Mercurial > repos > jbrayet > chipqc_1_0_docker
annotate ChIPQC_wrapper.sh @ 1:173b23aa37da draft
Uploaded
| author | jbrayet |
|---|---|
| date | Fri, 05 Feb 2016 10:07:55 -0500 |
| parents | |
| children |
| rev | line source |
|---|---|
| 1 | 1 #!/bin/bash |
| 2 | |
| 3 | |
| 4 while getopts "f:c:m:o:s:u:p:" optionName; do | |
| 5 case "$optionName" in | |
| 6 | |
| 7 f) CHIPFILE="$OPTARG";; | |
| 8 c) CONTROLFILE="$OPTARG";; | |
| 9 m) MINVAL="$OPTARG";; | |
| 10 s) MAXVAL="$OPTARG";; | |
| 11 o) OUTPUT="$OPTARG";; | |
| 12 u) OUTSTAT="$OPTARG";; | |
| 13 p) PDF="$OPTARG";; | |
| 14 | |
| 15 esac | |
| 16 done | |
| 17 | |
| 18 local_path=/usr/bin/ChIPQC | |
| 19 R_PATH='Rscript --slave ' | |
| 20 | |
| 21 echo "$R_PATH $local_path/ChIPQC.R --args $MINVAL $MAXVAL $CHIPFILE $CONTROLFILE $OUTPUT $OUTSTAT $PDF" | |
| 22 $R_PATH $local_path/ChIPQC.R --args $MINVAL $MAXVAL $CHIPFILE $CONTROLFILE $OUTPUT $OUTSTAT $PDF | |
| 23 |