[med-svn] [trinityrnaseq] branch upstream updated (aa97017 -> fdeb4cb)

[Michael Crusoe]

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

      from  aa97017   Imported Upstream version 2.1.1+dfsg
       new  fdeb4cb   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:
 galaxy-plugin/EdgeR_differentialExpression.xml     |   38 -
 .../EdgeR_differentialExpression_wrapper.py        |   40 -
 .../GauravGalaxy/EdgeR_differentialExpression.xml  |   38 -
 .../EdgeR_differentialExpression_wrapper.py        |   40 -
 .../GauravGalaxy/RSEM_estimates_to_matrix.xml      |   51 -
 galaxy-plugin/GauravGalaxy/Trinity                 | 2707 --------------------
 .../GauravGalaxy/__add_to_PATH_setting.txt         |    1 -
 .../abundance_estimation_to_matrix.xml             |   42 -
 .../abundance_estimation_to_matrix_wrapper.py      |   40 -
 .../GauravGalaxy/align_and_estimate_abundance.xml  |   90 -
 galaxy-plugin/GauravGalaxy/alignreads.xml          |  138 -
 galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml    |   41 -
 .../GauravGalaxy/analyze_diff_exp_wrapper.py       |   63 -
 .../GauravGalaxy/bash_command_executer.py          |   44 -
 galaxy-plugin/GauravGalaxy/cat.xml                 |   41 -
 galaxy-plugin/GauravGalaxy/diffExpress_edgeR.xml   |   47 -
 galaxy-plugin/GauravGalaxy/transcriptsToOrfs.xml   |   53 -
 galaxy-plugin/GauravGalaxy/trinityToolWrapper.py   |   82 -
 galaxy-plugin/GauravGalaxy/trinityrnaseq.xml       |  127 -
 .../trinityrnaseq.xml.Graham_version_022014        |  127 -
 galaxy-plugin/GauravGalaxy/trinityrnaseq_norm.xml  |  102 -
 galaxy-plugin/RSEM_abundance_estimation.xml        |   72 -
 galaxy-plugin/RSEM_estimates_to_matrix.xml         |   51 -
 galaxy-plugin/Trinity                              | 2707 --------------------
 galaxy-plugin/__add_to_PATH_setting.txt            |    1 -
 galaxy-plugin/abundance_estimation_to_matrix.xml   |   42 -
 .../abundance_estimation_to_matrix_wrapper.py      |   40 -
 galaxy-plugin/align_and_estimate_abundance.xml     |   90 -
 galaxy-plugin/alignreads.xml                       |  138 -
 galaxy-plugin/analyze_diff_exp.xml                 |   41 -
 galaxy-plugin/analyze_diff_exp_wrapper.py          |   63 -
 galaxy-plugin/bash_command_executer.py             |   44 -
 galaxy-plugin/cat.xml                              |   41 -
 galaxy-plugin/diffExpress_edgeR.xml                |   47 -
 galaxy-plugin/transcriptsToOrfs.xml                |   53 -
 galaxy-plugin/trinityToolWrapper.py                |   82 -
 galaxy-plugin/trinityrnaseq.xml                    |  127 -
 .../trinityrnaseq.xml.Graham_version_022014        |  127 -
 galaxy-plugin/trinityrnaseq_norm.xml               |  102 -
 39 files changed, 7820 deletions(-)
 delete mode 100644 galaxy-plugin/EdgeR_differentialExpression.xml
 delete mode 100644 galaxy-plugin/EdgeR_differentialExpression_wrapper.py
 delete mode 100644 galaxy-plugin/GauravGalaxy/EdgeR_differentialExpression.xml
 delete mode 100644 galaxy-plugin/GauravGalaxy/EdgeR_differentialExpression_wrapper.py
 delete mode 100644 galaxy-plugin/GauravGalaxy/RSEM_estimates_to_matrix.xml
 delete mode 100755 galaxy-plugin/GauravGalaxy/Trinity
 delete mode 100644 galaxy-plugin/GauravGalaxy/__add_to_PATH_setting.txt
 delete mode 100644 galaxy-plugin/GauravGalaxy/abundance_estimation_to_matrix.xml
 delete mode 100644 galaxy-plugin/GauravGalaxy/abundance_estimation_to_matrix_wrapper.py
 delete mode 100644 galaxy-plugin/GauravGalaxy/align_and_estimate_abundance.xml
 delete mode 100644 galaxy-plugin/GauravGalaxy/alignreads.xml
 delete mode 100644 galaxy-plugin/GauravGalaxy/analyze_diff_exp.xml
 delete mode 100644 galaxy-plugin/GauravGalaxy/analyze_diff_exp_wrapper.py
 delete mode 100755 galaxy-plugin/GauravGalaxy/bash_command_executer.py
 delete mode 100644 galaxy-plugin/GauravGalaxy/cat.xml
 delete mode 100644 galaxy-plugin/GauravGalaxy/diffExpress_edgeR.xml
 delete mode 100644 galaxy-plugin/GauravGalaxy/transcriptsToOrfs.xml
 delete mode 100755 galaxy-plugin/GauravGalaxy/trinityToolWrapper.py
 delete mode 100644 galaxy-plugin/GauravGalaxy/trinityrnaseq.xml
 delete mode 100644 galaxy-plugin/GauravGalaxy/trinityrnaseq.xml.Graham_version_022014
 delete mode 100644 galaxy-plugin/GauravGalaxy/trinityrnaseq_norm.xml
 delete mode 100644 galaxy-plugin/RSEM_abundance_estimation.xml
 delete mode 100644 galaxy-plugin/RSEM_estimates_to_matrix.xml
 delete mode 100755 galaxy-plugin/Trinity
 delete mode 100644 galaxy-plugin/__add_to_PATH_setting.txt
 delete mode 100644 galaxy-plugin/abundance_estimation_to_matrix.xml
 delete mode 100644 galaxy-plugin/abundance_estimation_to_matrix_wrapper.py
 delete mode 100644 galaxy-plugin/align_and_estimate_abundance.xml
 delete mode 100644 galaxy-plugin/alignreads.xml
 delete mode 100644 galaxy-plugin/analyze_diff_exp.xml
 delete mode 100644 galaxy-plugin/analyze_diff_exp_wrapper.py
 delete mode 100755 galaxy-plugin/bash_command_executer.py
 delete mode 100644 galaxy-plugin/cat.xml
 delete mode 100644 galaxy-plugin/diffExpress_edgeR.xml
 delete mode 100644 galaxy-plugin/transcriptsToOrfs.xml
 delete mode 100755 galaxy-plugin/trinityToolWrapper.py
 delete mode 100644 galaxy-plugin/trinityrnaseq.xml
 delete mode 100644 galaxy-plugin/trinityrnaseq.xml.Graham_version_022014
 delete mode 100644 galaxy-plugin/trinityrnaseq_norm.xml

-- 
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