util/misc/run_STAR_via_samples_file.pl | 2 2 + 0 - 0 !
1 file changed, 2 insertions(+)

 implement genomesaindexnbases

Butterfly/src/.classpath | 15 15 + 0 - 0 !
Butterfly/src/.err | 3 3 + 0 - 0 !
Butterfly/src/.project | 17 17 + 0 - 0 !
Butterfly/src/.settings/org.eclipse.jdt.core.prefs | 12 12 + 0 - 0 !
Butterfly/src/README | 12 12 + 0 - 0 !
Butterfly/src/_t_seqA.fa | 2 2 + 0 - 0 !
Butterfly/src/_t_seqB.fa | 2 2 + 0 - 0 !
Butterfly/src/build.xml | 67 67 + 0 - 0 !
Butterfly/src/runExample.sh | 11 11 + 0 - 0 !
Butterfly/src/run_NWalign.sh | 8 8 + 0 - 0 !
Butterfly/src/run_butterfly_nonJar.sh | 11 11 + 0 - 0 !
Butterfly/src/sample_data/c1.graph.out | 495 495 + 0 - 0 !
Butterfly/src/sample_data/c1.graph.reads | 47 47 + 0 - 0 !
Butterfly/src/src/AlignmentStats.java | 328 328 + 0 - 0 !
Butterfly/src/src/BFLY_GLOBALS.java | 19 19 + 0 - 0 !
Butterfly/src/src/BipartiteMatching.java | 65 65 + 0 - 0 !
Butterfly/src/src/DFS.java | 120 120 + 0 - 0 !
Butterfly/src/src/GraphPath.java | 134 134 + 0 - 0 !
Butterfly/src/src/IsoformExpressionLearning.java | 632 632 + 0 - 0 !
Butterfly/src/src/ListComparator.java | 43 43 + 0 - 0 !
Butterfly/src/src/LocInGraph.java | 67 67 + 0 - 0 !
Butterfly/src/src/My_DFS.java | 572 572 + 0 - 0 !
Butterfly/src/src/NWalign.java | 196 196 + 0 - 0 !
Butterfly/src/src/NumPathNodeLoopsEdgeComparator.java | 31 31 + 0 - 0 !
Butterfly/src/src/PairPath.java | 907 907 + 0 - 0 !
Butterfly/src/src/PairPathWOrig.java | 116 116 + 0 - 0 !
Butterfly/src/src/PasaVertex.java | 179 179 + 0 - 0 !
Butterfly/src/src/Path.java | 635 635 + 0 - 0 !
Butterfly/src/src/PathEndSeqVertexFinishTimeComparator.java | 33 33 + 0 - 0 !
Butterfly/src/src/PathExpressionComparator.java | 611 611 + 0 - 0 !
Butterfly/src/src/PathOverlap.java | 12 12 + 0 - 0 !
Butterfly/src/src/PathReadSupportComparator.java | 69 69 + 0 - 0 !
Butterfly/src/src/PathWithOrig.java | 120 120 + 0 - 0 !
Butterfly/src/src/Path_n_MM_count.java | 102 102 + 0 - 0 !
Butterfly/src/src/Read.java | 169 169 + 0 - 0 !
Butterfly/src/src/ScoredPath.java | 25 25 + 0 - 0 !
Butterfly/src/src/SeqComparator.java | 20 20 + 0 - 0 !
Butterfly/src/src/SeqVertex.java | 953 953 + 0 - 0 !
Butterfly/src/src/SeqVertexDepthComparator.java | 18 18 + 0 - 0 !
Butterfly/src/src/SeqVertexFinishTimeComparator.java | 19 19 + 0 - 0 !
Butterfly/src/src/SeqVertexNodeDepthComparator.java | 19 19 + 0 - 0 !
Butterfly/src/src/SimpleEdge.java | 132 132 + 0 - 0 !
Butterfly/src/src/SimpleEdgeComparator.java | 20 20 + 0 - 0 !
Butterfly/src/src/SimplePathNodeEdge.java | 46 46 + 0 - 0 !
Butterfly/src/src/TopologicalSort.java | 150 150 + 0 - 0 !
Butterfly/src/src/TransAssembly_allProbPaths.java | 15920 15920 + 0 - 0 !
Butterfly/src/src/UniquePathContentComparator.java | 96 96 + 0 - 0 !
Butterfly/src/src/Visitor.java | 63 63 + 0 - 0 !
Butterfly/src/src/ZipperAlignment.java | 92 92 + 0 - 0 !
Butterfly/src/src/edu/uci/ics/jung/algorithms/shortestpath/DijkstraDistanceWoVer.java | 125 125 + 0 - 0 !
Butterfly/src/src/numLoopsEdgeComparator.java | 78 78 + 0 - 0 !
51 files changed, 23638 insertions(+)

 upstream accidentally left out butterfly/src from their tarball

util/misc/run_jellyfish.pl | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

jellyfish path

Chrysalis/analysis/Chrysalis.cc | 2 1 + 1 - 0 !
Trinity | 4 2 + 2 - 0 !
trinity-plugins/bamsifter/Makefile | 2 1 + 1 - 0 !
util/misc/bam_gene_tests/write_trin_cmds.pl | 2 1 + 1 - 0 !
util/misc/compare_bflies.pl | 4 2 + 2 - 0 !
util/misc/sim_test_framework/run_Trinity_eval.pl | 2 1 + 1 - 0 !
6 files changed, 8 insertions(+), 8 deletions(-)

 updates the main trinity program to use fhs paths

Butterfly/src/src/edu/uci/ics/jung/algorithms/shortestpath/DijkstraDistanceWoVer.java | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 compatibility fix due to use of newer libcommons-collections4-java

Inchworm/src/sequenceUtil.cpp | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 fix_istream_failure_call

Upstream is using wrong test gor file open failure, comparing an int instead
of calling fail() method

Analysis/DifferentialExpression/PtR | 9 4 + 5 - 0 !
Analysis/DifferentialExpression/ROKU.pl | 3 1 + 2 - 0 !
Analysis/DifferentialExpression/analyze_diff_expr.pl | 13 6 + 7 - 0 !
Analysis/DifferentialExpression/cut_tree_into_clusters.pl | 3 1 + 2 - 0 !
Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl | 5 2 + 3 - 0 !
Analysis/DifferentialExpression/diff_expr_analysis_to_heatmap_html.pl | 5 2 + 3 - 0 !
Analysis/DifferentialExpression/diff_express.cgi | 3 1 + 2 - 0 !
Analysis/DifferentialExpression/extract_GO_enriched_genes.pl | 4 1 + 3 - 0 !
Analysis/DifferentialExpression/get_transcript_lengths.pl | 3 1 + 2 - 0 !
Analysis/DifferentialExpression/merge_matrices.pl | 3 1 + 2 - 0 !
Analysis/DifferentialExpression/prep_n_run_GOplot.pl | 5 2 + 3 - 0 !
Analysis/DifferentialExpression/prune_isoforms_fasta.pl | 3 1 + 2 - 0 !
Analysis/DifferentialExpression/prune_isoforms_gtf.pl | 1 0 + 1 - 0 !
Analysis/DifferentialExpression/remove_batch_effects_from_count_matrix.pl | 3 1 + 2 - 0 !
Analysis/DifferentialExpression/run_DE_analysis.pl | 11 5 + 6 - 0 !
Analysis/DifferentialExpression/run_GOseq.pl | 1 0 + 1 - 0 !
Analysis/DifferentialExpression/run_TMM_normalization_write_FPKM_matrix.pl | 4 1 + 3 - 0 !
Analysis/DifferentialExpression/stratify_diff_expression.pl | 3 1 + 2 - 0 !
Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.pl | 3 1 + 2 - 0 !
Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl | 5 2 + 3 - 0 !
Analysis/FL_reconstruction_analysis/compute_oracle.pl | 4 1 + 3 - 0 !
Analysis/FL_reconstruction_analysis/maps_file_to_paralog_representation.pl | 1 0 + 1 - 0 !
Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.pl | 5 2 + 3 - 0 !
Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl | 5 2 + 3 - 0 !
Analysis/FL_reconstruction_analysis/util/blat_psl_to_align_summary_stats.pl | 3 1 + 2 - 0 !
Analysis/FL_reconstruction_analysis/util/blat_top_tier_genes.pl | 3 1 + 2 - 0 !
Analysis/SuperTranscripts/AllelicVariants/VCF_to_annotated_SNP_report.pl | 3 1 + 2 - 0 !
Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/DTU/dexseq_wrapper.pl | 7 3 + 4 - 0 !
Trinity | 15 7 + 8 - 0 !
trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl | 7 3 + 4 - 0 !
trinity_ext_sample_data/test_GenomeGuidedTrinity/old/run_mouse_TrinityGG.sh | 2 1 + 1 - 0 !
trinity_ext_sample_data/test_align_and_estimate_abundance/align_and_estimate_tester.pl | 3 1 + 2 - 0 !
util/TrinityStats.pl | 3 1 + 2 - 0 !
util/abundance_estimates_to_matrix.pl | 5 2 + 3 - 0 !
util/align_and_estimate_abundance.pl | 7 3 + 4 - 0 !
util/analyze_blastPlus_topHit_coverage.pl | 3 1 + 2 - 0 !
util/filter_low_expr_transcripts.pl | 3 1 + 2 - 0 !
util/insilico_read_normalization.pl | 9 4 + 5 - 0 !
util/misc/Artemis/join_multi_wig_to_graph_plot.pl | 3 1 + 2 - 0 !
util/misc/ButterflyFastaToGraphDot.pl | 3 1 + 2 - 0 !
util/misc/HiCpipe_nameSortedSam_to_raw.pl | 4 1 + 3 - 0 !
util/misc/Monarch | 3 1 + 2 - 0 !
util/misc/N50.pl | 3 1 + 2 - 0 !
util/misc/SAM_coordsorted_max_reads_per_position.pl | 3 1 + 2 - 0 !
util/misc/SAM_intron_extractor.pl | 3 1 + 2 - 0 !
util/misc/SAM_nameSorted_to_uniq_count_stats.pl | 3 1 + 2 - 0 !
util/misc/SAM_pair_to_bed.pl | 3 1 + 2 - 0 !
util/misc/SAM_sortAny_to_count_stats.pl | 3 1 + 2 - 0 !
util/misc/SAM_toString.pl | 3 1 + 2 - 0 !
util/misc/SAM_to_bed.pl | 5 1 + 4 - 0 !
util/misc/SAM_to_fasta.pl | 3 1 + 2 - 0 !
util/misc/TophatCufflinksWrapper.pl | 1 0 + 1 - 0 !
util/misc/Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl | 3 1 + 2 - 0 !
util/misc/align_reads_launch_igv.pl | 3 1 + 2 - 0 !
util/misc/allele_simulator.pl | 3 1 + 2 - 0 !
util/misc/average.pl | 3 1 + 2 - 0 !
util/misc/bam_gene_tests/extract_bam_reads_per_target_gene.pl | 3 1 + 2 - 0 !
util/misc/bam_gene_tests/extract_bam_reads_per_target_transcript.pl | 3 1 + 2 - 0 !
util/misc/bam_gene_tests/write_trin_cmds.pl | 3 1 + 2 - 0 !
util/misc/blast_outfmt6_group_segments.pl | 3 1 + 2 - 0 !
util/misc/blast_outfmt6_group_segments.to_Markov_Clustering.pl | 3 1 + 2 - 0 !
util/misc/blat_util/blat_sam_add_reads2.pl | 3 1 + 2 - 0 !
util/misc/blat_util/blat_to_sam.pl | 9 3 + 6 - 0 !
util/misc/blat_util/process_BLAT_alignments.pl | 8 3 + 5 - 0 !
util/misc/blat_util/top_blat_sam_extractor.pl | 3 1 + 2 - 0 !
util/misc/capture_orig_n_unmapped_reads.pl | 3 1 + 2 - 0 !
util/misc/cdna_fasta_file_to_transcript_gtf.pl | 3 1 + 2 - 0 !
util/misc/check_fastQ_pair_ordering.pl | 3 1 + 2 - 0 !
util/misc/collate_fqs.pl | 3 1 + 2 - 0 !
util/misc/contig_ExN50_statistic.pl | 3 1 + 2 - 0 !
util/misc/count_trans_per_component.pl | 2 0 + 2 - 0 !
util/misc/determine_RF_strand_specificity.pl | 3 1 + 2 - 0 !
util/misc/ensure_paired_end_bam_file.pl | 3 1 + 2 - 0 !
util/misc/examine_strand_specificity.pl | 5 2 + 3 - 0 !
util/misc/extract_fastQ_pairings.pl | 3 1 + 2 - 0 !
util/misc/fastQ_rand_subset.SE.reservoir_sampling_reqiures_high_mem.pl | 3 1 + 2 - 0 !
util/misc/fastQ_rand_subset.pl | 3 1 + 2 - 0 !
util/misc/fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl | 3 1 + 2 - 0 !
util/misc/fasta_file_reformatter.pl | 3 1 + 2 - 0 !
util/misc/fasta_filter_by_min_length.pl | 3 1 + 2 - 0 !
util/misc/fasta_seq_length.pl | 3 1 + 2 - 0 !
util/misc/fasta_to_cmd_generator.pl | 3 1 + 2 - 0 !
util/misc/fasta_write_sense_n_anti.pl | 3 1 + 2 - 0 !
util/misc/fastq_interleave_pairs.pl | 3 1 + 2 - 0 !
util/misc/fastq_unweave_pairs.pl | 3 1 + 2 - 0 !
util/misc/filter_similar_seqs_expr_and_strand_aware.pl | 3 1 + 2 - 0 !
util/misc/flattened_gff_n_genome_to_Trinity_emulator.pl | 3 1 + 2 - 0 !
util/misc/frag_to_bed.pl | 1 0 + 1 - 0 !
util/misc/gene_gff3_to_introns.pl | 3 1 + 2 - 0 !
util/misc/genome_gff3_to_gene_gff3_partitions.pl | 1 0 + 1 - 0 !
util/misc/get_GC_content_dist.pl | 3 1 + 2 - 0 !
util/misc/get_longest_isoform_seq_per_trinity_gene.pl | 3 1 + 2 - 0 !
util/misc/gff3_file_to_cdna.pl | 3 1 + 2 - 0 !
util/misc/gff3_file_utr_coverage_trimmer.pl | 3 1 + 2 - 0 !
util/misc/gff3_to_genome_feature_base_encoding.parse_SAM.pl | 3 1 + 2 - 0 !
util/misc/gff3_to_genome_feature_base_encoding.pl | 3 1 + 2 - 0 !
util/misc/gmap_gff3_chimera_jaccard_analyzer.pl | 3 1 + 2 - 0 !
util/misc/gmap_gff3_to_percent_length_stats.pl | 3 1 + 2 - 0 !
util/misc/gmap_native_to_format_converter.pl | 3 1 + 2 - 0 !
util/misc/gtf_to_bed_format.pl | 3 1 + 2 - 0 !
util/misc/gtf_to_introns.pl | 3 1 + 2 - 0 !
util/misc/identify_distal_isoform_variations.pl | 3 1 + 2 - 0 !
util/misc/illustrate_ref_comparison.pl | 4 1 + 3 - 0 !
util/misc/jaccard_sam_pair_refiner.pl | 3 1 + 2 - 0 !
util/misc/kmer_counter.pl | 3 1 + 2 - 0 !
util/misc/m8_blastclust.pl | 3 1 + 2 - 0 !
util/misc/map_gtf_transcripts_to_genome_annots.pl | 3 1 + 2 - 0 !
util/misc/merge_blast_n_rsem_results.pl | 3 1 + 2 - 0 !
util/misc/nameSorted_SAM_to_FastQ.pl | 3 1 + 2 - 0 !
util/misc/nameSorted_SAM_to_paired_fastq.pl | 3 1 + 2 - 0 !
util/misc/pairwise_kmer_content_comparer.pl | 3 1 + 2 - 0 !
util/misc/plot_expressed_gene_dist.pl | 4 1 + 3 - 0 !
util/misc/print_kmers.pl | 3 1 + 2 - 0 !
util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl | 1 0 + 1 - 0 !
util/misc/prop_pair_sam_refiner.pl | 3 1 + 2 - 0 !
util/misc/randomly_sample_PE_fastq.pl | 3 1 + 2 - 0 !
util/misc/run_GSNAP.pl | 1 0 + 1 - 0 !
util/misc/run_HISAT.pl | 3 1 + 2 - 0 !
util/misc/run_HISAT2_via_samples_file.pl | 3 1 + 2 - 0 !
util/misc/run_HiCpipe_bowtie.pl | 5 1 + 4 - 0 !
util/misc/run_STAR.pl | 3 1 + 2 - 0 !
util/misc/run_STAR_via_samples_file.pl | 3 1 + 2 - 0 !
util/misc/run_TOPHAT.pl | 1 0 + 1 - 0 !
util/misc/run_bowtie2.pl | 3 1 + 2 - 0 !
util/misc/run_bwa.pl | 1 0 + 1 - 0 !
util/misc/run_jellyfish.pl | 1 0 + 1 - 0 !
util/misc/run_read_simulator_per_fasta_entry.pl | 5 2 + 3 - 0 !
util/misc/run_read_simulator_per_gene.pl | 4 1 + 3 - 0 !
util/misc/run_trimmomatic_qual_trimming.pl | 6 2 + 4 - 0 !
util/misc/sim_test_framework/info_files_to_eval_cmds.pl | 3 1 + 2 - 0 !
util/misc/sim_test_framework/partition_target_transcripts.pl | 1 0 + 1 - 0 !
util/misc/sim_test_framework/run_Trinity_eval.pl | 7 3 + 4 - 0 !
util/misc/sim_test_framework/run_simulate_reads.wgsim.pl | 3 1 + 2 - 0 !
util/misc/sim_test_framework/write_simulate_read_commands.pl | 3 1 + 2 - 0 !
util/misc/simulate_illuminaPE_from_transcripts.pl | 3 1 + 2 - 0 !
util/misc/simulate_illuminaPE_from_transcripts.wgsim.pl | 7 3 + 4 - 0 !
util/misc/simulate_reads_sam_and_fa.pl | 5 2 + 3 - 0 !
util/misc/sixFrameTranslation.pl | 3 1 + 2 - 0 !
util/misc/sort_fastq.pl | 3 1 + 2 - 0 !
util/misc/splice_path_analysis/assess_intron_path_sensitivity.pl | 3 1 + 2 - 0 !
util/misc/strip_fasta_header.pl | 3 1 + 2 - 0 !
util/misc/transcript_coverage_UTR_trimmer.pl | 5 2 + 3 - 0 !
util/misc/transcript_fasta_to_ORF_pics.pl | 3 1 + 2 - 0 !
util/misc/transcript_gff3_to_bed.pl | 4 1 + 3 - 0 !
util/misc/trinity_component_distribution.pl | 3 1 + 2 - 0 !
util/sift_bam_max_cov.pl | 3 1 + 2 - 0 !
util/support_scripts/SAM_coordSorted_fragment_Read_coverage_writer.pl | 3 1 + 2 - 0 !
util/support_scripts/SAM_coordSorted_fragment_coverage_writer2.pl | 3 1 + 2 - 0 !
util/support_scripts/SAM_extract_properly_mapped_pairs.pl | 3 1 + 2 - 0 !
util/support_scripts/SAM_extract_uniquely_mapped_reads.pl | 3 1 + 2 - 0 !
util/support_scripts/SAM_filter_out_unmapped_reads.pl | 3 1 + 2 - 0 !
util/support_scripts/SAM_ordered_pair_jaccard.pl | 3 1 + 2 - 0 !
util/support_scripts/SAM_set_transcribed_orient_info.pl | 3 1 + 2 - 0 !
util/support_scripts/SAM_strand_separator.pl | 3 1 + 2 - 0 !
util/support_scripts/SAM_to_frag_coords.pl | 3 1 + 2 - 0 !
util/support_scripts/bowtie2_wrapper.pl | 5 1 + 4 - 0 !
util/support_scripts/define_SAM_coverage_partitions2.pl | 3 1 + 2 - 0 !
util/support_scripts/define_coverage_partitions.pl | 3 1 + 2 - 0 !
util/support_scripts/ensure_coord_sorted_sam.pl | 3 1 + 2 - 0 !
util/support_scripts/extract_reads_per_partition.pl | 3 1 + 2 - 0 !
util/support_scripts/fastQ_to_fastA.pl | 3 1 + 2 - 0 !
util/support_scripts/fastQ_to_tab.pl | 2 0 + 2 - 0 !
util/support_scripts/fasta_find_duplicates.pl | 3 1 + 2 - 0 !
util/support_scripts/fasta_to_tab.pl | 3 1 + 2 - 0 !
util/support_scripts/filter_iworm_by_min_length_or_cov.pl | 3 1 + 2 - 0 !
util/support_scripts/filter_transcripts_require_min_cov.pl | 3 1 + 2 - 0 !
util/support_scripts/fragment_coverage_writer.pl | 3 1 + 2 - 0 !
util/support_scripts/inchworm_transcript_splitter.pl | 4 1 + 3 - 0 !
util/support_scripts/iworm_LR_to_scaff_pairs.pl | 3 1 + 2 - 0 !
util/support_scripts/jaccard_fasta_clipper.pl | 3 1 + 2 - 0 !
util/support_scripts/jaccard_wig_clipper.pl | 3 1 + 2 - 0 !
util/support_scripts/nbkc_merge_left_right_stats.pl | 3 1 + 2 - 0 !
util/support_scripts/nbkc_normalize.pl | 3 1 + 2 - 0 !
util/support_scripts/ordered_fragment_coords_to_jaccard.pl | 3 1 + 2 - 0 !
util/support_scripts/outfmt6_add_percent_match_length.pl | 3 1 + 2 - 0 !
util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl | 5 2 + 3 - 0 !
util/support_scripts/process_GMAP_alignments_gff3_chimeras_ok.pl | 1 0 + 1 - 0 !
util/support_scripts/run_TMM_scale_matrix.pl | 4 1 + 3 - 0 !
util/support_scripts/run_UpperQuartileNormalization_matrix.pl | 4 1 + 3 - 0 !
util/support_scripts/salmon_runner.pl | 3 1 + 2 - 0 !
util/support_scripts/scaffold_iworm_contigs.pl | 3 1 + 2 - 0 !
util/support_scripts/trinity_install_tests.sh | 2 1 + 1 - 0 !
util/support_scripts/write_partitioned_trinity_cmds.pl | 3 1 + 2 - 0 !
184 files changed, 217 insertions(+), 421 deletions(-)

 drop some use of findbin and hardcode paths

Trinity | 28 1 + 27 - 0 !
1 file changed, 1 insertion(+), 27 deletions(-)

 disable the version "phone home" for privacy

Trinity | 6 3 + 3 - 0 !
1 file changed, 3 insertions(+), 3 deletions(-)

 match the debian's path

Butterfly/src/src/NWalign.java | 2 1 + 1 - 0 !
Butterfly/src/src/NeedlemanWunschGotohBanded.java | 493 493 + 0 - 0 !
2 files changed, 494 insertions(+), 1 deletion(-)

---

Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/extract_supertranscript_from_reference.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Compact_graph_partial.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Compact_graph_pruner.py | 5 1 + 4 - 0 !
Analysis/SuperTranscripts/pylib/Compact_graph_whole.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/DP_matrix.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Gene_splice_modeler.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/GraphCycleException.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Node_alignment.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Node_path.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Splice_model_refiner.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/TGLOBALS.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/TGraph.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/TNode.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Topological_sort.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.py | 2 1 + 1 - 0 !
Analysis/SuperTranscripts/pylib/Trinity_util.py | 2 1 + 1 - 0 !
PyLib/Pipeliner.py | 2 1 + 1 - 0 !
trinity-plugins/COLLECTL/util/collectl_dat_to_time_matrix.py | 2 1 + 1 - 0 !
trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py | 2 1 + 1 - 0 !
util/misc/TPM_weighted_gene_length.py | 2 1 + 1 - 0 !
util/misc/alt_GG_read_partitioning_JCornish/genwig2.py | 2 1 + 1 - 0 !
util/support_scripts/trinity_installer.py | 2 1 + 1 - 0 !
23 files changed, 23 insertions(+), 26 deletions(-)

 default to running python 3

sample_data/test_Trinity_Assembly/misc_run_tests/__runMe.diff_kmer_length.sh | 4 2 + 2 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe.noSeqtk.sh | 3 2 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_CuffFly.sh | 4 2 + 2 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_PasaFly.sh | 4 2 + 2 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_as_DS.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_bowtie_components.sh | 4 2 + 2 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_full_cleanup.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_include_long_reads.sh | 3 2 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_include_supertranscripts.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_no_cleanup.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_no_para_iworm.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_no_salmon_no_cleanup.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_parallel_iworm_assembly.sh | 4 2 + 2 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_piecemeal.sh | 10 6 + 4 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_trin_complete.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_use_bowtie2.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_use_my_ramdisk.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_use_workdir.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_using_Grid_LSF.sh | 4 1 + 3 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_wSuperReads.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_w_monitoring.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming.sh | 3 2 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalization.sh | 3 2 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__runMe_with_qual_trimming_and_normalize_libs_separately.sh | 3 2 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe.singleFQ.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_NO_normalization.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_docker.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_include_normalization.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/__test_runMe_lenient_path_extension.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/misc_run_tests/runMe_no_qualTrim.sh | 4 3 + 1 - 0 !
sample_data/test_Trinity_Assembly/runMe.sh | 3 2 + 1 - 0 !
trinity_ext_sample_data/test_InSilicoReadNormalization/test_PE_normalization.mult_read_sets.sh | 4 3 + 1 - 0 !
trinity_ext_sample_data/test_InSilicoReadNormalization/test_PE_normalization.sh | 4 3 + 1 - 0 !
util/support_scripts/tests/tests.py | 9 5 + 4 - 0 !
34 files changed, 94 insertions(+), 47 deletions(-)

 don't hardcode number of --cpu (especially above 2)

blastn -num_threads will not accept a number larger than the cores/CPUs it
detects and will exit with an error. Some Debian test (virtual) machines only
have two cores and thus they failed our testing.

With this patch we detect in a unix/macOS friendly way the number of cores
using `nproc` or `sysctl -n hw.physicalcpu` (respectively). Thus execution of
the sample_data tests will be much faster for most developers/users.

Perhaps Trinity itself could be taught this trick and the --CPU option would
not be needed by default.

Chrysalis/Makefile | 4 2 + 2 - 0 !
trinity-plugins/scaffold_iworm_contigs/Makefile | 2 1 + 1 - 0 !
2 files changed, 3 insertions(+), 3 deletions(-)

 add standard cxxflags cppflags to chrysalis & scaffold_iworm_contigs

trinity-plugins/seqtk-trinity/Makefile | 6 3 + 3 - 0 !
1 file changed, 3 insertions(+), 3 deletions(-)

 add ldfalgs cppflags and unshadw cfalgs for seqtk-trinity-0.0.2

trinity_ext_sample_data/Makefile | 1 0 + 1 - 0 !
1 file changed, 1 deletion(-)

 skip tests that require gatk4 until it gets packaged

trinity_ext_sample_data/Makefile | 1 0 + 1 - 0 !
1 file changed, 1 deletion(-)

 r-bioc-tximportdata is 400mib+ package

Inchworm/Makefile | 4 2 + 2 - 0 !
Makefile | 10 5 + 5 - 0 !
sample_data/Makefile | 2 1 + 1 - 0 !
trinity-plugins/Makefile | 4 2 + 2 - 0 !
trinity_ext_sample_data/test_SuperTranscript/Makefile | 4 2 + 2 - 0 !
trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh | 3 2 + 1 - 0 !
trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh | 3 2 + 1 - 0 !
trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh | 3 2 + 1 - 0 !
trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh | 3 2 + 1 - 0 !
trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh | 3 2 + 1 - 0 !
trinity_ext_sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh | 3 2 + 1 - 0 !
trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh | 3 2 + 1 - 0 !
trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh | 3 2 + 1 - 0 !
trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh | 3 2 + 1 - 0 !
trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh | 3 2 + 1 - 0 !
trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh | 3 2 + 1 - 0 !
trinity_ext_sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh | 3 2 + 1 - 0 !
17 files changed, 36 insertions(+), 24 deletions(-)

 enable better use of sub-make

trinity_ext_sample_data/Makefile | 3 1 + 2 - 0 !
1 file changed, 1 insertion(+), 2 deletions(-)

 skip tests with a dependency on blat

trinity-plugins/bamsifter/sift_bam_max_cov.cpp | 1 1 + 0 - 0 !
1 file changed, 1 insertion(+)

 fix gcc-10 build issue
Bug-Debian: https://bugs.debian.org/966876

trinity-plugins/bamsifter/Makefile | 16 5 + 11 - 0 !
1 file changed, 5 insertions(+), 11 deletions(-)

 build bamsifter using the system htslib

trinity_ext_sample_data/test_DTU/Makefile | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 skip the star based dtu tests for now

Chrysalis/CMakeLists.txt | 2 1 + 1 - 0 !
Inchworm/CMakeLists.txt | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 remove -m64 flag, hopefully helps arm64 compile