[med-svn] [trinityrnaseq] branch master updated (9d01872 -> 11fefd4)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Fri May 20 13:32:26 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch master
in repository trinityrnaseq.
from 9d01872 d/watch: Use xz compression for upstream source
new 5ae7d24 fix local version mangle & update excludes
adds 0b7afc2 Imported Upstream version 2.2.0+dfsg
new 5ea6f53 Merge tag 'upstream/2.2.0+dfsg'
new 11fefd4 new upstream release
The 3 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
Analysis/DifferentialExpression/PtR | 80 +-
Analysis/DifferentialExpression/ROKU.pl | 2 +-
.../{ => TissueEnrichment}/DE_graph_to_dot.pl | 0
.../DE_results_to_pairwise_summary.pl} | 73 +-
.../TissueEnrichment/README.md | 5 +
.../pairwise_DE_summary_to_DE_classification.pl | 1 +
.../DifferentialExpression/analyze_diff_expr.pl | 8 +-
.../cluster_sample_data/cleanme.pl | 2 +-
.../cut_tree_into_clusters.pl | 2 +-
.../define_clusters_by_cutting_tree.pl | 9 +-
.../diff_expr_analysis_to_heatmap_html.pl | 4 +-
Analysis/DifferentialExpression/diff_express.cgi | 2 +-
.../extract_GO_enriched_genes.pl | 2 +-
.../get_transcript_lengths.pl | 2 +-
Analysis/DifferentialExpression/merge_matrices.pl | 12 +-
.../remove_batch_effects_from_count_matrix.pl | 2 +-
.../replicates_to_sample_averages_matrix.pl | 2 +-
Analysis/DifferentialExpression/run_DE_analysis.pl | 10 +-
Analysis/DifferentialExpression/run_GOseq.pl | 2 +-
.../run_TMM_normalization_write_FPKM_matrix.pl | 4 +-
.../stratify_diff_expression.pl | 2 +-
.../subcluster_to_canvasXpress_html.pl | 2 +-
.../FL_trans_analysis_pipeline.pl | 4 +-
.../FL_reconstruction_analysis/compute_oracle.pl | 2 +-
.../tier_gene_trans_alignments.pl | 4 +-
.../util/blat_full_length_mappings.pl | 2 +-
.../util/blat_top_tier_genes.pl | 2 +-
Butterfly/src/src/TransAssembly_allProbPaths.java | 144 ++-
Release.Notes => Changelog.txt | 95 +-
Chrysalis/MakeDepend.cc | 2 +-
Chrysalis/Makefile | 10 +-
Chrysalis/analysis/TranscriptomeGraph.cc | 2 +-
Inchworm/src/IRKE.cpp | 122 +--
Inchworm/src/fastaToKmerCoverageStats.cpp | 11 +-
PerlLib/Fastq_reader.pm | 17 +-
PerlLib/test_htc_gridrunner_LSF.pl | 4 +-
PerlLib/test_htc_gridrunner_SGE.pl | 4 +-
README | 2 +-
README.md | 2 +-
Trinity | 47 +-
debian/changelog | 11 +-
debian/control | 2 +-
debian/copyright | 8 -
debian/patches/chrysalis-make-tweak | 18 -
debian/patches/disable-version-check | 2 +-
debian/patches/fix_system_paths | 42 +-
debian/patches/hardening | 98 --
debian/patches/hashbang | 43 -
debian/patches/noExitTester | 2 +-
debian/patches/reproducible-build | 22 -
.../scaffold_iworm_contigs-Makefile-fix-clean | 17 -
debian/patches/series | 6 -
debian/patches/skip-kallisto-deseq2-tests | 30 +-
debian/patches/spelling | 35 -
debian/patches/update-paths | 2 +-
debian/rules | 3 +-
debian/trinityrnaseq.docs | 1 -
debian/watch | 2 +-
.../test_GraphFromFasta/runMe.sh | 1 +
sample_data/test_DE_analysis/Makefile | 6 +-
.../test_GOSeq_trinotate_pipe/Spombe/cleanme.pl | 2 +-
.../test_GOSeq_trinotate_pipe/Spombe/runMe.sh | 1 +
sample_data/test_GenomeGuidedTrinity/cleanme.pl | 2 +-
.../test_InSilicoReadNormalization/Makefile | 1 +
.../test_InSilicoReadNormalization/cleanme.pl | 10 +-
.../test_PE_normalization.mult_read_sets.sh | 11 +
sample_data/test_Inchworm/runMe_MPI.sh | 1 +
.../DE_results.tar.gz} | Bin 36329210 -> 37622593 bytes
sample_data/test_TissueSpecificityGraph/Makefile | 10 +
.../transcripts.TMM.fpkm.avg_reps.matrix.gz | Bin 0 -> 3467094 bytes
sample_data/test_Trinity_Assembly/Makefile | 14 +-
.../align_reads_via_bowtie.sh | 3 +-
.../__indiv_ex_sample_derived/ex05/runMe.clean.sh | 1 +
.../__indiv_ex_sample_derived/ex05/runMe.sh | 1 +
.../__indiv_ex_sample_derived/ex09/runMe.sh | 1 +
sample_data/test_Trinity_Assembly/cleanme.pl | 4 +-
.../misc_run_tests/__runMe_include_long_reads.sh | 2 +-
sample_data/test_Trinity_Assembly/runMe.sh | 2 +-
.../test_align_and_estimate_abundance/Makefile | 19 +-
.../PAIRED_END_ABUNDANCE_ESTIMATION/Makefile | 41 +
.../cleanme.pl | 22 +-
.../misc_tests/drosoph_denovo.samples.txt | 6 +
.../misc_tests/drosoph_ref.samples.txt | 6 +
.../misc_tests/mouse_denovo.samples.txt | 6 +
.../misc_tests/mouse_ref.samples.txt | 6 +
.../misc_tests/schizo_denovo.samples.txt | 6 +
.../misc_tests/schizo_ref.samples.txt | 6 +
.../misc_tests/test_Drosoph_denovo.sh | 1 +
.../misc_tests/test_Drosoph_ref.sh | 1 +
.../misc_tests/test_Mouse_denovo.sh | 1 +
.../misc_tests/test_Mouse_ref.sh | 1 +
.../misc_tests/test_Schizo_denovo.sh | 1 +
.../misc_tests/test_Schizo_ref.sh | 1 +
.../PAIRED_END_ABUNDANCE_ESTIMATION/samples.txt | 8 +
.../SINGLE_END_ABUNDANCE_ESTIMATION/Makefile | 41 +
.../cleanme.pl | 23 +-
.../misc_tests/drosoph_denovo.samples.txt | 5 +
.../misc_tests/drosoph_ref.samples.txt | 6 +
.../misc_tests/mouse_denovo.samples.txt | 6 +
.../misc_tests/mouse_ref.samples.txt | 6 +
.../misc_tests/schizo_denovo.samples.txt | 6 +
.../misc_tests/schizo_ref.samples.txt | 6 +
.../misc_tests/test_Drosoph_denovo.sh | 1 +
.../misc_tests/test_Drosoph_ref.sh | 1 +
.../misc_tests/test_Mouse_denovo.sh | 1 +
.../misc_tests/test_Mouse_ref.sh | 1 +
.../misc_tests/test_Schizo_denovo.sh | 1 +
.../misc_tests/test_Schizo_ref.sh | 1 +
.../SINGLE_END_ABUNDANCE_ESTIMATION/samples.txt | 8 +
.../align_and_estimate_tester.pl | 68 +-
.../pairs.Rscript | 6 +
.../test_align_and_estimate_abundance/samples.txt | 4 -
sample_data/test_full_edgeR_pipeline/cleanme.pl | 2 +-
trinity-plugins/Makefile | 10 +-
.../fstrozzi-Fastool-7c3e034f05/Makefile | 5 +-
trinity-plugins/scaffold_iworm_contigs/Makefile | 4 +-
trinity-plugins/slclust/src/Makefile | 21 +-
util/SAM_nameSorted_to_uniq_count_stats.pl | 12 +-
util/TrinityStats.pl | 2 +-
util/abundance_estimates_to_matrix.pl | 84 +-
util/align_and_estimate_abundance.pl | 344 ++++---
util/analyze_blastPlus_topHit_coverage.pl | 2 +-
util/bowtie_PE_separate_then_join.pl | 6 +-
util/fasta_tool | 1054 +++++++++++++++++++-
util/filter_low_expr_transcripts.pl | 286 ++++++
util/insilico_read_normalization.pl | 13 +-
util/misc/Artemis/join_multi_wig_to_graph_plot.pl | 2 +-
util/misc/BLAT_to_SAM.pl | 6 +-
util/misc/ButterflyFastaToGraphDot.pl | 2 +-
util/misc/HiCpipe_nameSortedSam_to_raw.pl | 2 +-
util/misc/Monarch | 2 +-
util/misc/N50.pl | 2 +-
.../misc/SAM_coordsorted_max_reads_per_position.pl | 2 +-
util/misc/SAM_intron_extractor.pl | 2 +-
util/misc/SAM_pair_to_bed.pl | 2 +-
util/misc/SAM_sortAny_to_count_stats.pl | 2 +-
util/misc/SAM_toString.pl | 2 +-
util/misc/SAM_to_bed.pl | 2 +-
util/misc/SAM_to_fasta.pl | 2 +-
util/misc/TophatCufflinksWrapper.pl | 2 +-
util/misc/allele_simulator.pl | 2 +-
util/misc/average.pl | 2 +-
.../extract_bam_reads_per_target_gene.pl | 2 +-
.../extract_bam_reads_per_target_transcript.pl | 2 +-
util/misc/bam_gene_tests/write_trin_cmds.pl | 2 +-
util/misc/blast_outfmt6_group_segments.pl | 2 +-
..._outfmt6_group_segments.to_Markov_Clustering.pl | 2 +-
util/misc/blat_util/blat_sam_add_reads2.pl | 2 +-
util/misc/blat_util/blat_to_sam.pl | 4 +-
util/misc/blat_util/process_BLAT_alignments.pl | 4 +-
util/misc/blat_util/top_blat_sam_extractor.pl | 2 +-
util/misc/capture_orig_n_unmapped_reads.pl | 2 +-
util/misc/cdna_fasta_file_to_transcript_gtf.pl | 2 +-
util/misc/check_fastQ_pair_ordering.pl | 2 +-
util/misc/contig_ExN50_statistic.pl | 15 +-
util/misc/extract_fastQ_pairings.pl | 2 +-
util/misc/fastQ_rand_subset.pl | 2 +-
..._subset.reservoir_sampling_reqiures_high_mem.pl | 2 +-
util/misc/fasta_file_reformatter.pl | 2 +-
util/misc/fasta_filter_by_min_length.pl | 2 +-
util/misc/fasta_seq_length.pl | 25 +
util/misc/fasta_to_cmd_generator.pl | 2 +-
util/misc/fasta_write_sense_n_anti.pl | 2 +-
util/misc/fastq_interleave_pairs.pl | 2 +-
util/misc/fastq_unweave_pairs.pl | 2 +-
util/misc/gene_gff3_to_introns.pl | 2 +-
.../get_longest_isoform_seq_per_trinity_gene.pl | 2 +-
util/misc/gff3_file_to_cdna.pl | 2 +-
util/misc/gff3_file_utr_coverage_trimmer.pl | 2 +-
...f3_to_genome_feature_base_encoding.parse_SAM.pl | 2 +-
util/misc/gff3_to_genome_feature_base_encoding.pl | 2 +-
util/misc/gmap_gff3_chimera_jaccard_analyzer.pl | 2 +-
util/misc/gmap_gff3_to_percent_length_stats.pl | 2 +-
util/misc/gmap_native_to_format_converter.pl | 2 +-
util/misc/gtf_to_bed_format.pl | 2 +-
util/misc/gtf_to_introns.pl | 2 +-
util/misc/identify_distal_isoform_variations.pl | 2 +-
util/misc/illustrate_ref_comparison.pl | 2 +-
util/misc/jaccard_sam_pair_refiner.pl | 2 +-
util/misc/kmer_counter.pl | 2 +-
util/misc/m8_blastclust.pl | 2 +-
util/misc/map_gtf_transcripts_to_genome_annots.pl | 2 +-
util/misc/merge_blast_n_rsem_results.pl | 2 +-
util/misc/nameSorted_SAM_to_FastQ.pl | 2 +-
util/misc/pairwise_kmer_content_comparer.pl | 2 +-
util/misc/plot_ExN50_statistic.Rscript | 14 +
util/misc/plot_expressed_gene_dist.pl | 2 +-
util/misc/print_kmers.pl | 2 +-
util/misc/prop_pair_sam_refiner.pl | 2 +-
util/misc/run_GSNAP.pl | 27 +-
util/misc/run_HISAT.pl | 2 +-
util/misc/run_HiCpipe_bowtie.pl | 4 +-
util/misc/run_bowtie2.pl | 39 +
util/misc/run_read_simulator_per_fasta_entry.pl | 4 +-
util/misc/run_read_simulator_per_gene.pl | 2 +-
util/misc/run_trimmomatic_qual_trimming.pl | 4 +-
util/misc/simulate_illuminaPE_from_transcripts.pl | 2 +-
util/misc/simulate_reads_sam_and_fa.pl | 4 +-
util/misc/sixFrameTranslation.pl | 2 +-
util/misc/sort_fastq.pl | 2 +-
.../assess_intron_path_sensitivity.pl | 2 +-
util/misc/strip_fasta_header.pl | 2 +-
util/misc/transcript_coverage_UTR_trimmer.pl | 4 +-
util/misc/transcript_fasta_to_ORF_pics.pl | 2 +-
util/misc/transcript_gff3_to_bed.pl | 2 +-
util/misc/trinity_component_distribution.pl | 2 +-
util/run_DE_analysis_from_samples_file.pl | 2 +-
util/run_RSEM_from_samples_file.pl | 2 +-
util/run_Trinity_edgeR_pipeline.pl | 22 +-
util/run_Trinity_from_samples_file.pl | 2 +-
...AM_coordSorted_fragment_Read_coverage_writer.pl | 2 +-
.../SAM_coordSorted_fragment_coverage_writer2.pl | 2 +-
.../SAM_extract_properly_mapped_pairs.pl | 2 +-
.../SAM_extract_uniquely_mapped_reads.pl | 2 +-
.../SAM_filter_out_unmapped_reads.pl | 2 +-
util/support_scripts/SAM_ordered_pair_jaccard.pl | 2 +-
.../SAM_set_transcribed_orient_info.pl | 2 +-
util/support_scripts/SAM_strand_separator.pl | 2 +-
util/support_scripts/SAM_to_frag_coords.pl | 2 +-
.../define_SAM_coverage_partitions2.pl | 2 +-
util/support_scripts/define_coverage_partitions.pl | 2 +-
.../support_scripts/extract_reads_per_partition.pl | 2 +-
util/support_scripts/fastQ_to_fastA.pl | 2 +-
util/support_scripts/fasta_to_tab.pl | 2 +-
util/support_scripts/fragment_coverage_writer.pl | 2 +-
.../inchworm_transcript_splitter.pl | 2 +-
util/support_scripts/jaccard_fasta_clipper.pl | 2 +-
util/support_scripts/jaccard_wig_clipper.pl | 2 +-
.../merge_left_right_nameSorted_SAMs.pl | 2 +-
.../support_scripts/nbkc_merge_left_right_stats.pl | 4 +
.../ordered_fragment_coords_to_jaccard.pl | 2 +-
...aseq_alignments_for_genome_assisted_assembly.pl | 2 +-
util/support_scripts/run_TMM_scale_matrix.pl | 4 +-
.../run_UpperQuartileNormalization_matrix.pl | 8 +-
..._results.pl => salmon_trans_to_gene_results.pl} | 60 +-
util/support_scripts/tests/sample_data_tests.py | 56 ++
util/support_scripts/tests/test.py | 187 ----
util/support_scripts/tests/test_prep.py | 55 +-
util/support_scripts/tests/tests.py | 34 +-
.../write_partitioned_trinity_cmds.pl | 2 +-
240 files changed, 2901 insertions(+), 1156 deletions(-)
copy Analysis/DifferentialExpression/{ => TissueEnrichment}/DE_graph_to_dot.pl (100%)
copy Analysis/DifferentialExpression/{pairwise_summaries/edgeR_to_pairwise_summary.pl => TissueEnrichment/DE_results_to_pairwise_summary.pl} (53%)
create mode 100644 Analysis/DifferentialExpression/TissueEnrichment/README.md
copy Analysis/DifferentialExpression/{pairwise_summaries => TissueEnrichment}/pairwise_DE_summary_to_DE_classification.pl (99%)
rename Release.Notes => Changelog.txt (90%)
delete mode 100644 debian/patches/chrysalis-make-tweak
delete mode 100644 debian/patches/hardening
delete mode 100644 debian/patches/hashbang
delete mode 100644 debian/patches/reproducible-build
delete mode 100644 debian/patches/scaffold_iworm_contigs-Makefile-fix-clean
delete mode 100644 debian/patches/spelling
create mode 100755 sample_data/test_InSilicoReadNormalization/test_PE_normalization.mult_read_sets.sh
copy sample_data/{test_GenomeGuidedTrinity/mm9chr17.tophat.bam => test_TissueSpecificityGraph/DE_results.tar.gz} (74%)
create mode 100644 sample_data/test_TissueSpecificityGraph/Makefile
create mode 100644 sample_data/test_TissueSpecificityGraph/transcripts.TMM.fpkm.avg_reps.matrix.gz
create mode 100644 sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/Makefile
copy sample_data/test_align_and_estimate_abundance/{ => PAIRED_END_ABUNDANCE_ESTIMATION}/cleanme.pl (56%)
create mode 100644 sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/drosoph_denovo.samples.txt
create mode 100644 sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/drosoph_ref.samples.txt
create mode 100644 sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/mouse_denovo.samples.txt
create mode 100644 sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/mouse_ref.samples.txt
create mode 100644 sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/schizo_denovo.samples.txt
create mode 100644 sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/schizo_ref.samples.txt
create mode 100644 sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh
create mode 100644 sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh
create mode 100644 sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh
create mode 100644 sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh
create mode 100644 sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh
create mode 100644 sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh
create mode 100644 sample_data/test_align_and_estimate_abundance/PAIRED_END_ABUNDANCE_ESTIMATION/samples.txt
create mode 100644 sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/Makefile
rename sample_data/test_align_and_estimate_abundance/{ => SINGLE_END_ABUNDANCE_ESTIMATION}/cleanme.pl (55%)
create mode 100644 sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/drosoph_denovo.samples.txt
create mode 100644 sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/drosoph_ref.samples.txt
create mode 100644 sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/mouse_denovo.samples.txt
create mode 100644 sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/mouse_ref.samples.txt
create mode 100644 sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/schizo_denovo.samples.txt
create mode 100644 sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/schizo_ref.samples.txt
create mode 100644 sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_denovo.sh
create mode 100644 sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Drosoph_ref.sh
create mode 100644 sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_denovo.sh
create mode 100644 sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Mouse_ref.sh
create mode 100644 sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_denovo.sh
create mode 100644 sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/misc_tests/test_Schizo_ref.sh
create mode 100644 sample_data/test_align_and_estimate_abundance/SINGLE_END_ABUNDANCE_ESTIMATION/samples.txt
create mode 100755 sample_data/test_align_and_estimate_abundance/pairs.Rscript
delete mode 100644 sample_data/test_align_and_estimate_abundance/samples.txt
mode change 120000 => 100755 util/fasta_tool
create mode 100755 util/filter_low_expr_transcripts.pl
create mode 100755 util/misc/fasta_seq_length.pl
create mode 100755 util/misc/plot_ExN50_statistic.Rscript
create mode 100755 util/misc/run_bowtie2.pl
copy util/support_scripts/{kallisto_trans_to_gene_results.pl => salmon_trans_to_gene_results.pl} (65%)
create mode 100644 util/support_scripts/tests/sample_data_tests.py
delete mode 100755 util/support_scripts/tests/test.py
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