[med-svn] [trinityrnaseq] branch master updated (910e489 -> 13145f1)

[Michael Crusoe]

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

      from  910e489   Upload to unstable
       new  7118b19   improve hardening & drop galaxy plugin
       new  fdeb4cb   Imported Upstream version 2.1.1+dfsg
       new  13145f1   Merge tag 'upstream/2.1.1+dfsg'

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:
 debian/changelog                                   |    7 +
 debian/copyright                                   |    2 +-
 debian/patches/hardening                           |   13 +-
 debian/rules                                       |    7 +-
 debian/trinityrnaseq.docs                          |    1 -
 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 -
 44 files changed, 25 insertions(+), 7825 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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