From 978d7a92911828b82452118273989b5a9a3d02d9 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 21 Jul 2017 08:34:18 +0000
Subject: github: fix links to gemma repo

---
 INSTALL.md         | 2 +-
 README.md          | 6 +++---
 test/test_suite.sh | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/INSTALL.md b/INSTALL.md
index e4da6ff..05b0eb8 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -23,7 +23,7 @@ dependencies:
 
 ### Bioconda
 
-(Note Bioconda install is a work in [progress](https://github.com/xiangzhou/GEMMA/issues/52)
+(Note Bioconda install is a work in [progress](https://github.com/genetics-statistics/GEMMA/issues/52)
 
 Recent versions of GEMMA can be installed with
 [BioConda](http://ddocent.com/bioconda/) without root permissions using the following
diff --git a/README.md b/README.md
index e196681..a614d0b 100644
--- a/README.md
+++ b/README.md
@@ -10,7 +10,7 @@ models (LMMs) and related models to genome-wide association studies
 Check out [NEWS.md](NEWS.md) to see what's new in each GEMMA release.
 
 Please post comments, feature requests or suspected bugs to
-[Github issues](https://github.com/xiangzhou/GEMMA/issues). We also
+[Github issues](https://github.com/genetics-statistics/GEMMA/issues). We also
 encourage contributions, for example, by forking the repository,
 making your changes to the code, and issuing a pull request.
 
@@ -19,7 +19,7 @@ platforms. *Windows is not currently supported.* If you are interested
 in helping to make GEMMA available on Windows platforms (e.g., by
 providing installation instructions for Windows, or by contributing
 Windows binaries) please post a note in the
-[Github issues](https://github.com/xiangzhou/GEMMA/issues).
+[Github issues](https://github.com/genetics-statistics/GEMMA/issues).
 
 *(The above image depicts physiological and behavioral trait
 loci identified in CFW mice using GEMMA, from [Parker et al, Nature
@@ -199,4 +199,4 @@ University of Michigan<br>
 Peter Carbonetto, Tim Flutre, Matthew Stephens, Pjotr Prins and others
 have also contributed to the development of this software.
 
-[latest_release]: https://github.com/xiangzhou/GEMMA/releases/tag/v0.96 "Most recent stable release"
+[latest_release]: https://github.com/genetics-statistics/GEMMA/releases/tag/v0.96 "Most recent stable release"
diff --git a/test/test_suite.sh b/test/test_suite.sh
index d1dbb3c..2b2ed0f 100755
--- a/test/test_suite.sh
+++ b/test/test_suite.sh
@@ -11,7 +11,7 @@ testCenteredRelatednessMatrixK() {
     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)
+    # FIXME: The following test fails in the Guix build system (https://github.com/genetics-statistics/GEMMA/issues/55)
     assertEquals "24.9799" `awk '{s+=substr($1,0,6)}END{print s}' output/mouse_hs1940.cXX.txt`
 }
 
-- 
cgit v1.2.3


From f4318e5545ad3afbf7b04a248806a4580af8b69b Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 26 Jul 2017 07:46:25 +0000
Subject: Added a line count test for K

---
 test/test_suite.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/test/test_suite.sh b/test/test_suite.sh
index 2b2ed0f..ca13ff7 100755
--- a/test/test_suite.sh
+++ b/test/test_suite.sh
@@ -8,6 +8,7 @@ testCenteredRelatednessMatrixK() {
     assertEquals 0 $?
     grep "total computation time" < output/mouse_hs1940.log.txt
     assertEquals 0 $?
+    assertEquals "1940" `wc -l < output/mouse_hs1940.cXX.txt`
     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`
-- 
cgit v1.2.3


From b31ec4f345979a2fb705fb274f4bac9b7ab0e4fe Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 26 Jul 2017 08:30:32 +0000
Subject: test_suite: replace awk with perl to compute file contents and
 default to shunit2 in repo             fixes
 https://github.com/genetics-statistics/GEMMA/issues/55

---
 test/test_suite.sh | 28 ++++++++++------------------
 1 file changed, 10 insertions(+), 18 deletions(-)

diff --git a/test/test_suite.sh b/test/test_suite.sh
index ca13ff7..821c5bf 100755
--- a/test/test_suite.sh
+++ b/test/test_suite.sh
@@ -8,12 +8,11 @@ testCenteredRelatednessMatrixK() {
     assertEquals 0 $?
     grep "total computation time" < output/mouse_hs1940.log.txt
     assertEquals 0 $?
-    assertEquals "1940" `wc -l < output/mouse_hs1940.cXX.txt`
-    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/genetics-statistics/GEMMA/issues/55)
-    assertEquals "24.9799" `awk '{s+=substr($1,0,6)}END{print s}' output/mouse_hs1940.cXX.txt`
+    outfn=output/mouse_hs1940.cXX.txt
+    assertEquals "1940" `wc -l < $outfn`
+    assertEquals "3763600" `wc -w < $outfn`
+    assertEquals "0.335" `head -c 5 $outfn`
+    assertEquals "24.9799" `perl -nle '$sum += substr($_,0,6) } END { print $sum' $outfn`
 }
 
 testUnivariateLinearMixedModel() {
@@ -23,8 +22,9 @@ testUnivariateLinearMixedModel() {
     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`
+    outfn=output/mouse_hs1940_CD8_lmm.assoc.txt
+    assertEquals "118459" `wc -w < $outfn`
+    assertEquals "92047" `perl -nle '$sum += substr($_,0,6) } END { print $sum' $outfn`
 }
 
 testMultivariateLinearMixedModel() {
@@ -37,19 +37,11 @@ testMultivariateLinearMixedModel() {
 
     outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt
     assertEquals "139867" `wc -w < $outfn`
-    assertEquals "92079" `awk '{s+=substr($1,0,6)}END{print s}' $outfn`
+    assertEquals "92079" `perl -nle '$sum += substr($_,0,6) } END { print $sum' $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
+if [ -e shunit2-2.0.3/src/shell/shunit2 ]; then
     . 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
-- 
cgit v1.2.3


From c91dfaef84d08ce151eecca50bf8ffdaf4b327f6 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 26 Jul 2017 09:06:34 +0000
Subject: test_suite: run shunit2 from system when available

---
 test/test_suite.sh | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/test/test_suite.sh b/test/test_suite.sh
index 821c5bf..ebbe4c7 100755
--- a/test/test_suite.sh
+++ b/test/test_suite.sh
@@ -39,8 +39,13 @@ testMultivariateLinearMixedModel() {
     assertEquals "139867" `wc -w < $outfn`
     assertEquals "92079" `perl -nle '$sum += substr($_,0,6) } END { print $sum' $outfn`
 }
+shunit2=`which shunit2`
 
-if [ -e shunit2-2.0.3/src/shell/shunit2 ]; then
+if [ -x "$shunit2" ]; then
+    echo run system shunit2
+    . $shunit2
+elif [ -e shunit2-2.0.3/src/shell/shunit2 ]; then
+    echo run shunit2 provided in gemma repo
     . shunit2-2.0.3/src/shell/shunit2
 else
     echo "Can not find shunit2 - see INSTALL.md"
-- 
cgit v1.2.3