[med-svn] [Git][med-team/prokka][master] 4 commits: Default database path is now ~/.local/lib/prokka/db (Closes: #924128)
Michael R. Crusoe
gitlab at salsa.debian.org
Wed Oct 14 10:34:40 BST 2020
Michael R. Crusoe pushed to branch master at Debian Med / prokka
Commits:
2c1039ff by Michael R. Crusoe at 2020-10-14T10:15:48+02:00
Default database path is now ~/.local/lib/prokka/db (Closes: #924128)
- - - - -
df0835af by Michael R. Crusoe at 2020-10-14T10:17:09+02:00
no need to forward hmmer3 patch
- - - - -
19e9f69d by Michael R. Crusoe at 2020-10-14T11:29:20+02:00
more fixes for new default DB path
- - - - -
2dbebb7c by Michael R. Crusoe at 2020-10-14T11:30:06+02:00
release 1.14.6+dfsg-2
- - - - -
10 changed files:
- + debian/NEWS
- debian/changelog
- debian/get-additional-data
- − debian/lintian-overrides
- debian/patches/hmmer_not_hmmer3
- debian/patches/set-db-dir
- − debian/prokka.postinst
- − debian/prokka.postrm
- debian/rules
- debian/watch
Changes:
=====================================
debian/NEWS
=====================================
@@ -0,0 +1,13 @@
+prokka (1.14.6+dfsg-2) unstable; urgency=medium
+
+ The default world writable shared database folder /var/lib/prokka/db
+ has been abandonded as a security measure.
+
+ Per-user database directories (~/.local/lib/prokka/db) are now the default.
+
+ To continue using a previously made shared database directory, please set
+ the PROKKA_DBDIR to the desired path.
+
+ -- Michael R. Crusoe <crusoe at debian.org> Wed, 14 Oct 2020 10:11:34 +0200
+
+
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+prokka (1.14.6+dfsg-2) unstable; urgency=medium
+
+ * debian/watch: new location
+ * Default database path is now ~/.local/lib/prokka/db (Closes: #924128)
+
+ -- Michael R. Crusoe <crusoe at debian.org> Wed, 14 Oct 2020 11:29:53 +0200
+
prokka (1.14.6+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
debian/get-additional-data
=====================================
@@ -1,6 +1,7 @@
#!/bin/sh -e
-PROKKADBPATH=/var/lib/prokka/db
+PROKKADBPATH=${PROKKA_DBDIR:-~/.local/lib/prokka/db}
+mkdir --parents ${PROKKADBPATH}
if which prokka >/dev/null ; then
# PROKKAVERSION=`prokka -v | sed 's/^.*[[:space:]]\+//'`
@@ -17,8 +18,7 @@ for data in hmm kingdom ; do
rm -rf ${PROKKADBPATH}/$data
mv prokka-${PROKKAVERSION}/db/$data ${PROKKADBPATH}
done
+cp -rf /usr/share/prokka/db/cm ${PROKKADBPATH}/
+cp -rf /usr/share/prokka/db/genus ${PROKKADBPATH}/
+
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 deleted
=====================================
@@ -1,2 +0,0 @@
-# /var/lib/prokka/db is intentionally writable for users
-prokka: non-standard-dir-perm var/lib/prokka/*
=====================================
debian/patches/hmmer_not_hmmer3
=====================================
@@ -1,8 +1,9 @@
-Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Author: Michael R. Crusoe <crusoe at debian.org>
Description: Use the Debian binary name for hmmer v3
+Forwarded: not-needed
--- prokka.orig/bin/prokka
+++ prokka/bin/prokka
-@@ -922,7 +922,7 @@
+@@ -970,7 +970,7 @@
push @database, {
DB => $dbfile,
SRC => "protein motif:$name:",
@@ -11,7 +12,7 @@ Description: Use the Debian binary name for hmmer v3
CMD => $HMMER3CMD,
VERSION => 3, # without this, latest Bioperl goes into infinite loop
}
-@@ -965,7 +965,7 @@
+@@ -1013,7 +1013,7 @@
unshift @database, {
DB => $hmms,
SRC => $compliant ? "" : "protein motif:$src:",
=====================================
debian/patches/set-db-dir
=====================================
@@ -1,8 +1,10 @@
-Description: Use a FHS path to the databases, not a relative path that would
- be non FHS compliant when the prokka script is installed to /usr/bin/
Forwarded: not-needed
-Author: Michael R. Crusoe <mcrusoe at msu.edu>
-Last-Update: 2015-02-21
+Author: Michael R. Crusoe <crusoe at debian.org>
+Last-Update: 2020-10-14
+Description: Database default path is a user path
+
+not a relative path that would be non FHS compliant
+when the prokka script is installed to /usr/bin/
---
@@ -28,12 +30,12 @@ Last-Update: 2015-02-21
# If you want a copy of the sprot file too (we do for git distribution)
--- prokka.orig/bin/prokka
+++ prokka/bin/prokka
-@@ -232,7 +232,7 @@
+@@ -235,7 +235,7 @@
$rfam, $norrna, $notrna, $rnammer, $rawproduct, $noanno, $accver,
$metagenome, $compliant, $listdb, $citation);
-$dbdir = $ENV{'PROKKA_DBDIR'} || abs_path("$FindBin::RealBin/../db");
-+$dbdir = $ENV{'PROKKA_DBDIR'} || "/var/lib/prokka/db";
++$dbdir = $ENV{'PROKKA_DBDIR'} || "$ENV{HOME}/.local/lib/prokka/db";
setOptions();
=====================================
debian/prokka.postinst deleted
=====================================
@@ -1,41 +0,0 @@
-#!/bin/sh
-# postinst script for Prokka
-#
-# see: dh_installdeb(1)
-
-set -e
-
-# summary of how this script can be called:
-# * <postinst> `configure' <most-recently-configured-version>
-# * <old-postinst> `abort-upgrade' <new version>
-# * <conflictor's-postinst> `abort-remove' `in-favour' <package>
-# <new-version>
-# * <postinst> `abort-remove'
-# * <deconfigured's-postinst> `abort-deconfigure' `in-favour'
-# <failed-install-package> <version> `removing'
-# <conflicting-package> <version>
-# for details, see http://www.debian.org/doc/debian-policy/ or
-# the debian-policy package
-
-#PROKKADBPATH=/var/lib/prokka/db
-
-case "$1" in
- configure)
- prokka --setupdb
- ;;
-
- abort-upgrade|abort-remove|abort-deconfigure)
- ;;
-
- *)
- echo "postinst called with unknown argument \`$1'" >&2
- exit 1
- ;;
-esac
-
-# dh_installdeb will replace this with shell code automatically
-# generated by other debhelper scripts.
-
-#DEBHELPER#
-
-exit 0
=====================================
debian/prokka.postrm deleted
=====================================
@@ -1,16 +0,0 @@
-#!/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
=====================================
@@ -4,8 +4,6 @@ DH_VERBOSE := 1
include /usr/share/dpkg/default.mk
-PROKKADBPATH=/var/lib/prokka
-
%:
dh $@
@@ -22,9 +20,3 @@ override_dh_link:
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
=====================================
debian/watch
=====================================
@@ -1,5 +1,5 @@
version=3
opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g" \
- https://www.github.com/Victorian-Bioinformatics-Consortium/prokka/releases .*/archive/v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+ https://github.com/tseemann/prokka/releases .*/archive/v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
View it on GitLab: https://salsa.debian.org/med-team/prokka/-/compare/030eaced3c8cebb27eac146c798d6833ab8ca7fa...2dbebb7c9b31ca5d01da1c85ae74dcf88194a4ee
--
View it on GitLab: https://salsa.debian.org/med-team/prokka/-/compare/030eaced3c8cebb27eac146c798d6833ab8ca7fa...2dbebb7c9b31ca5d01da1c85ae74dcf88194a4ee
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