[med-svn] [trinityrnaseq] branch upstream updated (a0eedbe -> 7558f2f)

[Michael Crusoe]

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

      from  a0eedbe   Imported Upstream version 2.0.4+dfsg
       new  7558f2f   Imported Upstream version 2.0.6+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:
 Butterfly/jar-in-jar-loader.zip                 | Bin 7269 -> 0 bytes
 Butterfly/src/src/PathExpressionComparator.java |   4 +-
 Inchworm/configure                              |   6 +-
 Inchworm/configure.ac                           |   6 +-
 Trinity                                         |  20 +--
 util/align_and_estimate_abundance.pl            |  51 +++++--
 util/misc/SRA_to_fastq.pl                       |  36 ++---
 util/misc/run_GSNAP.pl                          |  14 +-
 util/misc/run_HISAT.pl                          | 173 ++++++++++++++++++++++++
 9 files changed, 260 insertions(+), 50 deletions(-)
 delete mode 100644 Butterfly/jar-in-jar-loader.zip
 create mode 100755 util/misc/run_HISAT.pl

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