[med-svn] [Git][med-team/beagle][master] 2 commits: Update d/tests/ to use wrapper

[Dylan Aïssi]

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 <bob.dybian at gmail.com>
-# Last-Update: 2018-09-16
+# Author: Dylan Aïssi <daissi at debian.org>
+# 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
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