details: http://www.bx.psu.edu/hg/galaxy/rev/aa84d012cb50 changeset: 3806:aa84d012cb50 user: fubar/ross period lazarus at gmail d0t com date: Sat May 22 20:04:38 2010 -0400 description: Require 2 paths for rgtest.sh This script will overwrite all the snp/wga test outputs if you ask it to diffstat: tools/rgenetics/rgtest.sh | 27 +++++++++++++++++++++++---- 1 files changed, 23 insertions(+), 4 deletions(-) diffs (41 lines): diff -r 88afe0a30dc7 -r aa84d012cb50 tools/rgenetics/rgtest.sh --- a/tools/rgenetics/rgtest.sh Fri May 21 16:53:42 2010 -0400 +++ b/tools/rgenetics/rgtest.sh Sat May 22 20:04:38 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?