[Sashimi-commit] SF.net SVN: sashimi:[5057] trunk/trans_proteomic_pipeline/extern/hpctools/ grid/bin

[<sla...@us...>]

Revision: 5057
          http://sashimi.svn.sourceforge.net/sashimi/?rev=5057&view=rev
Author:   slagelwa
Date:     2010-07-14 20:55:36 +0000 (Wed, 14 Jul 2010)

Log Message:
-----------
Fixed issues with spaces in directory names, cleaned up some of the documentation

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qconvert
    trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qgrid_functions

Modified: trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qconvert
===================================================================
--- trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qconvert	2010-07-14 06:09:00 UTC (rev 5056)
+++ trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qconvert	2010-07-14 20:55:36 UTC (rev 5057)
@@ -127,7 +127,8 @@
 
 # Submit jobs
 for input in $INPUTS; do
-   dir=$(dirname $(rel2abs "$input"))           # base directory of input
+   abs=$(rel2abs "$input")
+   dir=`dirname "$abs"`	                        # base directory of input
    root=$(basename "${input%.*}")               # filename w/o extension
    
    write_qsub "$root.convert.qsub"

Modified: trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qgrid_functions
===================================================================
--- trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qgrid_functions	2010-07-14 06:09:00 UTC (rev 5056)
+++ trunk/trans_proteomic_pipeline/extern/hpctools/grid/bin/qgrid_functions	2010-07-14 20:55:36 UTC (rev 5057)
@@ -202,7 +202,7 @@
 #PBS ${QJOBNAME:+-N $QJOBNAME} ${QQUEUE:+-q $QQUEUE}
 #PBS -S /bin/bash
 #PBS -v PATH 
-#PBS -d $QSUB_DIR
+#PBS -d '$QSUB_DIR'
 #PBS -j oe ${QSUB_LOG:+-o $QSUB_LOG}
 #PBS ${QSUBFLAGS}
 
@@ -302,7 +302,7 @@
 
  Options:
    -h, --help           display this help and exit
-   -params <file>       file containing MS search algorithm parameters 
+   --params <file>      file containing MS search algorithm parameters 
    --dest <dir>         directory as the destination for output files  
    
  [qsub options]         all options following '--' are passed to qsub
@@ -324,7 +324,7 @@
 
 Specify the parameters file to use in the search.  If not provided then the
 program will default to a file named "I<search>.params" in the local current
-directory to use, where I<search> is the name of the search program to invoke.
+directory, where I<search> is the name of the search program to invoke.
 E.g. qtandem will defaults to "tandem.params".
 
 =item B<--dest DIR>
@@ -336,8 +336,9 @@
 
 =back
 
-NOTE: All other options provided will be passed to qsub.  This allows you to 
-be able to provide any additional qsub flags to the submission.
+Finally any options following "--" will be used as additional parameters to
+the qsub command.  So for example to change the queue that the job is submitted
+to you could run the command "qtandem *.mzXML -- -q serial".
 
 =head1 PREREQUSITES
 


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