[med-svn] [trinityrnaseq] branch master updated (c4f099d -> ac69c09)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Thu Oct 22 16:41:20 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch master
in repository trinityrnaseq.
from c4f099d Remove remaining lintian overrides
adds 7f4bee0 Imported Upstream version 2.1.0+dfsg
new 8cee320 Imported Upstream version 2.1.1+dfsg
new ce7ed9b Merge tag 'upstream/2.1.1+dfsg'
new ac69c09 bump version, refresh patches
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:
.gitmodules | 3 +
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 | 642 +-
debian/changelog | 4 +-
debian/control | 3 +-
debian/copyright | 14 +-
debian/patches/0001-fix_gcc5.patch.patch | 12 +-
debian/patches/0002-fix_istream_failure_call.patch | 11 +-
debian/patches/chrysalis-make-tweak | 2 +-
debian/patches/fix_system_paths | 168 +-
debian/patches/hardening | 4 +-
debian/patches/hashbang | 57 +-
debian/patches/jellyfish-path | 4 +-
debian/patches/noExitTester | 12 +-
debian/patches/update-paths | 13 +-
debian/rules | 1 +
debian/trinityrnaseq-examples.lintian-overrides | 2 +
debian/trinityrnaseq.lintian-overrides | 2 +
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/htslib-1.2.1.tar.bz2 | Bin 0 -> 911326 bytes
trinity-plugins/htslib.github.Aug182015.tar.gz | Bin 0 -> 7316027 bytes
trinity-plugins/samtools-0.1.19.tar.bz2 | Bin 0 -> 514507 bytes
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 +
util/misc/fastQ_rand_subset.pl | 158 +-
...subset.reservoir_sampling_reqiures_high_mem.pl} | 0
.../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 | 201 +
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
220 files changed, 31366 insertions(+), 3842 deletions(-)
create mode 100644 .gitmodules
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 debian/trinityrnaseq-examples.lintian-overrides
create mode 100644 debian/trinityrnaseq.lintian-overrides
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/htslib-1.2.1.tar.bz2
create mode 100644 trinity-plugins/htslib.github.Aug182015.tar.gz
create mode 100644 trinity-plugins/samtools-0.1.19.tar.bz2
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
copy util/misc/{fastQ_rand_subset.pl => fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl} (100%)
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} (92%)
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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