Andreas Tille pushed to branch master at Debian Med / prokka
Commits:
259437d3 by Andreas Tille at 2019-01-28T15:12:27Z
Move database to var to enable users recreation of the database
- - - - -
a97fba2f by Andreas Tille at 2019-01-28T15:12:50Z
Symlinks to data files on /var/lib to /usr/share
- - - - -
5867f570 by Andreas Tille at 2019-01-28T15:16:23Z
Cleanup on purge
- - - - -
fa66f09b by Andreas Tille at 2019-01-28T15:32:58Z
Make db dir user writable
- - - - -
1b3ad84c by Andreas Tille at 2019-01-28T17:22:31Z
Fix permissions
- - - - -
6 changed files:
- − debian/README.Debian
- debian/changelog
- debian/patches/set-db-dir
- debian/prokka.postinstall → debian/prokka.postinst
- + debian/prokka.postrm
- debian/rules
Changes:
=====================================
debian/README.Debian deleted
=====================================
@@ -1,20 +0,0 @@
-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 <[email protected]> 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
=====================================
@@ -0,0 +1,16 @@
+#!/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
View it on GitLab:
https://salsa.debian.org/med-team/prokka/compare/a04766af36e117512eff77c0bfd604d84acbe0c8...1b3ad84c682b9b2af283613be8a1c9d1fb1f7b32
--
View it on GitLab:
https://salsa.debian.org/med-team/prokka/compare/a04766af36e117512eff77c0bfd604d84acbe0c8...1b3ad84c682b9b2af283613be8a1c9d1fb1f7b32
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