Merge pull request #54 from genenetwork/tests

Added test suite, make check and openblas support. Need to fix one test that is still failing.

1 files changed, 54 insertions, 0 deletions

diff --git a/test/test_suite.sh b/test/test_suite.sh
new file mode 100755
index 0000000..f1a1c6f
--- /dev/null
+++ b/test/test_suite.sh
@@ -0,0 +1,54 @@
+#!/usr/bin/env bash
+
+gemma=../bin/gemma
+
+testCenteredRelatednessMatrixK() {
+    $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \
+           -a ../example/mouse_hs1940.anno.txt -gk -o mouse_hs1940
+    assertEquals 0 $?
+    grep "total computation time" < output/mouse_hs1940.log.txt
+    assertEquals 0 $?
+    assertEquals "3763600" `wc -w < output/mouse_hs1940.cXX.txt`
+    # assertEquals "15f680c" `md5sum < output/mouse_hs1940.cXX.txt | head -c 7`
+    assertEquals "0.335" `head -c 5 output/mouse_hs1940.cXX.txt`
+    # FIXME: The following test fails in the Guix build system (https://github.com/xiangzhou/GEMMA/issues/55)
+    assertEquals "29.691" `awk '{s+=substr($1,0,6)}END{print s}' output/mouse_hs1940.cXX.txt`
+}
+
+testUnivariateLinearMixedModel() {
+    $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt -n 1 \
+           -a ../example/mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt -lmm \
+           -o mouse_hs1940_CD8_lmm
+    assertEquals 0 $?
+    grep "total computation time" < output/mouse_hs1940_CD8_lmm.log.txt
+    assertEquals 0 $?
+    assertEquals "118459" `wc -w < output/mouse_hs1940_CD8_lmm.assoc.txt`
+    assertEquals "92047" `awk '{s+=substr($1,0,6)}END{print s}' output/mouse_hs1940_CD8_lmm.assoc.txt`
+}
+
+testMultivariateLinearMixedModel() {
+    $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \
+           -n 1 6 -a ../example/mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt \
+           -lmm -o mouse_hs1940_CD8MCH_lmm
+    assertEquals 0 $?
+    grep "total computation time" < output/mouse_hs1940_CD8MCH_lmm.log.txt
+    assertEquals 0 $?
+
+    outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt
+    assertEquals "139867" `wc -w < $outfn`
+    assertEquals "92079" `awk '{s+=substr($1,0,6)}END{print s}' $outfn`
+}
+
+shunit2=`which shunit2`
+if [ -e "../contrib/shunit2/source/2.0/src/shell/shunit2" ]; then
+    echo try to run the locally installed shunit2
+    . ../contrib/shunit2/source/2.0/src/shell/shunit2
+elif [ -e "../shunit2-2.0.3/src/shell/shunit2" ]; then
+    echo try to run the older locally installed shunit2
+    . ../shunit2-2.0.3/src/shell/shunit2
+elif [ -x "$shunit2" ]; then
+    echo run system shunit2
+    . $shunit2
+else
+    echo "Can not find shunit2 - see INSTALL.md"
+fi