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trinity-devel: Successful build, generate plist

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Sep 16 10:25:33 2018 -0500
Changeset:	7813ce923cd12cd07b86c1b010a1af93643331ff

Modified Files:
	trinity-devel/Makefile
	trinity-devel/PLIST
	trinity-devel/distinfo
Added Files:
	trinity-devel/patches/patch-trinity-plugins_seqtk-trinity-0.0.2_Makefile

Log Message:
trinity-devel: Successful build, generate plist

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=7813ce923cd12cd07b86c1b010a1af93643331ff

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

diffstat:
 trinity-devel/Makefile                             |  21 +-
 trinity-devel/PLIST                                | 615 +++++++++++++++++++++
 trinity-devel/distinfo                             |   1 +
 ...ch-trinity-plugins_seqtk-trinity-0.0.2_Makefile |  14 +
 4 files changed, 636 insertions(+), 15 deletions(-)

diffs:
diff --git a/trinity-devel/Makefile b/trinity-devel/Makefile
index cae62661b6..43f28a25b5 100644
--- a/trinity-devel/Makefile
+++ b/trinity-devel/Makefile
@@ -43,17 +43,14 @@ HOMEPAGE=	http://trinityrnaseq.github.io/
 COMMENT=	Assembles transcript sequences from Illumina RNA-Seq data
 LICENSE=	modified-bsd
 
-# MAKE_JOBS_SAFE=	no
-
 USE_LANGUAGES=	c c++
 USE_JAVA=	run
-USE_TOOLS+=	cmake gmake pax
-USE_CMAKE=	yes
+USE_TOOLS+=	cmake gmake pax perl
 
 REPLACE_BASH=	util/*/*.sh
 REPLACE_BASH+=	util/misc/alt_GG_read_partitioning_JCornish/genwig.sh
 REPLACE_BASH+=	Analysis/DifferentialExpression/cluster_sample_data/runMe.sh
-REPLACE_PERL=	util/*/*.pl Chrysalis/analysis/*.pl 
+REPLACE_PERL=	Trinity util/*.pl util/*/*.pl util/*/*/*.pl Chrysalis/analysis/*.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
@@ -115,20 +112,17 @@ PLUGINS_DIR=	${LIBEXEC_DIR}/trinity-plugins
 # Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
 # .include "../../mk/bsd.prefs.mk"
 
-INSTALLATION_DIRS=	bin include lib ${PKGMANDIR}/man1 share/doc share/examples
+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
 
 # FIXME: More may need to be installed
 do-install:
 	${INSTALL_SCRIPT} ${WRKSRC}/Trinity ${DESTDIR}${PREFIX}/bin
-	@${MKDIR} ${DESTDIR}${LIBEXEC_DIR}/Chrysalis/bin
 	${INSTALL_PROGRAM} ${WRKSRC}/Chrysalis/bin/* \
 		${DESTDIR}${LIBEXEC_DIR}/Chrysalis/bin
 	${INSTALL_SCRIPT} ${WRKSRC}/Chrysalis/analysis/ReadsToComponents.pl \
 		${DESTDIR}${LIBEXEC_DIR}/Chrysalis/bin
-	@${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 \
@@ -137,19 +131,16 @@ do-install:
 		${DESTDIR}${LIBEXEC_DIR}
 	cd ${WRKSRC} && pax -rw Analysis \
 		${DESTDIR}${LIBEXEC_DIR}
-	@${MKDIR} ${DESTDIR}${PLUGINS_DIR}/scaffold_iworm_contigs
 	${INSTALL_PROGRAM} ${WRKSRC}/trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs \
 		${DESTDIR}${PLUGINS_DIR}/scaffold_iworm_contigs
-	@${MKDIR} ${DESTDIR}${PLUGINS_DIR}/BIN
 	${INSTALL_PROGRAM} ${WRKSRC}/trinity-plugins/BIN/seqtk-trinity \
 		${DESTDIR}${PLUGINS_DIR}/BIN
-	cd ${WRKSRC}/sample_data && pax -rw \* \
+	cd ${WRKSRC}/sample_data && pax -rw * \
 		${DESTDIR}${EXAMPLESDIR}
-	${RLN} ${DESTDIR}${PREFIX}/bin/Trinity \
+	${LN} -fs ${PREFIX}/bin/Trinity \
 		${DESTDIR}${PREFIX}/libexec/trinity/Trinity
 
 .include "../../lang/python/application.mk"
 .include "../../biology/htslib/buildlink3.mk"
-# CentOS doesn't have zlib in the base, so uncomment if needed.
-# .include "../../devel/zlib/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/trinity-devel/PLIST b/trinity-devel/PLIST
index 48d96a5493..d3d104c695 100644
--- a/trinity-devel/PLIST
+++ b/trinity-devel/PLIST
@@ -1 +1,616 @@
 @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
+libexec/trinity/PerlLib/VCF_parser.pm
+libexec/trinity/PerlLib/WigParser.pm
+libexec/trinity/PerlLib/overlapping_nucs.ph
+libexec/trinity/PerlLib/test_Fasta_retriever.pl
+libexec/trinity/PerlLib/test_htc_gridrunner_LSF.pl
+libexec/trinity/PerlLib/test_htc_gridrunner_SGE.pl
+libexec/trinity/Trinity
+libexec/trinity/trinity-plugins/BIN/seqtk-trinity
+libexec/trinity/trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs
+libexec/trinity/util/PBS/N50stats.pl
+libexec/trinity/util/PBS/README
+libexec/trinity/util/PBS/TRINITY.CONFIG.template
+libexec/trinity/util/PBS/pbs_check.pl
+libexec/trinity/util/PBS/trinity_kill.pl
+libexec/trinity/util/PBS/trinity_kill.sh
+libexec/trinity/util/PBS/trinity_pbs.cont
+libexec/trinity/util/PBS/trinity_pbs.header
+libexec/trinity/util/PBS/trinity_pbs.p1
+libexec/trinity/util/PBS/trinity_pbs.p2
+libexec/trinity/util/PBS/trinity_pbs.p3
+libexec/trinity/util/PBS/trinity_pbs.p4a
+libexec/trinity/util/PBS/trinity_pbs.p4b
+libexec/trinity/util/PBS/trinity_pbs.p5b
+libexec/trinity/util/PBS/trinity_pbs.sh
+libexec/trinity/util/R/expression_analysis_lib.R
+libexec/trinity/util/R/get_Poisson_conf_intervals.R
+libexec/trinity/util/TrinityStats.pl
+libexec/trinity/util/abundance_estimates_to_matrix.pl
+libexec/trinity/util/align_and_estimate_abundance.pl
+libexec/trinity/util/analyze_blastPlus_topHit_coverage.pl
+libexec/trinity/util/filter_low_expr_transcripts.pl
+libexec/trinity/util/insilico_read_normalization.pl
+libexec/trinity/util/misc/Artemis/join_multi_wig_to_graph_plot.pl
+libexec/trinity/util/misc/BLAT_to_SAM.pl
+libexec/trinity/util/misc/ButterflyFastaToGraphDot.pl
+libexec/trinity/util/misc/HiCpipe_nameSortedSam_to_raw.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/N50.pl
+libexec/trinity/util/misc/PerlLib/SegmentGraph.pm
+libexec/trinity/util/misc/SAM_coordsorted_max_reads_per_position.pl
+libexec/trinity/util/misc/SAM_intron_extractor.pl
+libexec/trinity/util/misc/SAM_nameSorted_to_uniq_count_stats.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
+libexec/trinity/util/misc/SAM_toString.pl
+libexec/trinity/util/misc/SAM_to_bed.pl
+libexec/trinity/util/misc/SAM_to_fasta.pl
+libexec/trinity/util/misc/SRA_to_fastq.notes
+libexec/trinity/util/misc/SRA_to_fastq.pl
+libexec/trinity/util/misc/TEST_SUPPORT/BFLY_TESTING/graph_out_to_bfly_cmd.pl
+libexec/trinity/util/misc/TPM_weighted_gene_length.py
+libexec/trinity/util/misc/TophatCufflinksWrapper.pl
+libexec/trinity/util/misc/Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl
+libexec/trinity/util/misc/acc_list_to_fasta_entries.pl
+libexec/trinity/util/misc/alexie_analyze_blast.pl
+libexec/trinity/util/misc/align_reads_launch_igv.pl
+libexec/trinity/util/misc/allele_simulator.pl
+libexec/trinity/util/misc/alt_GG_read_partitioning_JCornish/genwig.sh
+libexec/trinity/util/misc/alt_GG_read_partitioning_JCornish/genwig2.py
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+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
index 8dacf5ca9e..f2fcfd1186 100644
--- a/trinity-devel/distinfo
+++ b/trinity-devel/distinfo
@@ -11,4 +11,5 @@ SHA1 (patch-Inchworm_Makefile) = 4aa9e682648484976e9cc611e2715b7fb9109e45
 SHA1 (patch-Makefile) = 07ca4b2a3f9157b822e9e05cf4f70b437b7fb5de
 SHA1 (patch-trinity-plugins_Makefile) = 173d54aa7a80edc3c429fe145cab841cdf4dca01
 SHA1 (patch-trinity-plugins_scaffold__iworm__contigs_Makefile) = e946e46209d0654c285f829017e5753eb3444fa0
+SHA1 (patch-trinity-plugins_seqtk-trinity-0.0.2_Makefile) = 30946c32223ae06311e7315a467af5c5de626f0c
 SHA1 (patch-util_support__scripts_plugin__install__tests.sh) = 5da1d3872d6632ffb33a84f4cd4ee57c367130f3
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
new file mode 100644
index 0000000000..e4978bb25f
--- /dev/null
+++ b/trinity-devel/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*
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