debian/README.Debian

+prokka for Debian
+=================
+
+Some data files of prokka are licensed CC-BY-ND-3 which is considered
+non-free by Debian.  These files are excluded from the distributed
+source.  You can obtain these files by calling
+
+    sh /usr/share/doc/prokka/get-additional-data
+
+ -- Andreas Tille <tille@debian.org>  Mon, 28 Jan 2019 18:52:07 +0100

debian/changelog

 prokka (1.13.4+dfsg-1) unstable; urgency=low
 
-  [ Michael R. Crusoe ]
   * Initial release (Closes: #778246)
 
- -- Andreas Tille <tille@debian.org>  Mon, 28 Jan 2019 18:52:07 +0100
+ -- Andreas Tille <tille@debian.org>  Mon, 04 Feb 2019 10:00:06 +0100

debian/copyright

@@ -2,28 +2,13 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: Prokka
 Source: https://github.com/tseemann/prokka/releases
 Files-Excluded: binaries/*
+                db/hmm
+                db/kingdom
 
 Files: *
 Copyright: Copyright (C) 2012-2018 Torsten Seemann
 License: GPL-3+
 
-Files: db/hmm/*
-       db/kingdom/*
-Copyright: UniProtKB/Swiss-Prot is copyrighted by the UniProt Consortium
-License: CC-BY-ND-3
-Comment: Email from upstream author:
- From: Torsten Seemann <torsten.seemann@monash.edu>
- Date: Sat, 14 Feb 2015 14:45:55 +1100
- Message-ID: <CAFrpSegC=noX+M-i-QXJvde-pECpy4uCPP8PQy5qHgHbu3PjaQ@mail.gmail.com>
- Subject: Re: Prokka Debian package?
- To: "Michael R. Crusoe" <mcrusoe@msu.edu>
- [...]
- > ./db/kingdom/Archaea/sprot
- > ./db/kingdom/Bacteria/sprot
- > ./db/kingdom/Mitochondria/sprot
- > ./db/kingdom/Viruses/sprot
- These 3 are derived from UniProt.
-
 Files: db/cm/*
 Copyright: Wellcome Trust Sanger Institute
 License: CC0-1
@@ -34,58 +19,6 @@ Copyright: 2015 Michael R. Crusoe <mcrusoe@msu.edu>
            2016-2019 Andreas Tille <tille@debian.org>
 License: GPL-3+
 
-License: CC-BY-ND-3
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- .
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-
 License: CC0-1
  Statement of Purpose
  .

debian/docs

 README.md
+debian/get-additional-data

debian/get-additional-data

+#!/bin/sh -e
+
+PROKKADBPATH=/var/lib/prokka/db
+
+if which prokka >/dev/null ; then
+   # PROKKAVERSION=`prokka -v | sed 's/^.*[[:space:]]\+//'`
+   # Sometimes prokka reports wrong version
+   PROKKAVERSION=`apt-cache policy prokka | grep "^ \*\*\*" | sed 's/^ \*\*\* \([.0-9]\+\)[+-].*/\1/'`
+else
+   echo "prokka not installed."
+   exit 1
+fi
+set -x
+wget -np -N https://github.com/tseemann/prokka/archive/v${PROKKAVERSION}.tar.gz
+for data in hmm kingdom ; do
+    tar -xaf v${PROKKAVERSION}.tar.gz --no-anchored "$data"
+    rm -rf ${PROKKADBPATH}/$data
+    mv prokka-${PROKKAVERSION}/db/$data ${PROKKADBPATH}
+done
+prokka --setupdb
+find ${PROKKADBPATH} -type f -exec chmod a+wr \{\} \;
+for data in hmm kingdom ; do
+    find ${PROKKADBPATH}/$data -type d -exec chmod a+wrx \{\} \;
+done

debian/lintian-overrides

 # /var/lib/prokka/db is intentionally writable for users
-prokka: non-standard-dir-perm var/lib/prokka/db/*
+prokka: non-standard-dir-perm var/lib/prokka/*

debian/rules

@@ -4,7 +4,7 @@ DH_VERBOSE := 1
 
 include /usr/share/dpkg/default.mk
 
-PROKKADBPATH=/var/lib/prokka/db
+PROKKADBPATH=/var/lib/prokka
 
 %:
 	dh $@