[med-svn] [roary] branch debian/jessie-backports updated (04e79e8 -> d4c3984)

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch debian/jessie-backports
in repository roary.

      from  04e79e8   releasing package roary version 3.6.3+dfsg-1~bpo8+1
      adds  322b69a   Imported Upstream version 3.6.4+dfsg
      adds  591d940   Merge tag 'upstream/3.6.4+dfsg'
      adds  749d790   update d/changelog
      adds  9ef604d   Imported Upstream version 3.6.5+dfsg
      adds  228ee8f   Merge tag 'upstream/3.6.5+dfsg'
      adds  d415024   Debian version bump
      adds  56c4c6f   Imported Upstream version 3.6.6+dfsg
      adds  0ce0e46   Merge tag 'upstream/3.6.6+dfsg'
      adds  41730a9   Debian version bump
      adds  e3a3aeb   Imported Upstream version 3.6.8+dfsg
      adds  fcdecbf   Merge tag 'upstream/3.6.8+dfsg'
      adds  5ebf8f0   Debian version bump
      adds  6805d50   fix autopkgtest by allowing stderr output
       new  aac360f   Merge tag 'debian/3.6.8+dfsg-2' into debian/jessie-backports
       new  d4c3984   releasing package roary version 3.6.8+dfsg-2~bpo8+1

The 2 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:
 .travis.yml                                        |   14 +-
 Dockerfile                                         |   19 +
 README.md                                          |   11 +-
 debian/changelog                                   |   38 +
 debian/tests/control                               |    1 +
 dist.ini                                           |    2 +-
 install_dependencies.sh                            |   12 +-
 lib/Bio/Roary/ExtractProteomeFromGFF.pm            |   27 +-
 lib/Bio/Roary/GeneNamesFromGFF.pm                  |    8 +
 lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm |   58 +-
 lib/Bio/Roary/ParseGFFAnnotationRole.pm            |    2 +-
 lib/Bio/Roary/SplitGroups.pm                       |    4 +
 t/Bio/Roary/AnnotateGroups.t                       |   17 +
 t/Bio/Roary/CommandLine/Roary.t                    |  174 +-
 t/Bio/Roary/ExtractProteomeFromGFFs.t              |   38 +
 t/data/allow_no_fasta_delimiter/annotation_1.gff   |  173 +
 .../annotation_1.gff.proteome.faa.expected         |   36 +
 t/data/allow_no_fasta_delimiter/annotation_2.gff   |  173 +
 .../annotation_2.gff.proteome.faa.expected         |   36 +
 ...on.gff => example_annotation_no_fasta_line.gff} |    1 -
 t/data/expected_core_60_summary_statistics.txt     |    4 +-
 ...xpected_mafft_real_data_core_gene_alignment.aln |  924 ++---
 t/data/expected_real_data_core_gene_alignment.aln  | 4074 ++++++++++----------
 t/data/gene_name_field/annotation_1.gff            |  173 +
 t/data/gene_name_field/annotation_2.gff            |  173 +
 .../expected_reannotated_groups_file               |    8 +
 t/data/gene_name_field/groups                      |    8 +
 27 files changed, 3520 insertions(+), 2688 deletions(-)
 create mode 100644 Dockerfile
 create mode 100644 t/data/allow_no_fasta_delimiter/annotation_1.gff
 create mode 100644 t/data/allow_no_fasta_delimiter/annotation_1.gff.proteome.faa.expected
 create mode 100644 t/data/allow_no_fasta_delimiter/annotation_2.gff
 create mode 100644 t/data/allow_no_fasta_delimiter/annotation_2.gff.proteome.faa.expected
 copy t/data/{example_annotation.gff => example_annotation_no_fasta_line.gff} (99%)
 create mode 100644 t/data/gene_name_field/annotation_1.gff
 create mode 100644 t/data/gene_name_field/annotation_2.gff
 create mode 100644 t/data/gene_name_field/expected_reannotated_groups_file
 create mode 100644 t/data/gene_name_field/groups

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/roary.git