[med-svn] [trinityrnaseq] branch upstream updated (b186ab4 -> aa97017)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Fri Jan 29 21:54:55 UTC 2016
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misterc-guest pushed a change to branch upstream
in repository trinityrnaseq.
from b186ab4 Imported Upstream version 2.1.1+dfsg
new aa97017 Imported Upstream version 2.1.1+dfsg
The 1 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:
.../deprecated/run_DESeq_all_vs_all.pl | 87 -
.../deprecated/run_DESeq_w_replicates.pl | 192 -
.../DifferentialExpression/deprecated/run_EdgeR.pl | 380 -
.../deprecated/run_EdgeR_wReplicates.pl | 157 -
.../deprecated/run_EdgeR_wReplicates_all_vs_all.pl | 87 -
.../summarize_stat_significant_results.pl | 74 -
Analysis/GenomeViewPlugin/test.html | 63 -
Analysis/GenomeViewPlugin/test_session.html | 63 -
.../GenomeViewPlugin/trinity_to_genomeview_html.pl | 124 -
Chrysalis/MakeDepend.dSYM/Contents/Info.plist | 20 -
.../Contents/Resources/DWARF/MakeDepend | Bin 960753 -> 0 bytes
galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml~ | 41 -
hpc_conf/deprecated/BroadInst_LSF.Trinity.conf | 7 -
hpc_conf/deprecated/BroadInst_LSF.blast.conf | 7 -
hpc_conf/deprecated/BroadInst_LSF.conf | 7 -
hpc_conf/deprecated/BroadInst_LSF.regev.10.conf | 7 -
hpc_conf/deprecated/BroadInst_LSF.regev.100.conf | 7 -
hpc_conf/deprecated/BroadInst_LSF.regev.1000.conf | 7 -
hpc_conf/deprecated/BroadInst_LSF.test.conf | 7 -
hpc_conf/deprecated/BroadInst_SGE.conf | 5 -
hpc_conf/deprecated/BroadInst_SGE.test.conf | 5 -
hpc_conf/deprecated/SLURM.FAS.conf | 7 -
.../example_DESeq2_analysis_pipeline/Makefile | 7 -
.../example_DESeq2_analysis_pipeline/cleanme.pl | 42 -
.../example_DESeq2_analysis_pipeline/counts.matrix | 80816 -------------------
.../example_DESeq2_analysis_pipeline/run_DESeq2.sh | 1 -
.../example_DESeq2_analysis_pipeline/samples.txt | 9 -
.../example_edgeR_analysis_pipeline/Makefile | 6 -
.../Trinity.fa.seqLens | 47999 -----------
.../__example_edgeR_output_dir/TMM_info.txt | 3 -
.../__example_edgeR_output_dir/__tmp_runTMM.R | 4 -
.../__tmp_run_edgeR.1820.R | 6 -
.../__tmp_targets.1820.dat | 3 -
.../__example_edgeR_output_dir/all_data_files.list | 3 -
.../__example_edgeR_output_dir/cysts.dat | 47999 -----------
.../example.matrix.normalized.FPKM | 48000 -----------
.../__example_edgeR_output_dir/myc.dat | 47999 -----------
.../__example_edgeR_output_dir/myc_vs_cysts.eps | 62775 --------------
.../myc_vs_cysts.results.txt | 12324 ---
.../example_edgeR_analysis_pipeline/cleanMe.sh | 2 -
.../example_edgeR_analysis_pipeline/example.matrix | 48000 -----------
.../example_edgeR_analysis_pipeline/runMe.sh | 1 -
.../deprecated/testEdgeRfuncs/Makefile | 6 -
.../deprecated/testEdgeRfuncs/cleanMe.sh | 1 -
.../deprecated/testEdgeRfuncs/dataA.dat | 47999 -----------
.../deprecated/testEdgeRfuncs/dataB.dat | 47999 -----------
.../deprecated/testEdgeRfuncs/runMe.sh | 1 -
.../testEdgeRfuncs/run_edgeR_on_sample_data.R | 7 -
.../deprecated/testEdgeRfuncs/targets.dat | 3 -
util/R/noiseq.r | 3312 -
util/deprecated/PairPathsToGraphDot.pl | 104 -
util/deprecated/RSEM_util/Nx_rsem_to_table.pl | 72 -
.../merge_RSEM_counts_and_labels_single_table.pl | 89 -
.../merge_RSEM_frag_counts_single_table.pl | 96 -
.../RSEM_util/merge_RSEM_output_to_matrix.pl | 142 -
.../RSEM_util/run_RSEM_align_n_estimate.pl | 318 -
util/deprecated/alignReads.pl | 1064 -
.../annot_genome_SAM_to_transcript_FPKM_simple.pl | 818 -
.../annot_genome_SAM_to_transcriptome_SAM.pl | 634 -
util/deprecated/blastn_illumina_to_SAM.pl | 199 -
util/deprecated/cigar_tweaker.pl | 92 -
util/deprecated/cmd_process_forker.pl | 222 -
util/deprecated/csfastX_to_defastA.pl | 191 -
util/deprecated/distribute_sam_aligned_reads.pl | 135 -
util/deprecated/eXpress_util/filter_contigs.py | 127 -
.../merge_eXpress_frag_counts_single_table.pl | 101 -
.../eXpress_util/run_eXpress_align_n_estimate.pl | 312 -
util/deprecated/eXpress_util/usage.txt | 48 -
util/deprecated/eXpress_util/use_express.py | 167 -
util/deprecated/fasta_to_deBruijn_graph.pl | 193 -
util/deprecated/purge_dir.pl | 36 -
util/deprecated/run_AllpathsLG_error_correction.pl | 170 -
util/deprecated/sort_fasta.sh | 16 -
util/deprecated/write_inchworm_cmds.pl | 36 -
74 files changed, 502063 deletions(-)
delete mode 100755 Analysis/DifferentialExpression/deprecated/run_DESeq_all_vs_all.pl
delete mode 100755 Analysis/DifferentialExpression/deprecated/run_DESeq_w_replicates.pl
delete mode 100755 Analysis/DifferentialExpression/deprecated/run_EdgeR.pl
delete mode 100755 Analysis/DifferentialExpression/deprecated/run_EdgeR_wReplicates.pl
delete mode 100755 Analysis/DifferentialExpression/deprecated/run_EdgeR_wReplicates_all_vs_all.pl
delete mode 100755 Analysis/DifferentialExpression/deprecated/summarize_stat_significant_results.pl
delete mode 100644 Analysis/GenomeViewPlugin/test.html
delete mode 100644 Analysis/GenomeViewPlugin/test_session.html
delete mode 100755 Analysis/GenomeViewPlugin/trinity_to_genomeview_html.pl
delete mode 100644 Chrysalis/MakeDepend.dSYM/Contents/Info.plist
delete mode 100644 Chrysalis/MakeDepend.dSYM/Contents/Resources/DWARF/MakeDepend
delete mode 100644 galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml~
delete mode 100644 hpc_conf/deprecated/BroadInst_LSF.Trinity.conf
delete mode 100644 hpc_conf/deprecated/BroadInst_LSF.blast.conf
delete mode 100644 hpc_conf/deprecated/BroadInst_LSF.conf
delete mode 100644 hpc_conf/deprecated/BroadInst_LSF.regev.10.conf
delete mode 100644 hpc_conf/deprecated/BroadInst_LSF.regev.100.conf
delete mode 100644 hpc_conf/deprecated/BroadInst_LSF.regev.1000.conf
delete mode 100644 hpc_conf/deprecated/BroadInst_LSF.test.conf
delete mode 100644 hpc_conf/deprecated/BroadInst_SGE.conf
delete mode 100644 hpc_conf/deprecated/BroadInst_SGE.test.conf
delete mode 100644 hpc_conf/deprecated/SLURM.FAS.conf
delete mode 100644 sample_data/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/Makefile
delete mode 100755 sample_data/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/cleanme.pl
delete mode 100644 sample_data/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/counts.matrix
delete mode 100755 sample_data/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/run_DESeq2.sh
delete mode 100644 sample_data/test_DE_analysis/deprecated/example_DESeq2_analysis_pipeline/samples.txt
delete mode 100644 sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/Makefile
delete mode 100644 sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/Trinity.fa.seqLens
delete mode 100644 sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/TMM_info.txt
delete mode 100644 sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_runTMM.R
delete mode 100644 sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_run_edgeR.1820.R
delete mode 100644 sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/__tmp_targets.1820.dat
delete mode 100644 sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/all_data_files.list
delete mode 100644 sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/cysts.dat
delete mode 100644 sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/example.matrix.normalized.FPKM
delete mode 100644 sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc.dat
delete mode 100644 sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc_vs_cysts.eps
delete mode 100644 sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/__example_edgeR_output_dir/myc_vs_cysts.results.txt
delete mode 100755 sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/cleanMe.sh
delete mode 100644 sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/example.matrix
delete mode 100755 sample_data/test_DE_analysis/deprecated/example_edgeR_analysis_pipeline/runMe.sh
delete mode 100644 sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/Makefile
delete mode 100755 sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/cleanMe.sh
delete mode 100644 sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/dataA.dat
delete mode 100644 sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/dataB.dat
delete mode 100755 sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/runMe.sh
delete mode 100644 sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/run_edgeR_on_sample_data.R
delete mode 100644 sample_data/test_DE_analysis/deprecated/testEdgeRfuncs/targets.dat
delete mode 100644 util/R/noiseq.r
delete mode 100755 util/deprecated/PairPathsToGraphDot.pl
delete mode 100755 util/deprecated/RSEM_util/Nx_rsem_to_table.pl
delete mode 100755 util/deprecated/RSEM_util/merge_RSEM_counts_and_labels_single_table.pl
delete mode 100755 util/deprecated/RSEM_util/merge_RSEM_frag_counts_single_table.pl
delete mode 100755 util/deprecated/RSEM_util/merge_RSEM_output_to_matrix.pl
delete mode 100755 util/deprecated/RSEM_util/run_RSEM_align_n_estimate.pl
delete mode 100755 util/deprecated/alignReads.pl
delete mode 100755 util/deprecated/annot_genome_SAM_to_transcript_FPKM_simple.pl
delete mode 100755 util/deprecated/annot_genome_SAM_to_transcriptome_SAM.pl
delete mode 100755 util/deprecated/blastn_illumina_to_SAM.pl
delete mode 100755 util/deprecated/cigar_tweaker.pl
delete mode 100755 util/deprecated/cmd_process_forker.pl
delete mode 100755 util/deprecated/csfastX_to_defastA.pl
delete mode 100755 util/deprecated/distribute_sam_aligned_reads.pl
delete mode 100755 util/deprecated/eXpress_util/filter_contigs.py
delete mode 100755 util/deprecated/eXpress_util/merge_eXpress_frag_counts_single_table.pl
delete mode 100755 util/deprecated/eXpress_util/run_eXpress_align_n_estimate.pl
delete mode 100644 util/deprecated/eXpress_util/usage.txt
delete mode 100755 util/deprecated/eXpress_util/use_express.py
delete mode 100755 util/deprecated/fasta_to_deBruijn_graph.pl
delete mode 100755 util/deprecated/purge_dir.pl
delete mode 100755 util/deprecated/run_AllpathsLG_error_correction.pl
delete mode 100755 util/deprecated/sort_fasta.sh
delete mode 100755 util/deprecated/write_inchworm_cmds.pl
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