[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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