[med-svn] [prokka] branch master updated (a5f1b37 -> 2caecb5)

[Michael Crusoe]

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

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

      from  a5f1b37   adding dfsg to version
       new  9b5a85f   arch:all as is just a Perl script
       new  1d0753e   prokka distributes via GitHub
       new  8f419a4   Imported Upstream version 1.11+dfsg
       new  b9a4e51   add get-orig-source target; ship README.md
       new  2caecb5   update copyright; new version; no ${shlibs} for Perl refresh manpages; add missing libswiss-perl dependency; fix paths

The 5 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:
 .gitignore                          |  24 ++
 README.md                           | 374 +++++++++++++++++++++++++++++
 bin/prokka                          | 179 ++++++++++----
 bin/prokka-genbank_to_fasta_db      |  62 +++--
 bin/prokka-uniprot_to_fasta_db      |   9 +-
 db/hmm/CLUSTERS.hmm                 | Bin 375777699 -> 0 bytes
 db/hmm/Pfam.hmm                     | Bin 327312167 -> 0 bytes
 debian/README.Debian                |   5 +
 debian/changelog                    |   2 +-
 debian/control                      |  10 +-
 debian/copyright                    |  30 ++-
 debian/createmanpages               |   2 +-
 debian/docs                         |   1 +
 debian/patches/set-db-dir           |  39 +++-
 debian/prokka-biocyc_to_fasta_db.1  |   2 +-
 debian/prokka-build_kingdom_dbs.1   |  41 ----
 debian/prokka-cdd_to_hmm.1          |   2 +-
 debian/prokka-clusters_to_hmm.1     |   2 +-
 debian/prokka-genbank_to_fasta_db.1 |   2 +-
 debian/prokka-genpept_to_fasta_db.1 |   2 +-
 debian/prokka-hamap_to_hmm.1        |   2 +-
 debian/prokka-make_tarball.1        |   6 -
 debian/prokka-tigrfams_to_hmm.1     |   6 -
 debian/prokka-uniprot_to_fasta_db.1 |  34 ++-
 debian/prokka.1                     |   2 +-
 debian/prokka.install               |   9 +-
 debian/prokka.manpages              |  12 +-
 debian/rules                        |  18 +-
 debian/watch                        |   2 +-
 doc/ChangeLog.txt                   |  19 ++
 doc/ToDoList.txt                    |   6 +-
 doc/prokka-manual.html              | 215 -----------------
 doc/prokka-manual.txt               | 454 ------------------------------------
 33 files changed, 723 insertions(+), 850 deletions(-)
 create mode 100644 .gitignore
 create mode 100644 README.md
 delete mode 100644 db/hmm/CLUSTERS.hmm
 delete mode 100644 db/hmm/Pfam.hmm
 create mode 100644 debian/README.Debian
 create mode 100644 debian/docs
 delete mode 100644 debian/prokka-build_kingdom_dbs.1
 delete mode 100644 debian/prokka-make_tarball.1
 delete mode 100644 debian/prokka-tigrfams_to_hmm.1
 delete mode 100644 doc/prokka-manual.html
 delete mode 100644 doc/prokka-manual.txt

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