1 files changed, 54 insertions, 0 deletions
diff --git a/test/lengthy_test_suite.sh b/test/lengthy_test_suite.sh
new file mode 100755
index 0000000..327b2b2
--- /dev/null
+++ b/test/lengthy_test_suite.sh
@@ -0,0 +1,54 @@
+#!/usr/bin/env bash
+#
+# Long running tests go here
+
+gemma=../bin/gemma
+
+testPlinkStandardRelatednessMatrixK() {
+    testname=testPlinkStandardRelatednessMatrixK
+    datadir=../example
+    outfn=output/$testname.sXX.txt
+    rm -f $outfn
+    $gemma -bfile $datadir/HLC \
+           -gk 2 -o $testname \
+           -debug
+    assertEquals 0 $?
+    assertEquals "427" `wc -l < $outfn`
+    assertEquals "-358.07" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+}
+
+testPlinkMultivariateLinearMixedModelMultiplePhenotypes_Issue58() {
+    # This test passes, but takes over 30 minutes to run!
+    # n=2 is original pheno in fam file
+    # n=1 is causal1
+    # n=3..12 is causal2
+    # n=13..22 is causal3
+    # -n 1 2 3 15 is independent
+    testname=testPlinkMultivariateLinearMixedModelMultiplePhenotypes
+    datadir=../example
+    $gemma -bfile $datadir/HLC \
+           -p $datadir/HLC.simu.pheno.txt \
+           -k output/testPlinkStandardRelatednessMatrixK.sXX.txt \
+           -lmm 1 \
+           -maf 0.1 \
+           -n 1 2 3 15 \
+           -c $datadir/HLC_covariates.txt \
+           -debug \
+           -o $testname
+    assertEquals 0 $?
+    outfn=output/$testname.assoc.txt
+    assertEquals "223243" `wc -l < $outfn`
+    assertEquals "89754977983.69" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+}
+
+shunit2=`which shunit2`
+
+if [ -x "$shunit2" ]; then
+    echo run system shunit2
+    . $shunit2
+elif [ -e ../contrib/shunit2-2.0.3/src/shell/shunit2 ]; then
+    echo run shunit2 provided in gemma repo
+    . ../contrib/shunit2-2.0.3/src/shell/shunit2
+else
+    echo "Can not find shunit2 - see INSTALL.md"
+fi