debian/README.Debian

-Prokka's databases are installed to /usr/share/prokka
-
-HAMAP.hmm is 224M, took 21 hours and 10 minutes, 15M of memory, single threaded?
-
-Shipped HAMAP.hmm is 88M ??
-
-
-After installing the package you need to run
-
-    prokka --setupdb
-
-as root.  This is creates files
-
-    /usr/share/prokka/db/kingdom/Archaea/sprot.{phr,pin,psq}
-
-which is not policy compliant.  It would be better to move the db to
-
-    /var/lib/prokka/db
-
-instead.

debian/changelog

@@ -2,6 +2,5 @@ prokka (1.13.4+dfsg-1) UNRELEASED; urgency=low
 
   [ Michael R. Crusoe ]
   * Initial release (Closes: #778246)
-  TODO: See README.Debian about user generated files in /usr
 
  -- Andreas Tille <tille@debian.org>  Mon, 28 Jan 2019 13:26:30 +0100

debian/patches/set-db-dir

@@ -13,7 +13,7 @@ Last-Update: 2015-02-21
  
  # where to put formatted database: /path/to/prokka/db/
 -ROOTDIR=$(dirname $0)
-+ROOTDIR=/usr/share/prokka/db
++ROOTDIR=/var/lib/prokka/db
  
  echo "*** NOTICE ***"
  echo "This script is about to download data from the Internet and overwrite your existing Prokka BLAST databases."
@@ -33,7 +33,7 @@ Last-Update: 2015-02-21
  	     $metagenome, $compliant, $listdb, $citation);
  
 -$dbdir = $ENV{'PROKKA_DBDIR'} || abs_path("$FindBin::RealBin/../db");
-+$dbdir = "/usr/share/prokka/db";
++$dbdir = "/var/lib/prokka/db";
  
  setOptions();
  

debian/prokka.postinstall → debian/prokka.postinst

@@ -17,6 +17,7 @@ set -e
 # for details, see http://www.debian.org/doc/debian-policy/ or
 # the debian-policy package
 
+#PROKKADBPATH=/var/lib/prokka/db
 
 case "$1" in
     configure)

debian/prokka.postrm

+#!/bin/sh
+
+set -e 
+
+PROKKADBPATH=/var/lib/prokka/db
+
+
+if [ "$1" = "purge" ] ; then
+   
+   if [ -d $PROKKADBPATH ]; then
+      rm -rf $(dirname $PROKKADBPATH)
+   fi
+fi
+
+#DEBHELPER#	
+

debian/rules

@@ -2,6 +2,10 @@
 
 DH_VERBOSE := 1
 
+include /usr/share/dpkg/default.mk
+
+PROKKADBPATH=/var/lib/prokka/db
+
 %:
 	dh $@
 
@@ -10,3 +14,17 @@ override_dh_install:
 	for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
 	    sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \
 	done
+
+override_dh_link:
+	for db in `find debian/$(DEB_SOURCE)/usr/share/prokka/db -type f` ; do \
+	    vardir=`echo $${db} | sed -e 's?.*/usr/share?/var/lib?'` ; \
+	    mkdir -p debian/$(DEB_SOURCE)/`dirname $${vardir}` ; \
+	    usrdir=`echo $${db} | sed -e 's?.*/usr?/usr?'` ; \
+	    dh_link $${usrdir} $${vardir} ; \
+	done
+
+override_dh_fixperms:
+	dh_fixperms
+	for db in `find debian/$(DEB_SOURCE)/$(PROKKADBPATH) -type d` ; do \
+	    chmod a+w $${db} ; \
+	done