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bioinfo
datautils
Commits
a6a486f2
Commit
a6a486f2
authored
Sep 17, 2015
by
Holger Brandl
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use snippet rendering for report if rendr_snippet is on path
parent
59a7297b
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6 deletions
+12
-6
bash/lsf_utils.sh
bash/lsf_utils.sh
+12
-6
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bash/lsf_utils.sh
View file @
a6a486f2
...
...
@@ -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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