[med-svn] [subread] 12/14: Run all tests

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch master
in repository subread.

commit c66fb682cb0a8d97a6ff16f70d0f365c3821e402
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Sat Apr 23 10:42:01 2016 +0200

    Run all tests
---
 debian/tests/subread-tests | 36 ++----------------------------------
 1 file changed, 2 insertions(+), 34 deletions(-)

diff --git a/debian/tests/subread-tests b/debian/tests/subread-tests
index e8e9455..37ba169 100755
--- a/debian/tests/subread-tests
+++ b/debian/tests/subread-tests
@@ -22,41 +22,9 @@ else
     WORKDIR=${TMPDIR}/adt_test
 fi
 
-cd $WORKDIR/featureCounts
-#featureCounts -a data/test-minimum.GTF -o test-minimum.FC data/test-minimum.sam
-#bash data/compare.sh data/corner-INDEL.sam data/corner-INDEL.ora data/test-minimum.GTF "-p" "indel reads"
-bash featureCounts-test.sh
-
-cd $WORKDIR/subjunc
-#mkdir tmp
-bash subjunc-test.sh
-#subread-buildindex -o tmp/small1 ../chr901.fa
-#subjunc --SAMoutput -i tmp/small1 -o junctions.sam -r data/junction-reads-A.fq \
-#-R data/junction-reads-B.fq
-#subjunc -i tmp/small1 -o junctionsNfusions.bam \
-#-r data/junction-reads-A.fq -R data/junction-reads-B.fq --allJunctions
-
-cd $WORKDIR/subread-align
-mkdir tmp
-subread-buildindex -B -F -o tmp/small1 -M100 ../chr901.fa
-subread-align --SAMoutput -t0 -i tmp/small1 -r data/test-noerror-r1.fq \
-    -o tmp/test-tmp.sam1 -H -J
-subread-align --SAMoutput -t0 -u -i tmp/small1 -r data/test-noerror-r1.fq \
-    -o tmp/test-tmp.sam2 -H -J
-subread-align --SAMoutput -t0 -i tmp/small1 -r data/test-noerror-r1.fq \
-    -R data/test-noerror-r2.fq -o tmp/test-tmp.sam3 -H -J
-subread-align --SAMoutput -t0 -u -i tmp/small1 -r data/test-noerror-r1.fq \
-    -R data/test-noerror-r2.fq -o tmp/test-tmp.sam4  -Q -J
-subread-align --SAMoutput -t0 -i tmp/small1 -r data/test-error-r1.fq \
-    -R data/test-error-r2.fq -o tmp/test-tmp.sam5 -H -J
-subread-align --SAMoutput -t0 -i tmp/small1 --gzFASTQinput -r data/test-err-mut-r1.fq.gz \
-    -R data/test-err-mut-r2.fq.gz -o tmp/test-tmp.sam6 -H -J \
-    --rg-id MyTestGroup --rg SM:sample1 --rg TP:1 --rg XX:YY
-
-cd $WORKDIR/exactSNP
-#exactSNP -g ../chr901.fa -o test-out.VCF -i data/test-in.BAM -b
-bash exactSNP-test.sh
+cd $WORKDIR
 
+bash test_all.sh
 
 if [ $# -eq 0 ]
 then

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/subread.git