[med-svn] [SCM] tophat annotated tag, precise-ppa/2.0.4-1_precise1, created. precise-ppa/2.0.4-1_precise1

[Carlos Borroto]

The annotated tag, precise-ppa/2.0.4-1_precise1 has been created
        at  25710bb0e0cd944fbea19bf6ed4963411e93c100 (tag)
   tagging  41a61988905b95ae7ae4c907e5865e46f7c84755 (commit)
  replaces  debian/1.4.1-1
 tagged by  Carlos Borroto
        on  Fri Jun 22 15:30:40 2012 -0400

- Shortlog ------------------------------------------------------------
Debian release 2.0.4-1~precise1

Alexandre Mestiashvili (11):
      Imported Upstream version 2.0.0
      Merge tag 'upstream/2.0.0'
      updated debian/patches
      debian/control added libboost-thread-dev dependency
      debian/control Standards-Version: 3.9.3 Depends: bowtie2
      debian/get-orig-source - removes shipped with tophat SeqAn files.
      Merge tag 'upstream/2.0.3'
      Imported Upstream version 2.0.3
      tophat depends on bowtie or bowtie2
      refreshed debian/patches/fix_includes_path.patch
      unreleased->unstable

Andreas Tille (12):
      Add patch for #660309 provided by Peter Green
      Fix bug in changelog
      Added myself as bug reviewer
      Mention author of patch in changelog
      Add name to e-mail in upstream contact
      Added references in debian/upstream file
      Upload to unstable
      BibTeX conform author syntax
      Fix bashism in shell script. UNTESTED - PLEASE TEST
      Debhelper 9; upload to unstable
      Add some manpages via help2man - please follow these examples and add more
      Prevent error message piped into manpage

Carlos Borroto (8):
      adds bowtie as a dependency and recommends cufflinks
      Make cufflinks a suggests and not a recommends
      Imported Upstream version 2.0.4
      Merge tag 'upstream/2.0.4'
      patch bashism_in_shell_script refreshed
      updated changelog to version 2.0.4
      Uploaded tophat_2.0.4-1~precise1_source.changes to Debian Med's PPA
      require boost 1.49

Charles Plessy (1):
      YAML syntax correction

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A spliced read mapper for RNA-Seq