diff options
| -rw-r--r-- | INSTALL.md | 2 | ||||
| -rw-r--r-- | README.md | 6 | ||||
| -rwxr-xr-x | test/test_suite.sh | 30 |
3 files changed, 18 insertions, 20 deletions
@@ -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 @@ -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..ebbe4c7 100755 --- a/test/test_suite.sh +++ b/test/test_suite.sh @@ -8,11 +8,11 @@ testCenteredRelatednessMatrixK() { 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 "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() { @@ -22,8 +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() { @@ -36,19 +37,16 @@ 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' $outfn` } - shunit2=`which shunit2` -if [ -e "../contrib/shunit2/source/2.0/src/shell/shunit2" ]; then - echo try to run the locally installed shunit2 - . ../contrib/shunit2/source/2.0/src/shell/shunit2 -elif [ -e "shunit2-2.0.3/src/shell/shunit2" ]; then - echo try to run the older locally installed shunit2 - . shunit2-2.0.3/src/shell/shunit2 -elif [ -x "$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" fi |