[med-svn] [trinityrnaseq] branch upstream updated (7558f2f -> 7f4bee0)

Michael Crusoe misterc-guest at moszumanska.debian.org
Tue Sep 29 19:43:51 UTC 2015


This is an automated email from the git hooks/post-receive script.

misterc-guest pushed a change to branch upstream
in repository trinityrnaseq.

      from  7558f2f   Imported Upstream version 2.0.6+dfsg
      adds  7f4bee0   Imported Upstream version 2.1.0+dfsg

No new revisions were added by this update.

Summary of changes:
 Analysis/DifferentialExpression/DE_graph_to_dot.pl |   55 +
 Analysis/DifferentialExpression/PtR                |   48 +-
 .../group_isoforms_by_tissue_enrichment.pl         |   54 +
 .../add_blastx_hit_to_trinity_id.pl                |   11 +-
 .../DifferentialExpression/analyze_diff_expr.pl    |    8 +-
 .../define_clusters_by_cutting_tree.pl             |    3 +
 Analysis/DifferentialExpression/run_DE_analysis.pl |  343 +-
 .../FL_trans_analysis_pipeline.pl                  |    8 +-
 .../util/blat_full_length_mappings.pl              |   13 +-
 Butterfly/src/src/TransAssembly_allProbPaths.java  |    7 +
 Chrysalis/GraphFromFasta_MPI.cc                    |   30 +-
 .../Contents/Resources/DWARF/MakeDepend            |  Bin 875386 -> 960753 bytes
 Chrysalis/Makefile                                 |    3 +
 Chrysalis/ReadsToTranscripts_MPI.cc                |    2 +-
 Chrysalis/ReadsToTranscripts_MPI_chang.cc          |    2 +-
 Chrysalis/analysis/BreakTransByPairs.cc            |    4 +-
 Chrysalis/analysis/Chrysalis.cc                    |   16 +-
 Chrysalis/analysis/CreateIwormFastaBundle.cc       |    8 +-
 Chrysalis/analysis/DNAVector.cc                    |   52 +-
 Chrysalis/analysis/DNAVector.h                     |   14 +-
 Chrysalis/analysis/GraphFromFasta.cc               |   40 +-
 Chrysalis/analysis/IsoformAugment.cc               |    4 +-
 Chrysalis/analysis/JoinTransByPairs.cc             |   10 +-
 Chrysalis/analysis/KmerTable.cc                    |   12 +-
 Chrysalis/analysis/NonRedKmerTable.cc              |   35 +-
 Chrysalis/analysis/NonRedKmerTable.h               |   12 +-
 Chrysalis/analysis/QuantifyGraph.cc                |    2 +-
 Chrysalis/analysis/ReadsToTranscripts.cc           |    4 +-
 Chrysalis/analysis/TranscriptomeFromVaryK.cc       |    8 +-
 Chrysalis/analysis/TranscriptomeGraph.cc           |   23 +-
 Chrysalis/base/SVector.h                           |   30 +-
 Chrysalis/util/mutil.h                             |    6 +-
 Inchworm/configure                                 |    2 +-
 Inchworm/src/Cigar.hpp                             |    2 +-
 Inchworm/src/DeBruijnGraph.cpp                     |    9 +-
 Inchworm/src/FastaToDeBruijn.cpp                   |   10 +-
 Inchworm/src/IRKE.cpp                              |   21 +-
 Inchworm/src/IRKE_run.cpp                          |    1 +
 Inchworm/src/fastaToKmerCoverageStats.cpp          |   12 +-
 Inchworm/src/sequenceUtil.cpp                      |    8 +-
 PerlLib/Fastq_reader.pm                            |    4 +
 PerlLib/HPC/PBS_handler.pm                         |   19 +-
 PerlLib/HPC/SGE_handler.pm                         |    2 +-
 PerlLib/Pipeliner.pm                               |   60 +-
 PerlLib/Process_cmd.pm                             |   15 +-
 PerlLib/SAM_entry.pm                               |   14 +
 Release.Notes                                      |   16 +
 Trinity                                            |  610 +-
 galaxy-plugin/EdgeR_differentialExpression.xml     |   21 +-
 .../EdgeR_differentialExpression_wrapper.py        |   40 +
 .../EdgeR_differentialExpression.xml               |   21 +-
 .../EdgeR_differentialExpression_wrapper.py        |   40 +
 .../RSEM_estimates_to_matrix.xml                   |    0
 Trinity => galaxy-plugin/GauravGalaxy/Trinity      | 1554 ++---
 .../{ => GauravGalaxy}/__add_to_PATH_setting.txt   |    0
 .../abundance_estimation_to_matrix.xml             |    0
 .../abundance_estimation_to_matrix_wrapper.py      |    2 +-
 .../align_and_estimate_abundance.xml               |    0
 galaxy-plugin/{ => GauravGalaxy}/alignreads.xml    |    0
 galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml    |   41 +
 galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml~   |   41 +
 .../GauravGalaxy/analyze_diff_exp_wrapper.py       |   63 +
 .../{ => GauravGalaxy}/bash_command_executer.py    |    0
 galaxy-plugin/{ => GauravGalaxy}/cat.xml           |    0
 .../{ => GauravGalaxy}/diffExpress_edgeR.xml       |    0
 .../{ => GauravGalaxy}/transcriptsToOrfs.xml       |    0
 .../{ => GauravGalaxy}/trinityToolWrapper.py       |    3 +-
 galaxy-plugin/{ => GauravGalaxy}/trinityrnaseq.xml |    4 +-
 .../trinityrnaseq.xml.Graham_version_022014        |    0
 .../{ => GauravGalaxy}/trinityrnaseq_norm.xml      |    0
 Trinity => galaxy-plugin/Trinity                   | 1554 ++---
 .../abundance_estimation_to_matrix_wrapper.py      |    2 +-
 galaxy-plugin/analyze_diff_exp.xml                 |   41 +
 galaxy-plugin/analyze_diff_exp_wrapper.py          |   63 +
 galaxy-plugin/trinityToolWrapper.py                |    3 +-
 galaxy-plugin/trinityrnaseq.xml                    |    4 +-
 notes                                              |   22 +
 sample_data/Makefile                               |    8 +-
 .../Sp_ds.10k.left.fq.gz                           |  Bin
 .../Sp_ds.10k.right.fq.gz                          |  Bin
 .../Sp_hs.10k.left.fq.gz                           |  Bin
 .../Sp_hs.10k.right.fq.gz                          |  Bin
 .../Sp_log.10k.left.fq.gz                          |  Bin
 .../Sp_log.10k.right.fq.gz                         |  Bin
 .../Sp_plat.10k.left.fq.gz                         |  Bin
 .../Sp_plat.10k.right.fq.gz                        |  Bin
 sample_data/test_DATA/Trinity.fasta                | 4443 ++++++++++++
 sample_data/test_DE_analysis/Makefile              |   30 +
 .../test_DE_analysis/Trinity_trans.TMM.EXPR.matrix | 7240 ++++++++++++++++++++
 .../Trinity_trans.TPM.not_cross_norm               | 7240 ++++++++++++++++++++
 .../test_DE_analysis/Trinity_trans.counts.matrix   | 7240 ++++++++++++++++++++
 .../example_DESeq2_analysis_pipeline/Makefile      |    0
 .../example_DESeq2_analysis_pipeline/cleanme.pl    |    0
 .../example_DESeq2_analysis_pipeline/counts.matrix |    0
 .../example_DESeq2_analysis_pipeline/run_DESeq2.sh |    0
 .../example_DESeq2_analysis_pipeline/samples.txt   |    0
 .../example_edgeR_analysis_pipeline/Makefile       |    0
 .../Trinity.fa.seqLens                             |    0
 .../__example_edgeR_output_dir/TMM_info.txt        |    0
 .../__example_edgeR_output_dir/__tmp_runTMM.R      |    0
 .../__tmp_run_edgeR.1820.R                         |    0
 .../__tmp_targets.1820.dat                         |    0
 .../__example_edgeR_output_dir/all_data_files.list |    0
 .../__example_edgeR_output_dir/cysts.dat           |    0
 .../example.matrix.normalized.FPKM                 |    0
 .../__example_edgeR_output_dir/myc.dat             |    0
 .../__example_edgeR_output_dir/myc_vs_cysts.eps    |    0
 .../myc_vs_cysts.results.txt                       |    0
 .../example_edgeR_analysis_pipeline/cleanMe.sh     |    0
 .../example_edgeR_analysis_pipeline/example.matrix |    0
 .../example_edgeR_analysis_pipeline/runMe.sh       |    0
 .../deprecated}/testEdgeRfuncs/Makefile            |    0
 .../deprecated}/testEdgeRfuncs/cleanMe.sh          |    0
 .../deprecated}/testEdgeRfuncs/dataA.dat           |    0
 .../deprecated}/testEdgeRfuncs/dataB.dat           |    0
 .../deprecated}/testEdgeRfuncs/runMe.sh            |    0
 .../testEdgeRfuncs/run_edgeR_on_sample_data.R      |    0
 .../deprecated}/testEdgeRfuncs/targets.dat         |    0
 sample_data/test_DE_analysis/notes                 |    1 +
 sample_data/test_DE_analysis/samples.txt           |   14 +
 ...nome-guided_Trinity_use_existing_bam.use_LSF.sh |    0
 ...nome-guided_Trinity_use_existing_bam.use_PBS.sh |    0
 ...nome-guided_Trinity_use_existing_bam.use_SGE.sh |    0
 .../{ => old}/run_Schizo_TrinityGG.SE.sh           |    0
 .../{ => old}/run_Schizo_TrinityGG.sh              |    0
 .../{ => old}/run_genome-guided_Trinity.sh         |    0
 .../{ => old}/run_mouse_TrinityGG.sh               |    0
 sample_data/test_Trinity_Assembly/Makefile         |   23 +-
 sample_data/test_Trinity_Assembly/README           |    4 +-
 sample_data/test_Trinity_Assembly/cleanme.pl       |    6 +
 .../misc_run_tests/__runMe_include_long_reads.sh   |    2 +-
 ..._qual_trimming_and_normalize_libs_separately.sh |   15 +-
 sample_data/test_Trinity_Assembly/runMe.sh         |   16 +-
 .../test_Trinity_Coding_Extraction/Makefile        |    6 -
 .../Trinity.fasta.gz                               |  Bin 39206 -> 0 bytes
 .../test_Trinity_Coding_Extraction/cleanme.pl      |   39 -
 .../test_Trinity_Coding_Extraction/runMe.sh        |   17 -
 .../test_align_and_estimate_abundance/Makefile     |   15 +-
 .../Trinity.fasta.gene_trans_map                   |  124 -
 .../Trinity.fasta.gz                               |  Bin 54372 -> 0 bytes
 .../align_and_estimate_tester.pl                   |   93 +
 .../test_align_and_estimate_abundance/cleanme.pl   |   27 +-
 .../plot_paired_comparisons.Rscript                |   14 +
 .../reads.left.fq.gz                               |    1 -
 .../reads.right.fq.gz                              |    1 -
 .../run_eXpress.sh                                 |    1 -
 .../test_align_and_estimate_abundance/run_rsem.sh  |   14 -
 .../test_align_and_estimate_abundance/samples.txt  |    4 +
 sample_data/test_edgeR_diff_expr/Makefile          |   17 -
 sample_data/test_full_edgeR_pipeline/cleanme.pl    |    1 -
 .../samples_n_reads_decribed.txt                   |    8 +-
 trinity-plugins/BIN/README                         |    2 +
 trinity-plugins/Makefile                           |   47 +-
 .../fstrozzi-Fastool-7c3e034f05/fastool.c          |    7 +-
 trinity-plugins/scaffold_iworm_contigs/Makefile    |   10 +
 .../ScaffoldIwormContigs.cpp                       |  216 +
 .../scaffold_iworm_contigs/error_checker.cpp       |   40 +
 .../scaffold_iworm_contigs/error_checker.h         |   24 +
 trinity-plugins/slclust/Makefile.bak               |   10 -
 util/abundance_estimates_to_matrix.pl              |  117 +-
 util/align_and_estimate_abundance.pl               |  262 +-
 util/filter_fasta_by_rsem_values.pl                |    6 +-
 util/insilico_read_normalization.pl                |    6 +
 util/misc/blast_outfmt6_group_segments.pl          |  165 +
 ..._outfmt6_group_segments.to_Markov_Clustering.pl |  167 +
 ...blast_outfmt6_group_segments.tophit_coverage.pl |  110 +
 ...ig_E_statistic.pl => contig_ExN50_statistic.pl} |   72 +-
 .../count_features_given_MIN_FPKM_threshold.pl     |    2 +-
 ...unt_matrix_features_given_MIN_FPKM_threshold.pl |   52 -
 ...ount_matrix_features_given_MIN_TPM_threshold.pl |   52 +
 .../get_longest_isoform_seq_per_trinity_gene.pl    |   62 +
 util/misc/gmap_gff3_to_percent_length_stats.pl     |    1 +
 .../merge_RSEM_output_to_matrix.pl                 |    0
 util/misc/pair_up_fastq_files_1_2.pl               |   30 +
 util/misc/pair_up_fastq_files_LeftRight.pl         |   32 +
 util/misc/pair_up_fastq_files_R1_R2.pl             |   30 +
 util/misc/run_GSNAP.pl                             |    2 +-
 util/misc/run_HISAT.pl                             |   29 +-
 util/misc/run_STAR.pl                              |  186 +
 util/misc/run_trimmomatic_qual_trimming.pl         |   24 +-
 util/misc/simulate_illuminaPE_from_transcripts.pl  |  239 +-
 util/misc/sixFrameTranslation.pl                   |   38 +
 ...ine.pl => run_DE_analysis_from_samples_file.pl} |  195 +-
 ...R_pipeline.pl => run_RSEM_from_samples_file.pl} |  151 +-
 util/run_Trinity_edgeR_pipeline.pl                 |    6 +-
 ...ipeline.pl => run_Trinity_from_samples_file.pl} |  139 +-
 ...tor.pl => GG_partitioned_trinity_aggregator.pl} |    2 +-
 .../eXpress_trans_to_gene_results.pl               |   18 +-
 util/support_scripts/fastQ_to_tab.pl               |   15 +-
 ...esults.pl => kallisto_trans_to_gene_results.pl} |   36 +-
 .../merge_left_right_nameSorted_SAMs.pl            |    6 +-
 .../partitioned_trinity_aggregator.pl              |   12 +-
 util/support_scripts/plugin_install_tests.sh       |    7 -
 util/support_scripts/run_TMM_scale_matrix.pl       |    1 +
 util/support_scripts/{tests.py => tests/test.py}   |   42 +-
 util/support_scripts/tests/test_prep.py            |  122 +
 util/support_scripts/{ => tests}/tests.py          |   38 +-
 util/support_scripts/trinity_install_tests.sh      |    6 +
 ...y_cmds.pl => write_partitioned_trinity_cmds.pl} |    0
 199 files changed, 31088 insertions(+), 3603 deletions(-)
 create mode 100755 Analysis/DifferentialExpression/DE_graph_to_dot.pl
 create mode 100755 Analysis/DifferentialExpression/TissueEnrichment/group_isoforms_by_tissue_enrichment.pl
 create mode 100644 galaxy-plugin/EdgeR_differentialExpression_wrapper.py
 copy galaxy-plugin/{ => GauravGalaxy}/EdgeR_differentialExpression.xml (56%)
 create mode 100644 galaxy-plugin/GauravGalaxy/EdgeR_differentialExpression_wrapper.py
 copy galaxy-plugin/{ => GauravGalaxy}/RSEM_estimates_to_matrix.xml (100%)
 copy Trinity => galaxy-plugin/GauravGalaxy/Trinity (69%)
 copy galaxy-plugin/{ => GauravGalaxy}/__add_to_PATH_setting.txt (100%)
 copy galaxy-plugin/{ => GauravGalaxy}/abundance_estimation_to_matrix.xml (100%)
 copy galaxy-plugin/{ => GauravGalaxy}/abundance_estimation_to_matrix_wrapper.py (95%)
 copy galaxy-plugin/{ => GauravGalaxy}/align_and_estimate_abundance.xml (100%)
 copy galaxy-plugin/{ => GauravGalaxy}/alignreads.xml (100%)
 create mode 100644 galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml
 create mode 100644 galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml~
 create mode 100644 galaxy-plugin/GauravGalaxy/analyze_diff_exp_wrapper.py
 copy galaxy-plugin/{ => GauravGalaxy}/bash_command_executer.py (100%)
 copy galaxy-plugin/{ => GauravGalaxy}/cat.xml (100%)
 copy galaxy-plugin/{ => GauravGalaxy}/diffExpress_edgeR.xml (100%)
 copy galaxy-plugin/{ => GauravGalaxy}/transcriptsToOrfs.xml (100%)
 copy galaxy-plugin/{ => GauravGalaxy}/trinityToolWrapper.py (92%)
 copy galaxy-plugin/{ => GauravGalaxy}/trinityrnaseq.xml (98%)
 copy galaxy-plugin/{ => GauravGalaxy}/trinityrnaseq.xml.Graham_version_022014 (100%)
 copy galaxy-plugin/{ => GauravGalaxy}/trinityrnaseq_norm.xml (100%)
 copy Trinity => galaxy-plugin/Trinity (69%)
 create mode 100644 galaxy-plugin/analyze_diff_exp.xml
 create mode 100644 galaxy-plugin/analyze_diff_exp_wrapper.py
 rename sample_data/{test_full_edgeR_pipeline/rnaseq_reads => test_DATA}/Sp_ds.10k.left.fq.gz (100%)
 rename sample_data/{test_full_edgeR_pipeline/rnaseq_reads => test_DATA}/Sp_ds.10k.right.fq.gz (100%)
 rename sample_data/{test_full_edgeR_pipeline/rnaseq_reads => test_DATA}/Sp_hs.10k.left.fq.gz (100%)
 rename sample_data/{test_full_edgeR_pipeline/rnaseq_reads => test_DATA}/Sp_hs.10k.right.fq.gz (100%)
 rename sample_data/{test_full_edgeR_pipeline/rnaseq_reads => test_DATA}/Sp_log.10k.left.fq.gz (100%)
 rename sample_data/{test_full_edgeR_pipeline/rnaseq_reads => test_DATA}/Sp_log.10k.right.fq.gz (100%)
 rename sample_data/{test_full_edgeR_pipeline/rnaseq_reads => test_DATA}/Sp_plat.10k.left.fq.gz (100%)
 rename sample_data/{test_full_edgeR_pipeline/rnaseq_reads => test_DATA}/Sp_plat.10k.right.fq.gz (100%)
 create mode 100644 sample_data/test_DATA/Trinity.fasta
 create mode 100644 sample_data/test_DE_analysis/Makefile
 create mode 100644 sample_data/test_DE_analysis/Trinity_trans.TMM.EXPR.matrix
 create mode 100644 sample_data/test_DE_analysis/Trinity_trans.TPM.not_cross_norm
 create mode 100644 sample_data/test_DE_analysis/Trinity_trans.counts.matrix
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_DESeq2_analysis_pipeline/Makefile (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_DESeq2_analysis_pipeline/cleanme.pl (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_DESeq2_analysis_pipeline/counts.matrix (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_DESeq2_analysis_pipeline/run_DESeq2.sh (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_DESeq2_analysis_pipeline/samples.txt (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_edgeR_analysis_pipeline/Makefile (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_edgeR_analysis_pipeline/Trinity.fa.seqLens (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/TMM_info.txt (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_runTMM.R (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_run_edgeR.1820.R (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_targets.1820.dat (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/all_data_files.list (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/cysts.dat (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/example.matrix.normalized.FPKM (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc.dat (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc_vs_cysts.eps (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc_vs_cysts.results.txt (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_edgeR_analysis_pipeline/cleanMe.sh (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_edgeR_analysis_pipeline/example.matrix (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/example_edgeR_analysis_pipeline/runMe.sh (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/testEdgeRfuncs/Makefile (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/testEdgeRfuncs/cleanMe.sh (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/testEdgeRfuncs/dataA.dat (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/testEdgeRfuncs/dataB.dat (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/testEdgeRfuncs/runMe.sh (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/testEdgeRfuncs/run_edgeR_on_sample_data.R (100%)
 rename sample_data/{test_edgeR_diff_expr => test_DE_analysis/deprecated}/testEdgeRfuncs/targets.dat (100%)
 create mode 100644 sample_data/test_DE_analysis/notes
 create mode 100644 sample_data/test_DE_analysis/samples.txt
 rename sample_data/test_GenomeGuidedTrinity/{ => old}/__run_genome-guided_Trinity_use_existing_bam.use_LSF.sh (100%)
 rename sample_data/test_GenomeGuidedTrinity/{ => old}/__run_genome-guided_Trinity_use_existing_bam.use_PBS.sh (100%)
 rename sample_data/test_GenomeGuidedTrinity/{ => old}/__run_genome-guided_Trinity_use_existing_bam.use_SGE.sh (100%)
 rename sample_data/test_GenomeGuidedTrinity/{ => old}/run_Schizo_TrinityGG.SE.sh (100%)
 rename sample_data/test_GenomeGuidedTrinity/{ => old}/run_Schizo_TrinityGG.sh (100%)
 rename sample_data/test_GenomeGuidedTrinity/{ => old}/run_genome-guided_Trinity.sh (100%)
 rename sample_data/test_GenomeGuidedTrinity/{ => old}/run_mouse_TrinityGG.sh (100%)
 delete mode 100644 sample_data/test_Trinity_Coding_Extraction/Makefile
 delete mode 100644 sample_data/test_Trinity_Coding_Extraction/Trinity.fasta.gz
 delete mode 100755 sample_data/test_Trinity_Coding_Extraction/cleanme.pl
 delete mode 100755 sample_data/test_Trinity_Coding_Extraction/runMe.sh
 delete mode 100644 sample_data/test_align_and_estimate_abundance/Trinity.fasta.gene_trans_map
 delete mode 100644 sample_data/test_align_and_estimate_abundance/Trinity.fasta.gz
 create mode 100755 sample_data/test_align_and_estimate_abundance/align_and_estimate_tester.pl
 create mode 100755 sample_data/test_align_and_estimate_abundance/plot_paired_comparisons.Rscript
 delete mode 120000 sample_data/test_align_and_estimate_abundance/reads.left.fq.gz
 delete mode 120000 sample_data/test_align_and_estimate_abundance/reads.right.fq.gz
 delete mode 100755 sample_data/test_align_and_estimate_abundance/run_eXpress.sh
 delete mode 100755 sample_data/test_align_and_estimate_abundance/run_rsem.sh
 create mode 100644 sample_data/test_align_and_estimate_abundance/samples.txt
 delete mode 100644 sample_data/test_edgeR_diff_expr/Makefile
 create mode 100644 trinity-plugins/BIN/README
 create mode 100644 trinity-plugins/scaffold_iworm_contigs/Makefile
 create mode 100755 trinity-plugins/scaffold_iworm_contigs/ScaffoldIwormContigs.cpp
 create mode 100755 trinity-plugins/scaffold_iworm_contigs/error_checker.cpp
 create mode 100755 trinity-plugins/scaffold_iworm_contigs/error_checker.h
 delete mode 100644 trinity-plugins/slclust/Makefile.bak
 create mode 100755 util/misc/blast_outfmt6_group_segments.pl
 create mode 100755 util/misc/blast_outfmt6_group_segments.to_Markov_Clustering.pl
 create mode 100755 util/misc/blast_outfmt6_group_segments.tophit_coverage.pl
 rename util/misc/{contig_E_statistic.pl => contig_ExN50_statistic.pl} (54%)
 delete mode 100755 util/misc/count_matrix_features_given_MIN_FPKM_threshold.pl
 create mode 100755 util/misc/count_matrix_features_given_MIN_TPM_threshold.pl
 create mode 100755 util/misc/get_longest_isoform_seq_per_trinity_gene.pl
 copy util/{deprecated/RSEM_util => misc}/merge_RSEM_output_to_matrix.pl (100%)
 create mode 100755 util/misc/pair_up_fastq_files_1_2.pl
 create mode 100755 util/misc/pair_up_fastq_files_LeftRight.pl
 create mode 100755 util/misc/pair_up_fastq_files_R1_R2.pl
 create mode 100755 util/misc/run_STAR.pl
 create mode 100755 util/misc/sixFrameTranslation.pl
 copy util/{run_Trinity_edgeR_pipeline.pl => run_DE_analysis_from_samples_file.pl} (51%)
 copy util/{run_Trinity_edgeR_pipeline.pl => run_RSEM_from_samples_file.pl} (64%)
 copy util/{run_Trinity_edgeR_pipeline.pl => run_Trinity_from_samples_file.pl} (63%)
 copy util/support_scripts/{partitioned_trinity_aggregator.pl => GG_partitioned_trinity_aggregator.pl} (93%)
 copy util/support_scripts/{eXpress_trans_to_gene_results.pl => kallisto_trans_to_gene_results.pl} (78%)
 copy util/support_scripts/{tests.py => tests/test.py} (80%)
 mode change 100644 => 100755
 create mode 100644 util/support_scripts/tests/test_prep.py
 rename util/support_scripts/{ => tests}/tests.py (81%)
 rename util/support_scripts/{GG_write_trinity_cmds.pl => write_partitioned_trinity_cmds.pl} (100%)

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