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3 bytes added
, 01:51, 8 January 2013
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| ====Required on Command-Line or in Config File==== | | ====Required on Command-Line or in Config File==== |
| The following Command-Line or Config File Settings must be specified by the user: | | The following Command-Line or Config File Settings must be specified by the user: |
− | * --outdir/OUTDIR= path to desired output directory | + | * --outdir/OUT_DIR= path to desired output directory |
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| ====Targeted/Exome Sequencing Settings==== | | ====Targeted/Exome Sequencing Settings==== |
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| ** WRITE_TARGET_LOCI = TRUE | | ** WRITE_TARGET_LOCI = TRUE |
| * Specify the output sub-directory to store target information, for example: targetDir | | * Specify the output sub-directory to store target information, for example: targetDir |
− | ** Should not be a full path as this will co under the OUTDIR directory. | + | ** Should not be a full path as this will co under the OUT_DIR directory. |
| ** TARGET_DIR = targetDir | | ** TARGET_DIR = targetDir |
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| Replace umake.conf with the approprate path/name of the user's configuration file. | | Replace umake.conf with the approprate path/name of the user's configuration file. |
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− | If <code>OUTDIR</code> is not defined in the configuration file, add <code>--outdir</code> followed by the path to the user's desired output directory. | + | If <code>OUT_DIR</code> is not defined in the configuration file, add <code>--outdir</code> followed by the path to the user's desired output directory. |
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| Update the value following <code>--numjobs</code> to the appropriate number of jobs to be run in parallel. | | Update the value following <code>--numjobs</code> to the appropriate number of jobs to be run in parallel. |