details: http://www.bx.psu.edu/hg/galaxy/rev/72d709b2c198 changeset: 3807:72d709b2c198 user: fubar: ross Lazarus at gmail period com date: Sat May 22 19:47:50 2010 -0400 description: Require two paths for rgtest.sh galaxyroot and outroot test with a /tmp path for outroot...this script will recreate all the snp/wga test outputs if you ask it to - which may or may not be what you want...
diffstat:
tools/rgenetics/rgEigPCA.xml | 2 +- tools/rgenetics/rgtest.sh | 27 +++++++++++++++++++++++---- 2 files changed, 24 insertions(+), 5 deletions(-)
diffs (53 lines):
diff -r 3b8e4af25be2 -r 72d709b2c198 tools/rgenetics/rgEigPCA.xml --- a/tools/rgenetics/rgEigPCA.xml Fri May 21 15:50:49 2010 -0400 +++ b/tools/rgenetics/rgEigPCA.xml Sat May 22 19:47:50 2010 -0400 @@ -48,7 +48,7 @@ <param name="t" value="2" /> <param name="s" value="2" /> <output name='out_file1' file='rgtestouts/rgEigPCA/rgEigPCAtest1.html' ftype='html' compare='diff' lines_diff='195'> - <extra_files type="file" name='rgEigPCAtest1_PCAPlot.pdf' value="rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf" compare="sim_size" delta="30000"/> + <extra_files type="file" name='rgEigPCAtest1_PCAPlot.pdf' value="rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf" compare="sim_size" delta="3000"/> </output> <output name='pca' file='rgtestouts/rgEigPCA/rgEigPCAtest1.txt' compare='diff'/> </test> diff -r 3b8e4af25be2 -r 72d709b2c198 tools/rgenetics/rgtest.sh --- a/tools/rgenetics/rgtest.sh Fri May 21 15:50:49 2010 -0400 +++ b/tools/rgenetics/rgtest.sh Sat May 22 19:47:50 2010 -0400 @@ -1,14 +1,33 @@ #!/bin/sh # script to generate all functional test outputs for each rgenetics tool # could be run at installation to ensure all dependencies are in place? -GALAXYROOT=`pwd` -echo "using $GALAXYROOT" +if test $# -lt 2 +then + echo "We need to agree on 2 parameters - GalaxyRoot and OutRoot - use paths to galaxy and galaxy to re-create all test outputs" + echo "or more prudently, galaxy and /tmp/foo for checking without updating all your test-data" + echo "Exiting with no changes" + exit 1 +fi +if [ $1 ] +then + GALAXYROOT=$1 +else + GALAXYROOT=`pwd` +fi +if [ $2 ] +then + OUTROOT=$2 +else + OUTROOT=`pwd` + OUTROOT="$OUTROOT/test-data" +fi +echo "using $GALAXYROOT as galaxyroot and $OUTROOT as outroot" # change this as needed for your local install INPATH="${GALAXYROOT}/test-data" BINPATH="${GALAXYROOT}/tool-data/rg/bin" TOOLPATH="${GALAXYROOT}/tools/rgenetics" -OROOT="${GALAXYROOT}/test-data/rgtestouts" -NORMALOROOT="${GALAXYROOT}/test-data" +OROOT="${OUTROOT}/test-data/rgtestouts" +NORMALOROOT="${OUTROOT}/test-data" mkdir -p $OROOT rm -rf $OROOT/* # needed for testing - but tool versions should be bumped if this is rerun?