[med-svn] [trinityrnaseq] 03/04: Merge tag 'upstream/2.1.1+dfsg'

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository trinityrnaseq.

commit 93e094599da3624a1c90e6451ee404437832f642
Merge: 32e052f aa97017
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Fri Jan 29 13:33:23 2016 -0800

    Merge tag 'upstream/2.1.1+dfsg'
    
    Upstream version 2.1.1+dfsg

 .../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(-)

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