Mercurial > repos > jbrayet > chipqc_1_0_docker
changeset 1:173b23aa37da draft
Uploaded
| author | jbrayet |
|---|---|
| date | Fri, 05 Feb 2016 10:07:55 -0500 |
| parents | b8e8b0a4b41c |
| children | 0c3402cdee70 |
| files | ChIPQC_wrapper.sh |
| diffstat | 1 files changed, 23 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ChIPQC_wrapper.sh Fri Feb 05 10:07:55 2016 -0500 @@ -0,0 +1,23 @@ +#!/bin/bash + + +while getopts "f:c:m:o:s:u:p:" optionName; do +case "$optionName" in + +f) CHIPFILE="$OPTARG";; +c) CONTROLFILE="$OPTARG";; +m) MINVAL="$OPTARG";; +s) MAXVAL="$OPTARG";; +o) OUTPUT="$OPTARG";; +u) OUTSTAT="$OPTARG";; +p) PDF="$OPTARG";; + +esac +done + +local_path=/usr/bin/ChIPQC +R_PATH='Rscript --slave ' + +echo "$R_PATH $local_path/ChIPQC.R --args $MINVAL $MAXVAL $CHIPFILE $CONTROLFILE $OUTPUT $OUTSTAT $PDF" +$R_PATH $local_path/ChIPQC.R --args $MINVAL $MAXVAL $CHIPFILE $CONTROLFILE $OUTPUT $OUTSTAT $PDF +