[med-svn] [Git][med-team/qcumber][master] 9 commits: feed config.txt with default Kraken DB

[Étienne Mollier]

Étienne Mollier pushed to branch master at Debian Med / qcumber


Commits:
8e490c00 by Étienne Mollier at 2021-01-09T23:04:33+01:00
feed config.txt with default Kraken DB

- - - - -
9c134cb3 by Étienne Mollier at 2021-01-09T23:05:02+01:00
reinforce config script

- - - - -
afbfd76f by Étienne Mollier at 2021-01-09T23:05:38+01:00
reinforce postinst script

- - - - -
36aaa451 by Étienne Mollier at 2021-01-09T23:06:47+01:00
update changelog

- - - - -
35097df4 by Étienne Mollier at 2021-01-09T23:08:40+01:00
d/config: remove unused variable

- - - - -
db557cc4 by Étienne Mollier at 2021-01-09T23:10:09+01:00
routine-update: Standards-Version: 4.5.1

- - - - -
44df372c by Étienne Mollier at 2021-01-09T23:10:13+01:00
routine-update: Remove trailing whitespace in debian/rules

- - - - -
5b0957ab by Étienne Mollier at 2021-01-09T23:10:13+01:00
routine-update: Add salsa-ci file

- - - - -
9139e934 by Étienne Mollier at 2021-01-09T23:10:59+01:00
routine-update: Ready to upload to unstable

- - - - -


7 changed files:

- debian/changelog
- debian/config
- debian/config.txt
- debian/control
- debian/postinst
- debian/rules
- + debian/salsa-ci.yml


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+qcumber (2.3.0-2) unstable; urgency=medium
+
+  * Team upload.
+  * Feed debian/config.txt with default Kraken DB directory:
+    - fixes piuparts error due to altered /etc/qcumber/config.txt;
+    - reinforced config and postinst scripts while investigating the issue.
+  * Standards-Version: 4.5.1 (routine-update)
+  * Remove trailing whitespace in debian/rules (routine-update)
+  * Add salsa-ci file (routine-update)
+
+ -- Étienne Mollier <etienne.mollier at mailoo.org>  Sat, 09 Jan 2021 23:10:14 +0100
+
 qcumber (2.3.0-1) unstable; urgency=medium
 
   * Team Upload.


=====================================
debian/config
=====================================
@@ -3,14 +3,13 @@
 set -e
 
 conffile=/etc/qcumber/config.txt
-DEFAULTKRAKENDB="/var/lib/kraken/minikraken_20141208"
 CHECKKRAKENDBFILE="database.idx"
 
 . /usr/share/debconf/confmodule
 
 if [ -f $conffile ] ; then
-    krakendb=`sed '/\[PATH\]/,$d' $conffile | grep "^kraken_db" | head -n 1 | sed 's/^kraken_db *= *\([^ ]\+\) *$/\1/'`
-    db_set qcumber/krakendb ${krakendb}
+    krakendb="`sed '/\[PATH\]/,$d' $conffile | grep ^kraken_db | head -n 1 | sed 's/^kraken_db *= *\([^ ]\+\) *$/\1/'`"
+    db_set qcumber/krakendb "${krakendb}"
 fi
 
 if [ ! -e "${krakendb}/${CHECKKRAKENDBFILE}" ] ; then


=====================================
debian/config.txt
=====================================
@@ -1,3 +1,3 @@
 [DEFAULT]
-kraken_db =
+kraken_db = /var/lib/kraken/minikraken_20141208
 adapter = /usr/share/trimmomatic


=====================================
debian/control
=====================================
@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
                bowtie2,
                kraken,
                texlive-latex-base
-Standards-Version: 4.5.0
+Standards-Version: 4.5.1
 Vcs-Browser: https://salsa.debian.org/med-team/qcumber
 Vcs-Git: https://salsa.debian.org/med-team/qcumber.git
 Homepage: https://gitlab.com/RKIBioinformaticsPipelines/QCumber


=====================================
debian/postinst
=====================================
@@ -9,10 +9,10 @@ CHECKKRAKENDBFILE="database.idx"
 
 db_get qcumber/krakendb || true
 
-DEFAULTKRAKENDB=$RET
+DEFAULTKRAKENDB="$RET"
 
 if [ "$DEFAULTKRAKENDB" = "" ] ; then
-    DEFAULTKRAKENDB=`sed '/\[PATH\]/,$d' $conffile | grep "^kraken_db" | head -n 1 | sed 's/^kraken_db *= *\([^ ]\+\) *$/\1/'`
+    DEFAULTKRAKENDB="`sed '/\[PATH\]/,$d' $conffile | grep ^kraken_db | head -n 1 | sed 's/^kraken_db *= *\([^ ]\+\) *$/\1/'`"
 else
     # check whether configfile has the same dir as the user has input in config step
     if ! grep -q "^kraken_db *= *$DEFAULTKRAKENDB *$" $conffile ; then


=====================================
debian/rules
=====================================
@@ -20,7 +20,7 @@ override_dh_fixperms:
 	chmod a-x debian/*/usr/share/*/*.tex
 	chmod a-x debian/*/etc/*/*.txt
 	chmod a-x debian/*/usr/share/*/*.html
-	chmod a-x debian/*/usr/share/*/*.py	
+	chmod a-x debian/*/usr/share/*/*.py
 	chmod a-x debian/*/usr/share/*/Rscripts/*.R
 	chmod a-x debian/*/usr/share/*/modules/*.snakefile
 	chmod a-x debian/*/etc/qcumber/adapters.fa


=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml



View it on GitLab: https://salsa.debian.org/med-team/qcumber/-/compare/05bfeff79dc6aef9d9262d284e7ffbfb339f1d56...9139e93432920e52c80cc66b3245fd195593bf19

-- 
View it on GitLab: https://salsa.debian.org/med-team/qcumber/-/compare/05bfeff79dc6aef9d9262d284e7ffbfb339f1d56...9139e93432920e52c80cc66b3245fd195593bf19
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