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Last change
on this file since 14065 was 13399, checked in by Daniela Dorner, 13 years ago |
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added (scripts and setup for MC processing)
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-
Property svn:executable
set to
*
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File size:
1.7 KB
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| 1 | #!/bin/bash
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| 2 | #
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| 3 | # This script is launching star for mc sequences.
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| 4 | #
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| 5 |
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| 6 | source `dirname $0`/../Sourcefile.sh
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| 7 | printprocesslog "INFO starting $0"
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| 8 | program=star
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| 9 | step=Star
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| 10 |
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| 11 | set -C
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| 12 |
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| 13 | # get sequence #
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| 14 | numchanged=0
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| 15 | while (( 0 < 21 ))
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| 16 | do
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| 17 | if ! [ $numchanged -eq 1 ]
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| 18 | then
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| 19 | if ! [ "$sequence" = "" ] && ! [ "$cereskey" = "" ]
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| 20 | then
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| 21 | printprocesslog "INFO $program for sequence $sequence cereskey $cereskey is already running => request new number "
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| 22 | fi
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| 23 | gettodo "1"
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| 24 | sequence=${primaries[0]}
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| 25 | cereskey=${primaries[1]}
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| 26 | if [ "$sequence" = "" ] || [ "$cereskey" = "" ]
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| 27 | then
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| 28 | printprocesslog "INFO nothing to do for $program "
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| 29 | fi
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| 30 | else
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| 31 | printprocesslog "INFO starting $program for sequence $sequence cereskey $cereskey"
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| 32 | break
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| 33 | fi
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| 34 | setstatus "start"
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| 35 | done
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| 36 |
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| 37 | cd $mars
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| 38 |
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| 39 | # run calibration for sequence
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| 40 |
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| 41 | # define files and paths
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| 42 | sequfile="$mcsequpath/`printf %08d $sequence | cut -c 1-4`/sequence`printf %08d $sequence`.txt"
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| 43 | outpath=$mcpath/$program/`printf %03d $cereskey`/`printf %08d $sequence | cut -c 1-4`/`printf %08d $sequence | cut -c 5-8`
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| 44 | makedir $outpath
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| 45 | log=$outpath/$program`printf %08d $sequence`
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| 46 | inpath=$mcpath/callisto/`printf %03d $cereskey`/`printf %08d $sequence | cut -c 1-4`/`printf %08d $sequence | cut -c 5-8`
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| 47 |
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| 48 | command="./star -b -q -v4 -f --ind=$inpath --out=$outpath --log=$log.log --html=$log.html $sequfile"
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| 49 | printprocesslog "INFO executing "$command
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| 50 | $command
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| 51 | check1=$?
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| 52 |
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| 53 | case $check1 in
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| 54 | 0) printprocesslog "INFO $program finished successfully for sequence $sequence cereskey $cereskey (return code $check1)"
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| 55 | ;;
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| 56 | *) printprocesslog "ERROR $program failed for sequence $sequence cereskey $cereskey (return code $check1)"
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| 57 | check=$check1
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| 58 | ;;
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| 59 | esac
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| 60 |
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| 61 | setstatus "stop"
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| 62 |
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| 63 | finish
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| 64 |
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