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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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