) $(LDFLAGS) -I$(LOCALBASE)/include -L$(LOCALBASE)/lib ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs
-
- clean:
- rm -f scaffold_iworm_contigs
diff --git a/trinity-devel/patches/patch-trinity-plugins_seqtk-trinity-0.0.2_Makefile b/trinity-devel/patches/patch-trinity-plugins_seqtk-trinity-0.0.2_Makefile
deleted file mode 100644
index e4978bb25f..0000000000
--- a/trinity-devel/patches/patch-trinity-plugins_seqtk-trinity-0.0.2_Makefile
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD$
-
-# Respect env
---- trinity-plugins/seqtk-trinity-0.0.2/Makefile.orig 2018-09-16 14:53:41.191563645 +0000
-+++ trinity-plugins/seqtk-trinity-0.0.2/Makefile
-@@ -4,7 +4,7 @@ CFLAGS=-g -Wall -O2 -Wno-unused-function
- all:seqtk-trinity
-
- seqtk-trinity:seqtk.c khash.h kseq.h
-- $(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm
-+ $(CC) $(CFLAGS) seqtk.c -o $@ $(LDFLAGS) -lz -lm
-
- clean:
- rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session*
diff --git a/trinity-devel/patches/patch-util_support__scripts_plugin__install__tests.sh b/trinity-devel/patches/patch-util_support__scripts_plugin__install__tests.sh
deleted file mode 100644
index e947754ea3..0000000000
--- a/trinity-devel/patches/patch-util_support__scripts_plugin__install__tests.sh
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD$
-
-# Unbundle slclust
---- util/support_scripts/plugin_install_tests.sh.orig 2018-09-01 15:43:40 UTC
-+++ util/support_scripts/plugin_install_tests.sh
-@@ -3,7 +3,7 @@
- echo "## Checking plugin installations:"
- echo
-
--if [ -e "trinity-plugins/slclust/bin/slclust" ]
-+if [ -e "${LOCALBASE}/bin/slclust" ]
- then
- echo "slclust: has been Installed Properly"
- else
diff --git a/trinity/DESCR b/trinity/DESCR
new file mode 100644
index 0000000000..7752b73aa7
--- /dev/null
+++ b/trinity/DESCR
@@ -0,0 +1,4 @@
+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
new file mode 100644
index 0000000000..3ef0276936
--- /dev/null
+++ b/trinity/Makefile
@@ -0,0 +1,154 @@
+# $NetBSD$
+#
+###########################################################
+# Generated by fbsd2pkg #
+# Fri Sep 14 20:48:17 CDT 2018 #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+# 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.
+# To-do:
+# Unbundle collectl (low priority)
+## Should work on other 64-bit archs, but untested
+#ONLY_FOR_ARCH= amd64
+
+# Should salmon use bl3?
+# bowtie should not have bl3
+DEPENDS= coreutils>=0:../../sysutils/coreutils
+DEPENDS+= slclust>=0.0.0.20100202:../../wip/slclust
+DEPENDS+= salmon>=0.11.3:../../wip/salmon
+DEPENDS+= bowtie>=1.1.2:../../wip/bowtie
+DEPENDS+= bowtie2>=2.3.4.2:../../wip/bowtie2
+DEPENDS+= samtools>=1.9:../../wip/samtools
+DEPENDS+= jellyfish>=2.2.10:../../wip/jellyfish2
+DEPENDS+= parafly>=2013.01.21:../../wip/parafly
+DEPENDS+= fastool>=0.1.4:../../wip/fastool
+DEPENDS+= p5-transdecoder>=5.3.0:../../wip/p5-transdecoder
+DEPENDS+= Trimmomatic>=0.38:../../wip/trimmomatic
+DEPENDS+= rsem>=1.2.30:../../wip/rsem
+
+DISTNAME= trinity-${PV}
+CATEGORIES= biology
+MASTER_SITES= ${MASTER_SITE_GITHUB:=trinityrnaseq/}
+GITHUB_PROJECT= trinityrnaseq
+GITHUB_TAG= Trinity-v${PV}
+
+MAINTAINER= bacon%NetBSD.org@localhost
+HOMEPAGE= http://trinityrnaseq.github.io/
+COMMENT= Assembles transcript sequences from Illumina RNA-Seq data
+LICENSE= modified-bsd
+
+USE_LANGUAGES= c c++
+USE_JAVA= run
+USE_TOOLS+= bash cmake gmake pax perl
+
+REPLACE_BASH= util/*/*.sh
+REPLACE_BASH+= util/*/*/*.sh
+REPLACE_BASH+= Analysis/*/*/*.sh
+REPLACE_PERL= Trinity util/misc/Monarch
+REPLACE_PERL+= util/*.pl util/*/*.pl util/*/*/*.pl util/*/*/*/*.pl
+REPLACE_PERL+= Chrysalis/analysis/*.pl
+REPLACE_PERL+= Analysis/*/*.pl Analysis/*/*/*.pl Analysis/*/*/*/*.pl
+REPLACE_PERL+= Analysis/*/*.cgi Analysis/*/PtR
+REPLACE_PERL+= PerlLib/*.pm PerlLib/*/*.pm PerlLib/*.ph PerlLib/*.pl
+REPLACE_PYTHON= util/support_scripts/trinity_installer.py
+REPLACE_PYTHON+=util/misc/alt_GG_read_partitioning_JCornish/genwig2.py
+REPLACE_PYTHON+=util/misc/sim_test_framework/run_Trinity_eval.sh
+REPLACE_PYTHON+=util/misc/TPM_weighted_gene_length.py
+REPLACE_PYTHON+=Analysis/SuperTranscripts/*.py
+REPLACE_PYTHON+=Analysis/SuperTranscripts/*/*.py
+REPLACE_RSCRIPT+= Analysis/*/*.Rscript
+REPLACE_RSCRIPT+= util/misc/*.Rscript
+
+SUBST_CLASSES+= paths
+SUBST_STAGE.paths= post-patch
+SUBST_SED.paths+= -e 's|$$FindBin::Bin|$$FindBin::Bin/../libexec/trinity|g'
+SUBST_SED.paths+= -e 's|$$FindBin::RealBin|$$FindBin::RealBin/../libexec/trinity|g'
+SUBST_SED.paths+= -e 's|$$ROOTDIR/trinity-plugins/BIN/ParaFly|ParaFly|g'
+SUBST_SED.paths+= -e 's|$$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar|${JAVAJARDIR}/trimmomatic.jar|g'
+SUBST_SED.paths+= -e 's|$$ROOTDIR/trinity-plugins/Trimmomatic|${PREFIX}/share/Trimmomatic|g'
+SUBST_FILES.paths+= ${WRKSRC}/Trinity
+
+SUBST_CLASSES+= jelly
+SUBST_STAGE.jelly= post-patch
+SUBST_SED.jelly+= -e 's|$$JELLYFISH_DIR/bin/jellyfish|jellyfish|g'
+SUBST_FILES.jelly+= ${WRKSRC}/util/misc/run_jellyfish.pl
+
+SUBST_CLASSES+= trimmo
+SUBST_STAGE.trimmo= post-patch
+SUBST_SED.trimmo+= -e 's|$$FindBin::RealBin/../../trinity-plugins/Trimmomatic/trimmomatic.jar|${JAVAJARDIR}/trimmomatic.jar|g'
+SUBST_SED.trimmo+= -e 's|/seq/regev_genome_portal/SOFTWARE/BIN/trimmomatic.jar|${JAVAJARDIR}/trimmomatic.jar|g'
+SUBST_FILES.trimmo+= ${WRKSRC}/util/misc/run_trimmomatic_qual_trimming.pl
+
+SUBST_CLASSES+= rpath
+SUBST_STAGE.rpath= post-patch
+SUBST_SED.rpath+= -e "s|-lm -pthread|-lm -pthread -Wl,-rpath=${_GCC_RUNTIME}|g"
+SUBST_FILES.rpath+= ${WRKSRC}/Chrysalis/Makefile
+
+SUBST_CLASSES+= trinity
+SUBST_STAGE.trinity= post-patch
+SUBST_SED.trinity+= -e 's|$$FindBin::Bin/../../Trinity|Trinity|g'
+SUBST_FILES.trinity+= ${WRKSRC}/util/support_scripts/write_partitioned_trinity_cmds.pl
+
+SUBST_CLASSES+= build
+SUBST_STAGE.build= post-build
+SUBST_SED.build+= -e "s|/usr/bin/perl|${PREFIX}/bin/perl|g"
+SUBST_FILES.build+= ${WRKSRC}/trinity-plugins/COLLECTL/collectl/collectl
+SUBST_FILES.build+= ${WRKSRC}/trinity-plugins/COLLECTL/collectl/*.pl
+
+CFLAGS+= -fopenmp
+CXXFLAGS= -fopenmp
+
+PV= 2.8.3
+EXAMPLESDIR= ${PREFIX}/share/examples/trinity
+LIBEXEC_DIR= ${PREFIX}/libexec/trinity
+PLUGINS_DIR= ${LIBEXEC_DIR}/trinity-plugins
+
+REPLACE_INTERPRETER+= Rscript
+REPLACE.Rscript.old= .*Rscript
+REPLACE.Rscript.new= ${PREFIX}/bin/Rscript
+REPLACE_FILES.Rscript= ${REPLACE_RSCRIPT}
+
+# Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
+# .include "../../mk/bsd.prefs.mk"
+
+INSTALLATION_DIRS= bin libexec/trinity/Chrysalis/bin libexec/trinity/Inchworm/bin libexec/trinity/Butterfly libexec/trinity/trinity-plugins/scaffold_iworm_contigs libexec/trinity/trinity-plugins/BIN share/examples
+
+post-extract:
+ ${CHMOD} -R g-w ${WRKSRC}
+
+# FIXME: More may need to be installed
+do-install:
+ ${INSTALL_SCRIPT} ${WRKSRC}/Trinity ${DESTDIR}${PREFIX}/bin
+ ${INSTALL_PROGRAM} ${WRKSRC}/Chrysalis/bin/* \
+ ${DESTDIR}${LIBEXEC_DIR}/Chrysalis/bin
+ ${INSTALL_SCRIPT} ${WRKSRC}/Chrysalis/analysis/ReadsToComponents.pl \
+ ${DESTDIR}${LIBEXEC_DIR}/Chrysalis/bin
+ ${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 \
+ ${DESTDIR}${LIBEXEC_DIR}
+ cd ${WRKSRC} && pax -rw util \
+ ${DESTDIR}${LIBEXEC_DIR}
+ cd ${WRKSRC} && pax -rw Analysis \
+ ${DESTDIR}${LIBEXEC_DIR}
+ ${INSTALL_PROGRAM} ${WRKSRC}/trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs \
+ ${DESTDIR}${PLUGINS_DIR}/scaffold_iworm_contigs
+ ${INSTALL_PROGRAM} ${WRKSRC}/trinity-plugins/BIN/seqtk-trinity \
+ ${DESTDIR}${PLUGINS_DIR}/BIN
+ cd ${WRKSRC}/sample_data && pax -rw * \
+ ${DESTDIR}${EXAMPLESDIR}
+ ${LN} -fs ${PREFIX}/bin/Trinity \
+ ${DESTDIR}${PREFIX}/libexec/trinity/Trinity
+ ${RM} ${DESTDIR}${PREFIX}/libexec/trinity/util/support_scripts/plugin_install_tests.sh.orig
+
+.include "../../lang/python/application.mk"
+.include "../../wip/htslib/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/trinity/PLIST b/trinity/PLIST
new file mode 100644
index 0000000000..d04d0ed9af
--- /dev/null
+++ b/trinity/PLIST
@@ -0,0 +1,615 @@
+@comment $NetBSD$
+bin/Trinity
+libexec/trinity/Analysis/DifferentialExpression/DE_graph_to_dot.pl
+libexec/trinity/Analysis/DifferentialExpression/DTE_to_DTU.pl
+libexec/trinity/Analysis/DifferentialExpression/GOplot.Rscript
+libexec/trinity/Analysis/DifferentialExpression/Glimma.Trinity.Rscript
+libexec/trinity/Analysis/DifferentialExpression/PtR
+libexec/trinity/Analysis/DifferentialExpression/R/edgeR_funcs.R
+libexec/trinity/Analysis/DifferentialExpression/R/get_cluster_info.R
+libexec/trinity/Analysis/DifferentialExpression/R/heatmap.3.R
+libexec/trinity/Analysis/DifferentialExpression/R/jaccard_distance.R
+libexec/trinity/Analysis/DifferentialExpression/R/manually_define_clusters.R
+libexec/trinity/Analysis/DifferentialExpression/R/misc_rnaseq_funcs.R
+libexec/trinity/Analysis/DifferentialExpression/R/pairs3.R
+libexec/trinity/Analysis/DifferentialExpression/R/rnaseq_plot_funcs.R
+libexec/trinity/Analysis/DifferentialExpression/R/test.heatmap.3.R
+libexec/trinity/Analysis/DifferentialExpression/R/tests/test_heatmap_w_pca.R
+libexec/trinity/Analysis/DifferentialExpression/R/vioplot2.R
+libexec/trinity/Analysis/DifferentialExpression/ROKU.pl
+libexec/trinity/Analysis/DifferentialExpression/TissueEnrichment/DE_graph_to_dot.pl
+libexec/trinity/Analysis/DifferentialExpression/TissueEnrichment/DE_results_to_pairwise_summary.pl
+libexec/trinity/Analysis/DifferentialExpression/TissueEnrichment/README.md
+libexec/trinity/Analysis/DifferentialExpression/TissueEnrichment/group_isoforms_by_tissue_enrichment.pl
+libexec/trinity/Analysis/DifferentialExpression/TissueEnrichment/pairwise_DE_summary_to_DE_classification.pl
+libexec/trinity/Analysis/DifferentialExpression/add_annot_to_trans_id.pl
+libexec/trinity/Analysis/DifferentialExpression/add_annotations_to_GO_and_lengths_file.R
+libexec/trinity/Analysis/DifferentialExpression/add_blastx_hit_to_trinity_id.pl
+libexec/trinity/Analysis/DifferentialExpression/analyze_diff_expr.pl
+libexec/trinity/Analysis/DifferentialExpression/assign_tissue_specific.pl
+libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/Islam_scde_data/es.mef.fpkm.matrix
+libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/MLF_ESC_NPC.cuff.genes.fpkm.matrix.gz
+libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/cleanme.pl
+libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/orig.samples.txt
+libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/runMe.sh
+libexec/trinity/Analysis/DifferentialExpression/cluster_sample_data/samples.txt
+libexec/trinity/Analysis/DifferentialExpression/compare_gene_trans_DE_ranks.pl
+libexec/trinity/Analysis/DifferentialExpression/cut_tree_into_clusters.pl
+libexec/trinity/Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl
+libexec/trinity/Analysis/DifferentialExpression/diff_expr_analysis_to_heatmap_html.pl
+libexec/trinity/Analysis/DifferentialExpression/diff_express.cgi
+libexec/trinity/Analysis/DifferentialExpression/downsample_count_matrix.pl
+libexec/trinity/Analysis/DifferentialExpression/extract_GO_enriched_genes.pl
+libexec/trinity/Analysis/DifferentialExpression/filter_diff_expr.pl
+libexec/trinity/Analysis/DifferentialExpression/filter_matrix_min_sum_rowcounts.pl
+libexec/trinity/Analysis/DifferentialExpression/get_tissue_enriched_DE_one_vs_all.pl
+libexec/trinity/Analysis/DifferentialExpression/get_transcript_lengths.pl
+libexec/trinity/Analysis/DifferentialExpression/identify_diff_isoform_splicing.pl
+libexec/trinity/Analysis/DifferentialExpression/log2_transform_matrix.pl
+libexec/trinity/Analysis/DifferentialExpression/log2_transform_median_center_fpkm_matrix.pl
+libexec/trinity/Analysis/DifferentialExpression/matrix_to_gene_plots.pl
+libexec/trinity/Analysis/DifferentialExpression/merge_matrices.pl
+libexec/trinity/Analysis/DifferentialExpression/merge_subclusters.pl
+libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/DE_pair_counts_to_matrix.pl
+libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/EBSeq_to_pairwise_summary.pl
+libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/add_counts_to_classes.pl
+libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/class_to_separate_fpkm_matrices.pl
+libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/edgeR_to_pairwise_summary.pl
+libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/examine_rank_correlation.pl
+libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/extract_venn_agree_from_summaries.pl
+libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/mmdiff_to_pairwise_summary.pl
+libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/notes
+libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/pairwise_DE_summary_to_DE_classification.pl
+libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/venn_pairwise_summaries.pair_stats.pl
+libexec/trinity/Analysis/DifferentialExpression/pairwise_summaries/venn_pairwise_summaries.pl
+libexec/trinity/Analysis/DifferentialExpression/plot_all_DE_MAplots.Rscript
+libexec/trinity/Analysis/DifferentialExpression/plot_all_DE_volcanos.Rscript
+libexec/trinity/Analysis/DifferentialExpression/plot_expression_patterns.pl
+libexec/trinity/Analysis/DifferentialExpression/plot_log2FC_hist.Rscript
+libexec/trinity/Analysis/DifferentialExpression/prep_n_run_GOplot.pl
+libexec/trinity/Analysis/DifferentialExpression/prune_isoforms_fasta.pl
+libexec/trinity/Analysis/DifferentialExpression/prune_isoforms_gtf.pl
+libexec/trinity/Analysis/DifferentialExpression/rank_roku_by_expr.pl
+libexec/trinity/Analysis/DifferentialExpression/remove_batch_effects_from_count_matrix.pl
+libexec/trinity/Analysis/DifferentialExpression/rename_matrix_column_labels.pl
+libexec/trinity/Analysis/DifferentialExpression/rename_matrix_feature_identifiers.pl
+libexec/trinity/Analysis/DifferentialExpression/replicates_to_sample_averages_matrix.pl
+libexec/trinity/Analysis/DifferentialExpression/run_DE_analysis.pl
+libexec/trinity/Analysis/DifferentialExpression/run_GOseq.pl
+libexec/trinity/Analysis/DifferentialExpression/run_TMM_normalization_write_FPKM_matrix.pl
+libexec/trinity/Analysis/DifferentialExpression/stratify_diff_expression.pl
+libexec/trinity/Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.make_index_html.pl
+libexec/trinity/Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.pl
+libexec/trinity/Analysis/DifferentialExpression/summarize_diff_expr_across_min_threshold_ranges.pl
+libexec/trinity/Analysis/DifferentialExpression/validate_UP_subset.Rscript
+libexec/trinity/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
+libexec/trinity/Analysis/FL_reconstruction_analysis/R/boot.tree.R
+libexec/trinity/Analysis/FL_reconstruction_analysis/compute_oracle.pl
+libexec/trinity/Analysis/FL_reconstruction_analysis/count_by_expression_quintile.pl
+libexec/trinity/Analysis/FL_reconstruction_analysis/fusion_comparisons_via_maps_files.pl
+libexec/trinity/Analysis/FL_reconstruction_analysis/get_genes_from_maps_file.pl
+libexec/trinity/Analysis/FL_reconstruction_analysis/maps_file_to_paralog_representation.pl
+libexec/trinity/Analysis/FL_reconstruction_analysis/oracle_counter.pl
+libexec/trinity/Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.pl
+libexec/trinity/Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.tiers_to_boxplot.pl
+libexec/trinity/Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl
+libexec/trinity/Analysis/FL_reconstruction_analysis/util/blat_map_filter_with_isoforms.pl
+libexec/trinity/Analysis/FL_reconstruction_analysis/util/blat_psl_to_align_summary_stats.pl
+libexec/trinity/Analysis/FL_reconstruction_analysis/util/blat_query_top_hit_extractor.pl
+libexec/trinity/Analysis/FL_reconstruction_analysis/util/blat_top_tier_genes.pl
+libexec/trinity/Analysis/GenomeViewPlugin/test.html
+libexec/trinity/Analysis/GenomeViewPlugin/test_session.html
+libexec/trinity/Analysis/GenomeViewPlugin/trinity_to_genomeview_html.pl
+libexec/trinity/Analysis/SuperTranscripts/AllelicVariants/VCF_to_annotated_SNP_report.pl
+libexec/trinity/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
+libexec/trinity/Analysis/SuperTranscripts/AllelicVariants/util/clean_bam.pl
+libexec/trinity/Analysis/SuperTranscripts/DTU/README.md
+libexec/trinity/Analysis/SuperTranscripts/DTU/dexseq_wrapper.pl
+libexec/trinity/Analysis/SuperTranscripts/DTU/util/reformat_featureCounts.pl
+libexec/trinity/Analysis/SuperTranscripts/README.md
+libexec/trinity/Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py
+libexec/trinity/Analysis/SuperTranscripts/_misc/aln_before_after.pl
+libexec/trinity/Analysis/SuperTranscripts/extract_supertranscript_from_reference.py
+libexec/trinity/Analysis/SuperTranscripts/pylib/Compact_graph_partial.py
+libexec/trinity/Analysis/SuperTranscripts/pylib/Compact_graph_pruner.py
+libexec/trinity/Analysis/SuperTranscripts/pylib/Compact_graph_whole.py
+libexec/trinity/Analysis/SuperTranscripts/pylib/DP_matrix.py
+libexec/trinity/Analysis/SuperTranscripts/pylib/Gene_splice_modeler.py
+libexec/trinity/Analysis/SuperTranscripts/pylib/GraphCycleException.py
+libexec/trinity/Analysis/SuperTranscripts/pylib/Node_alignment.py
+libexec/trinity/Analysis/SuperTranscripts/pylib/Node_path.py
+libexec/trinity/Analysis/SuperTranscripts/pylib/Splice_model_refiner.py
+libexec/trinity/Analysis/SuperTranscripts/pylib/TGLOBALS.py
+libexec/trinity/Analysis/SuperTranscripts/pylib/TGraph.py
+libexec/trinity/Analysis/SuperTranscripts/pylib/TNode.py
+libexec/trinity/Analysis/SuperTranscripts/pylib/Topological_sort.py
+libexec/trinity/Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.py
+libexec/trinity/Analysis/SuperTranscripts/pylib/Trinity_util.py
+libexec/trinity/Analysis/SuperTranscripts/pylib/__init__.py
+libexec/trinity/Butterfly/Butterfly.jar
+libexec/trinity/Chrysalis/bin/BubbleUpClustering
+libexec/trinity/Chrysalis/bin/Chrysalis
+libexec/trinity/Chrysalis/bin/CreateIwormFastaBundle
+libexec/trinity/Chrysalis/bin/GraphFromFasta
+libexec/trinity/Chrysalis/bin/QuantifyGraph
+libexec/trinity/Chrysalis/bin/ReadsToComponents.pl
+libexec/trinity/Chrysalis/bin/ReadsToTranscripts
+libexec/trinity/Inchworm/bin/FastaToDeBruijn
+libexec/trinity/Inchworm/bin/fastaToKmerCoverageStats
+libexec/trinity/Inchworm/bin/inchworm
+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/DelimParser.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/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
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+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/__indiv_ex_sample_derived/refSeqs.fa.gene_trans_map
+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_full_cleanup.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_include_supertranscripts.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_piecemeal.sh
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_trin_complete.sh
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_use_bowtie2.sh
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_use_my_ramdisk.sh
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__runMe_use_workdir.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_PE_samples_file.min_kmer_cov_3.sh
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__run_PE_samples_file.sh
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__run_SE_samples_file.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_NO_normalization.sh
+share/examples/trinity/test_Trinity_Assembly/misc_run_tests/__test_runMe_docker.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_lenient_path_extension.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.fa.gz
+share/examples/trinity/test_Trinity_Assembly/reads.left.fq.gz
+share/examples/trinity/test_Trinity_Assembly/reads.right.fa.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/samples.PE.txt
+share/examples/trinity/test_Trinity_Assembly/samples.SE.txt
+share/examples/trinity/test_Trinity_Assembly/test_FL.sh
diff --git a/trinity/distinfo b/trinity/distinfo
new file mode 100644
index 0000000000..1a18fb467e
--- /dev/null
+++ b/trinity/distinfo
@@ -0,0 +1,15 @@
+$NetBSD$
+
+SHA1 (trinity-2.8.3.tar.gz) = e9553095eb526bb478eac8237fae2bab7d143126
+RMD160 (trinity-2.8.3.tar.gz) = 92a7a81b15a220ff70f3ff5cb3fb80617d041c9d
+SHA512 (trinity-2.8.3.tar.gz) = 45f0712b2732591688697d3b4726e3c2f64a507d97f080b1cfeaf2d16647b196b2a3b45aac45640877bb0c4eced8578ca16fc57cd778b7a1c84908c76cee299f
+Size (trinity-2.8.3.tar.gz) = 21707766 bytes
+SHA1 (patch-Chrysalis_CMakeLists.txt) = cc637a1b8dbbd95e49c94ac3c1bd361612bc01ee
+SHA1 (patch-Chrysalis_Makefile) = 151e0c2838db9822858879fa15c47a76f75f33bb
+SHA1 (patch-Inchworm_CMakeLists.txt) = 0a00585801893b2ebac759ecf5db91b76218238f
+SHA1 (patch-Inchworm_Makefile) = 43279c6a1d6c2d1a00d5f993c734122b351ff517
+SHA1 (patch-Makefile) = a428497a9d0a674d210ab5dde97d18ac9b0adba2
+SHA1 (patch-trinity-plugins_Makefile) = a7f6526429ed3007d0336fc765fd61161f9a3ed5
+SHA1 (patch-trinity-plugins_scaffold__iworm__contigs_Makefile) = 65b8d5c5bb46448080515968f6bb49df463567be
+SHA1 (patch-trinity-plugins_seqtk-trinity-0.0.2_Makefile) = 30946c32223ae06311e7315a467af5c5de626f0c
+SHA1 (patch-util_support__scripts_plugin__install__tests.sh) = ecfe2717a827a16df01834fba8e73a8fc09ed6d7
diff --git a/trinity/patches/patch-Chrysalis_CMakeLists.txt b/trinity/patches/patch-Chrysalis_CMakeLists.txt
new file mode 100644
index 0000000000..49a7dbae42
--- /dev/null
+++ b/trinity/patches/patch-Chrysalis_CMakeLists.txt
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# Portability
+--- Chrysalis/CMakeLists.txt.orig 2018-09-01 15:19:53 UTC
++++ Chrysalis/CMakeLists.txt
+@@ -18,7 +18,7 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}
+ set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O2 -march=native -DNDEBUG ")
+ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g -O0")
+
+-set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lm -ldl ")
++set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lm ")
+
+ MESSAGE(STATUS "system: ${CMAKE_SYSTEM_NAME}")
+ if (${CMAKE_SYSTEM_NAME} STREQUAL "Linux")
diff --git a/trinity/patches/patch-Chrysalis_Makefile b/trinity/patches/patch-Chrysalis_Makefile
new file mode 100644
index 0000000000..b77ae5f267
--- /dev/null
+++ b/trinity/patches/patch-Chrysalis_Makefile
@@ -0,0 +1,22 @@
+$NetBSD$
+
+# Must use gmake
+--- Chrysalis/Makefile.orig 2018-09-01 15:20:04 UTC
++++ Chrysalis/Makefile
+@@ -1,13 +1,13 @@
+ all:
+ mkdir -p build
+- cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && make DESTDIR=../ install
++ cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && ${MAKE} DESTDIR=../ install
+
+ debug:
+ mkdir -p build
+- cd build && cmake -DCMAKE_INSTALL_PREFIX="" -DCMAKE_BUILD_TYPE=Debug ../ && make DESTDIR=../ install
++ cd build && cmake -DCMAKE_INSTALL_PREFIX="" -DCMAKE_BUILD_TYPE=Debug ../ && ${MAKE} DESTDIR=../ install
+
+
+ clean:
+ @echo cleaning
+- (cd build && make clean) || :
++ (cd build && ${MAKE} clean) || :
+ rm -rf ./build ./bin
diff --git a/trinity/patches/patch-Inchworm_CMakeLists.txt b/trinity/patches/patch-Inchworm_CMakeLists.txt
new file mode 100644
index 0000000000..784afd9776
--- /dev/null
+++ b/trinity/patches/patch-Inchworm_CMakeLists.txt
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# Portability
+--- Inchworm/CMakeLists.txt.orig 2018-09-01 15:19:04 UTC
++++ Inchworm/CMakeLists.txt
+@@ -18,7 +18,7 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}
+ set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O2 -march=native -DNDEBUG ")
+ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g -O0")
+
+-set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lm -ldl ")
++set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lm ")
+
+ MESSAGE(STATUS "system: ${CMAKE_SYSTEM_NAME}")
+ if (${CMAKE_SYSTEM_NAME} STREQUAL "Linux")
diff --git a/trinity/patches/patch-Inchworm_Makefile b/trinity/patches/patch-Inchworm_Makefile
new file mode 100644
index 0000000000..fe44c2675f
--- /dev/null
+++ b/trinity/patches/patch-Inchworm_Makefile
@@ -0,0 +1,16 @@
+$NetBSD$
+
+# Must use gmake
+--- Inchworm/Makefile.orig 2018-09-01 15:18:14 UTC
++++ Inchworm/Makefile
+@@ -1,8 +1,8 @@
+ all:
+ mkdir -p build
+- cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && make DESTDIR=../ install
++ cd build && cmake -DCMAKE_INSTALL_PREFIX="" ../ && ${MAKE} DESTDIR=../ install
+
+ clean:
+ @echo cleaning
+- (cd build && make clean) || :
++ (cd build && ${MAKE} clean) || :
+ rm -rf ./build ./bin
diff --git a/trinity/patches/patch-Makefile b/trinity/patches/patch-Makefile
new file mode 100644
index 0000000000..28d726fc08
--- /dev/null
+++ b/trinity/patches/patch-Makefile
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# Build plugins
+--- Makefile.orig 2018-09-01 14:38:58 UTC
++++ Makefile
+@@ -17,7 +17,7 @@ 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
+
+
diff --git a/trinity/patches/patch-trinity-plugins_Makefile b/trinity/patches/patch-trinity-plugins_Makefile
new file mode 100644
index 0000000000..95677e3641
--- /dev/null
+++ b/trinity/patches/patch-trinity-plugins_Makefile
@@ -0,0 +1,35 @@
+$NetBSD$
+
+# Unbundle deps, build scaffold_iworm_contigs
+--- trinity-plugins/Makefile.orig 2018-08-22 01:25:08 UTC
++++ trinity-plugins/Makefile
+@@ -9,12 +9,11 @@ TRIMMOMATIC_CODE=Trimmomatic-0.36
+
+
+
+-trinity_essentials: seqtk_target parafly_target trimmomatic_target
++trinity_essentials: scaffold_iworm_contigs_target seqtk_target
+
+ trimmomatic_target:
+ ln -sf ${TRIMMOMATIC_CODE} Trimmomatic
+
+-
+ seqtk_target:
+ cd seqtk-trinity-0.0.2 && $(MAKE) CXX=$(CXX) CC=$(CC)
+ mv seqtk-trinity-0.0.2/seqtk-trinity ./BIN/.
+@@ -24,12 +23,14 @@ parafly_target:
+ cd ${PARAFLY_CODE} && sh ./configure --prefix=`pwd` CXX=$(CXX) CC=$(CC) CFLAGS="-fopenmp" CXXFLAGS="-fopenmp" && $(MAKE) install && \
+ cp bin/ParaFly ../BIN/
+
++scaffold_iworm_contigs_target:
++ cd scaffold_iworm_contigs && $(MAKE)
+
+ ##################################
+ ### Needed for downstream analyses
+ ##################################
+
+-plugins: slclust_target collectl_target
++plugins: collectl_target
+ @echo "\n\n** Done building plugins **\n\n"
+
+
diff --git a/trinity/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile b/trinity/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile
new file mode 100644
index 0000000000..40007968f5
--- /dev/null
+++ b/trinity/patches/patch-trinity-plugins_scaffold__iworm__contigs_Makefile
@@ -0,0 +1,16 @@
+$NetBSD$
+
+# Respect pkgsrc env
+--- trinity-plugins/scaffold_iworm_contigs/Makefile.orig 2018-08-22 01:25:08 UTC
++++ trinity-plugins/scaffold_iworm_contigs/Makefile
+@@ -1,8 +1,8 @@
+-CXX = g++
++CXX ?= g++
+ prefix = ../htslib
+
+ ScaffoldIwormContigs:
+- $(CXX) $(LDFLAGS) -I$(prefix) -L$(prefix) ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs
++ $(CXX) $(LDFLAGS) -I$(LOCALBASE)/include -L$(LOCALBASE)/lib ScaffoldIwormContigs.cpp error_checker.cpp -lhts -o scaffold_iworm_contigs
+
+ clean:
+ rm -f scaffold_iworm_contigs
diff --git a/trinity/patches/patch-trinity-plugins_seqtk-trinity-0.0.2_Makefile b/trinity/patches/patch-trinity-plugins_seqtk-trinity-0.0.2_Makefile
new file mode 100644
index 0000000000..e4978bb25f
--- /dev/null
+++ b/trinity/patches/patch-trinity-plugins_seqtk-trinity-0.0.2_Makefile
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# Respect env
+--- trinity-plugins/seqtk-trinity-0.0.2/Makefile.orig 2018-09-16 14:53:41.191563645 +0000
++++ trinity-plugins/seqtk-trinity-0.0.2/Makefile
+@@ -4,7 +4,7 @@ CFLAGS=-g -Wall -O2 -Wno-unused-function
+ all:seqtk-trinity
+
+ seqtk-trinity:seqtk.c khash.h kseq.h
+- $(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm
++ $(CC) $(CFLAGS) seqtk.c -o $@ $(LDFLAGS) -lz -lm
+
+ clean:
+ rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session*
diff --git a/trinity/patches/patch-util_support__scripts_plugin__install__tests.sh b/trinity/patches/patch-util_support__scripts_plugin__install__tests.sh
new file mode 100644
index 0000000000..e947754ea3
--- /dev/null
+++ b/trinity/patches/patch-util_support__scripts_plugin__install__tests.sh
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# Unbundle slclust
+--- util/support_scripts/plugin_install_tests.sh.orig 2018-09-01 15:43:40 UTC
++++ util/support_scripts/plugin_install_tests.sh
+@@ -3,7 +3,7 @@
+ echo "## Checking plugin installations:"
+ echo
+
+-if [ -e "trinity-plugins/slclust/bin/slclust" ]
++if [ -e "${LOCALBASE}/bin/slclust" ]
+ then
+ echo "slclust: has been Installed Properly"
+ else
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