[med-svn] [roary] branch master updated (41730a9 -> 5ebf8f0)

[Sascha Steinbiss]

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satta pushed a change to branch master
in repository roary.

      from  41730a9   Debian version bump
       new  e3a3aeb   Imported Upstream version 3.6.8+dfsg
       new  fcdecbf   Merge tag 'upstream/3.6.8+dfsg'
       new  5ebf8f0   Debian version bump

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:
 .travis.yml                                        |   10 +-
 Dockerfile                                         |   19 +
 README.md                                          |    7 +-
 debian/changelog                                   |    6 +
 dist.ini                                           |    2 +-
 install_dependencies.sh                            |   10 +-
 lib/Bio/Roary/ExtractProteomeFromGFF.pm            |   22 +-
 lib/Bio/Roary/GeneNamesFromGFF.pm                  |    8 +
 lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm |   27 +-
 t/Bio/Roary/AnnotateGroups.t                       |   17 +
 t/Bio/Roary/CommandLine/Roary.t                    |  174 +-
 t/Bio/Roary/ExtractProteomeFromGFFs.t              |   25 +
 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 +
 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 +
 23 files changed, 3430 insertions(+), 2679 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
 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

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