Changeset 83:b20402a843c1

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Timestamp:
02/16/07 16:21:24 (2 years ago)
Author:
Nate Coraor <nate@bx.psu.edu>
branch:
default
convert_revision:
svn:9bcadc22-80f8-0310-8a53-c8f022958886/galaxy/trunk@1366
Message:

Made run.sh Bourne-friendly and added path fix for cluster nodes.

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  • lib/galaxy/jobs/runners/pbs.py

    r78 r83  
    136136 
    137137        # write the job script 
    138         script = pbs_template % (os.environ['LC_ALL'], os.environ['PATH'], os.environ['PYTHONPATH'], exec_dir, command_line) 
     138        script = pbs_template % (os.environ['LC_ALL'], os.environ['NODEPATH'], os.environ['PYTHONPATH'], exec_dir, command_line) 
    139139        job_file = "%s/database/pbs/%s.sh" % (os.getcwd(), job_name) 
    140140        fh = file(job_file, "w") 

  • run.sh

    r51 r83  
    33## Set MACHTYPE to something,  
    44MACHTYPE=`uname -m` 
    5 if [[ $MACHTYPE = "Power Macintosh" ]]; then MACHTYPE="powerpc"; fi 
    6 export MACHTYPE  
    7 export LC_ALL=POSIX 
     5[ "$MACHTYPE" = "Power Macintosh" ] && MACHTYPE="powerpc" 
     6LC_ALL=POSIX 
     7export MACHTYPE LC_ALL 
    88 
    99KERNEL=`uname -s | tr "A-Z" "a-z"` 
    …… 
    1212echo "Architecture appears to be $ARCH" 
    1313 
    14 export UNIVERSE_HOME=`pwd` 
    15 export PATH=$PATH:/depot/apps/$MACHTYPE/bin:/home/universe/$ARCH/EMBOSS/EMBOSS-3.0.0/bin:/home/universe/$ARCH/EMBOSS/bin:/home/universe/$ARCH/ImageMagick/bin:/home/universe/$ARCH/PAML/paml3.15/bin 
    16 export PYTHONPATH=$UNIVERSE_HOME/lib:$UNIVERSE_HOME/eggs 
     14UNIVERSE_HOME=`pwd` 
     15PYTHONPATH=$UNIVERSE_HOME/lib:$UNIVERSE_HOME/eggs 
     16export UNIVERSE_HOME PYTHONPATH 
     17 
     18## For PBS - if you need to force node paths (i.e. the arch the frontend 
     19## runs on is not the same arch as the compute nodes or Galaxy is 
     20## installed in a different path on the node). 
     21#NODEMACH="i686" 
     22#NODEARCH="linux-i686" 
     23#NODEPATH=$PATH 
     24 
     25## Certain tools (EMBOSS, PAML...) are not distributed with Galaxy. 
     26## If you have them installed, add their bin directories to the PATH. 
     27PATH=$PATH:/depot/apps/$MACHTYPE/bin:/home/universe/$ARCH/EMBOSS/bin:/home/universe/$ARCH/ImageMagick/bin:/home/universe/$ARCH/PAML/paml3.15/bin 
     28 
     29## NODEPATH defaults to $PATH 
     30: ${NODEPATH:=$PATH} 
     31 
     32export PATH NODEPATH 
    1733 
    1834echo "python path: $PYTHONPATH"