Dylan Aïssi pushed to branch master at Debian Med / beagle
Commits: d3135f77 by Dylan Aïssi at 2019-09-19T19:03:03Z Update d/tests/ to use wrapper - - - - - ed81b24f by Dylan Aïssi at 2019-09-19T19:19:16Z Upload to unstable - - - - - 2 changed files: - debian/changelog - debian/tests/run-sample-analysis Changes: ===================================== debian/changelog ===================================== @@ -1,4 +1,4 @@ -beagle (5.1-190824+dfsg-2) UNRELEASED; urgency=medium +beagle (5.1-190824+dfsg-2) unstable; urgency=medium * Team upload. ===================================== debian/tests/run-sample-analysis ===================================== @@ -1,8 +1,8 @@ #!/bin/sh -e # http://dep.debian.net/deps/dep8/ # Autopkgtest: Test if beagle run analysis correctly -# Author: Dylan Aïssi <[email protected]> -# Last-Update: 2018-09-16 +# Author: Dylan Aïssi <[email protected]> +# Last-Update: 2019-09-19 pkg=beagle if [ "$ADTTMP" = "" ] ; then @@ -11,21 +11,19 @@ fi cd $ADTTMP cp -a /usr/share/doc/${pkg}/examples/* $ADTTMP -BEAGLE_TEST='java -jar /usr/share/beagle/beagle.jar' - # Generate necessary files gzip test.vcf zcat test.vcf.gz | cut -f1-190 | tr '/' '|' | gzip > ref.vcf.gz zcat test.vcf.gz | cut -f1-9,191-200 | gzip > target.vcf.gz -java -jar /usr/share/beagle/bref3.jar ref.vcf.gz > ref.bref3 +bref3 ref.vcf.gz > ref.bref3 # Beagle with gt argument -$BEAGLE_TEST gt=test.vcf.gz out=out.gt +beagle gt=test.vcf.gz out=out.gt # Beagle with ref and gt argument -$BEAGLE_TEST ref=ref.vcf.gz gt=target.vcf.gz out=out.ref +beagle ref=ref.vcf.gz gt=target.vcf.gz out=out.ref # Beagle with bref3 file -$BEAGLE_TEST ref=ref.bref3 gt=target.vcf.gz out=out.bref3 +beagle ref=ref.bref3 gt=target.vcf.gz out=out.bref3 rm -f $ADTTMP/* View it on GitLab: https://salsa.debian.org/med-team/beagle/compare/a5f00fabec95a94c987ed178b52912cb9717827a...ed81b24f9962f9c6937a023b2f16ad4bb816ab57 -- View it on GitLab: https://salsa.debian.org/med-team/beagle/compare/a5f00fabec95a94c987ed178b52912cb9717827a...ed81b24f9962f9c6937a023b2f16ad4bb816ab57 You're receiving this email because of your account on salsa.debian.org.
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