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Integration test for #219. This fixes #219. Integration tests incorpo…

…rated int Travic-CI pipeline.
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dbolotin committed Mar 2, 2017
1 parent ea3c51c commit 7069820cf613152b07ef587a064477a5638d49ea
Showing with 45 additions and 9 deletions.
  1. +3 −0 .travis.yml
  2. +42 −9 itests.sh
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@@ -14,6 +14,9 @@ before_install:
- mvn clean install -DskipTests -B && cd ..
- mv ./repseqio/.cache .cache
script:
- mvn install -DskipTests=true -Dmaven.javadoc.skip=true -B -V && mvn test -B && ./itests.sh test
jdk:
- openjdk7
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@@ -1,5 +1,8 @@
#!/bin/bash
set -e
set -o pipefail
# "Integration" tests for MiXCR
# Test standard analysis pipeline results
@@ -46,6 +49,26 @@ case $os in
;;
esac
create_standard_results=false
run_tests=false
while [[ $# > 0 ]]
do
key="$1"
shift
case $key in
std)
create_standard_results=true
;;
test)
run_tests=true
;;
*)
echo "Unknown option $key";
exit 1
;;
esac
done
rm -rf ${dir}/test_target
mkdir ${dir}/test_target
@@ -60,17 +83,27 @@ which mixcr
mixcr -v
function go_assemble {
mixcr assemble -r $1.clns.report $1.vdjca $1.clns || exit 1
mixcr assemble -r $1.clns.report $1.vdjca $1.clns
for c in TCR IG TRB TRA TRG TRD IGH IGL IGK ALL
do
mixcr exportClones -c ${c} -s $1.clns $1.clns.${c}.txt || exit 1
mixcr exportClones -c ${c} -s $1.clns $1.clns.${c}.txt
done
}
for s in sample_IGH test;
do
mixcr align -r ${s}_paired.vdjca.report ${s}_R1.fastq ${s}_R2.fastq ${s}_paired.vdjca || exit 1
go_assemble ${s}_paired
mixcr align -r ${s}_single.vdjca.report ${s}_R1.fastq ${s}_single.vdjca || exit 1
go_assemble ${s}_single
done
if [[ $create_standard_results == true ]]; then
for s in sample_IGH test;
do
mixcr align -r ${s}_paired.vdjca.report ${s}_R1.fastq ${s}_R2.fastq ${s}_paired.vdjca
go_assemble ${s}_paired
mixcr align -r ${s}_single.vdjca.report ${s}_R1.fastq ${s}_single.vdjca
go_assemble ${s}_single
done
fi
# UseCase 1
if [[ $run_tests == true ]]; then
echo "Running test case 1"
mixcr align -OvParameters.geneFeatureToAlign=VGeneWithP test_R1.fastq test_R2.fastq case1.vdjca
mixcr assemble case1.vdjca case1.clns
fi

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