Mercurial > repos > jbrayet > chipqc_1_0_docker

view ChIPQC_wrapper.sh @ 1:173b23aa37da draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jbrayet
date Fri, 05 Feb 2016 10:07:55 -0500
parents
children
line wrap: on
line source

#!/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