[med-svn] [Git][med-team/soapdenovo][master] Autopkgtest: modified run-unit-test

[Liubov Chuprikova]

Liubov Chuprikova pushed to branch master at Debian Med / soapdenovo


Commits:
4e9bbb2e by Liubov Chuprikova at 2018-06-09T00:19:33+02:00
Autopkgtest: modified run-unit-test

- - - - -


1 changed file:

- debian/tests/run-unit-test


Changes:

=====================================
debian/tests/run-unit-test
=====================================
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -10,35 +10,41 @@ cd $AUTOPKGTEST_TMP
 cp -a /usr/share/doc/${pkg}/test-data/* .
 tar -xzvf *.tar.gz; rm *.tar.gz
 
-echo ">>>>>Starting soapdenovo test..."
-echo ">>>>>Step 1: pregraph"
-soapdenovo-31mer pregraph -s example.config -o graph
-[ -s graph.kmerFreq ]
-[ -s graph.edge ]
-[ -s graph.preArc ]
-[ -s graph.vertex ]
-[ -s graph.preGraphBasic ]
+for command in soapdenovo-31mer soapdenovo-63mer; do
+	echo ">>>>>Starting $command test..."
+	echo ">>>>>Step 1: pregraph"
+	$command pregraph -s example.config -o graph
+	[ -s graph.kmerFreq ]
+	[ -s graph.edge ]
+	[ -s graph.preArc ]
+	[ -s graph.vertex ]
+	[ -s graph.preGraphBasic ]
 
-echo ">>>>>Step 2: contig"
-soapdenovo-31mer contig -g graph
-[ -s graph.contig ]
-[ -s graph.Arc ]
-[ -s graph.updated.edge ]
-[ -s graph.ContigIndex ]
+	echo ">>>>>Step 2: contig"
+	$command contig -g graph
+	[ -s graph.contig ]
+	[ -s graph.Arc ]
+	[ -s graph.updated.edge ]
+	[ -s graph.ContigIndex ]
+	
+	echo ">>>>>Step 3: map"
+	$command map -s example.config -g graph
+	[ -s graph.peGrads ]
+	[ -s graph.readOnContig ]
+	[ -s graph.readInGap ]
+	
+	echo ">>>>>Step 4: scaff"
+	$command scaff -g graph
+	[ -s graph.newContigIndex ]
+	[ -s graph.links ]
+	[ -s graph.scaf_gap ]
+	[ -s graph.scaf ]
+	[ -e graph.gapSeq ]
+	[ -s graph.scafSeq ]
+	
+	rm graph.*
+	echo ""; echo "OK"; echo ""
+done
 
-echo ">>>>>Step 3: map"
-soapdenovo-31mer map -s example.config -g graph
-[ -s graph.peGrads ]
-[ -s graph.readOnContig ]
-[ -s graph.readInGap ]
+# soapdenovo-127mer testing requires lots of memory->Skipped
 
-echo ">>>>>Step 4: scaff"
-soapdenovo-31mer scaff -g graph
-[ -s graph.newContigIndex ]
-[ -s graph.links ]
-[ -s graph.scaf_gap ]
-[ -s graph.scaf ]
-[ -e graph.gapSeq ]
-[ -s graph.scafSeq ]
-
-echo ""; echo "PASS"; echo ""



View it on GitLab: https://salsa.debian.org/med-team/soapdenovo/commit/4e9bbb2e1b964ca2df7347c4d10443993d9f857c

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View it on GitLab: https://salsa.debian.org/med-team/soapdenovo/commit/4e9bbb2e1b964ca2df7347c4d10443993d9f857c
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