Commit a6a486f2 authored by Holger Brandl's avatar Holger Brandl

use snippet rendering for report if rendr_snippet is on path

parent 59a7297b
......@@ -72,13 +72,19 @@ jlistReport(){
# ## add spin.R
# export PATH=/projects/bioinfo/holger/bioinfo_templates/misc:$PATH
# source $(which spin_utils.sh)
wget --no-check-certificate https://raw.githubusercontent.com/holgerbrandl/datautils/master/bash/CreateJobReport.R
chmod u+x CreateJobReport.R
CreateJobReport.R $joblistFile
# echo "Creating report for $joblistFile"
# echo "reportName='$joblistFile'; devtools::source_url('https://raw.githubusercontent.com/holgerbrandl/datautils/v1.9/bash/CreateJobReport.R',local=T)" | spinsnip $(echo $joblistFile | tr -d ".")
rm CreateJobReport.R
# if [ -n "$(which rend.R)" ]; then
if [ -n "$(type rendr_snippet)" ]; then
curl https://raw.githubusercontent.com/holgerbrandl/datautils/master/bash/CreateJobReport.R 2>&1 2>/dev/null | rendr_snippet ${joblistFile}.report $joblistFile
else
## fall back to plain execution of the report. This will just create a generic Rplots.pdf
wget --no-check-certificate https://raw.githubusercontent.com/holgerbrandl/datautils/master/bash/CreateJobReport.R
chmod u+x CreateJobReport.R
CreateJobReport.R $joblistFile
rm CreateJobReport.R
fi
}
export -f jlistReport
......
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