|
Last change
on this file since 19536 was 13399, checked in by Daniela Dorner, 13 years ago |
|
added (scripts and setup for MC processing)
|
-
Property svn:executable
set to
*
|
|
File size:
1.7 KB
|
| Line | |
|---|
| 1 | #!/bin/bash
|
|---|
| 2 | #
|
|---|
| 3 | # This script is launching star for mc sequences.
|
|---|
| 4 | #
|
|---|
| 5 |
|
|---|
| 6 | source `dirname $0`/../Sourcefile.sh
|
|---|
| 7 | printprocesslog "INFO starting $0"
|
|---|
| 8 | program=star
|
|---|
| 9 | step=Star
|
|---|
| 10 |
|
|---|
| 11 | set -C
|
|---|
| 12 |
|
|---|
| 13 | # get sequence #
|
|---|
| 14 | numchanged=0
|
|---|
| 15 | while (( 0 < 21 ))
|
|---|
| 16 | do
|
|---|
| 17 | if ! [ $numchanged -eq 1 ]
|
|---|
| 18 | then
|
|---|
| 19 | if ! [ "$sequence" = "" ] && ! [ "$cereskey" = "" ]
|
|---|
| 20 | then
|
|---|
| 21 | printprocesslog "INFO $program for sequence $sequence cereskey $cereskey is already running => request new number "
|
|---|
| 22 | fi
|
|---|
| 23 | gettodo "1"
|
|---|
| 24 | sequence=${primaries[0]}
|
|---|
| 25 | cereskey=${primaries[1]}
|
|---|
| 26 | if [ "$sequence" = "" ] || [ "$cereskey" = "" ]
|
|---|
| 27 | then
|
|---|
| 28 | printprocesslog "INFO nothing to do for $program "
|
|---|
| 29 | fi
|
|---|
| 30 | else
|
|---|
| 31 | printprocesslog "INFO starting $program for sequence $sequence cereskey $cereskey"
|
|---|
| 32 | break
|
|---|
| 33 | fi
|
|---|
| 34 | setstatus "start"
|
|---|
| 35 | done
|
|---|
| 36 |
|
|---|
| 37 | cd $mars
|
|---|
| 38 |
|
|---|
| 39 | # run calibration for sequence
|
|---|
| 40 |
|
|---|
| 41 | # define files and paths
|
|---|
| 42 | sequfile="$mcsequpath/`printf %08d $sequence | cut -c 1-4`/sequence`printf %08d $sequence`.txt"
|
|---|
| 43 | outpath=$mcpath/$program/`printf %03d $cereskey`/`printf %08d $sequence | cut -c 1-4`/`printf %08d $sequence | cut -c 5-8`
|
|---|
| 44 | makedir $outpath
|
|---|
| 45 | log=$outpath/$program`printf %08d $sequence`
|
|---|
| 46 | inpath=$mcpath/callisto/`printf %03d $cereskey`/`printf %08d $sequence | cut -c 1-4`/`printf %08d $sequence | cut -c 5-8`
|
|---|
| 47 |
|
|---|
| 48 | command="./star -b -q -v4 -f --ind=$inpath --out=$outpath --log=$log.log --html=$log.html $sequfile"
|
|---|
| 49 | printprocesslog "INFO executing "$command
|
|---|
| 50 | $command
|
|---|
| 51 | check1=$?
|
|---|
| 52 |
|
|---|
| 53 | case $check1 in
|
|---|
| 54 | 0) printprocesslog "INFO $program finished successfully for sequence $sequence cereskey $cereskey (return code $check1)"
|
|---|
| 55 | ;;
|
|---|
| 56 | *) printprocesslog "ERROR $program failed for sequence $sequence cereskey $cereskey (return code $check1)"
|
|---|
| 57 | check=$check1
|
|---|
| 58 | ;;
|
|---|
| 59 | esac
|
|---|
| 60 |
|
|---|
| 61 | setstatus "stop"
|
|---|
| 62 |
|
|---|
| 63 | finish
|
|---|
| 64 |
|
|---|
Note:
See
TracBrowser
for help on using the repository browser.
