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Revision as of 18:13, 19 October 2014
, 18:13, 19 October 2014→Command-Line Options
* help - print usage
* help - print usage
* test OUTPUT_DIR - run the test example placing the output in a user specified OUTPUT_DIR. No other options are required.
* test OUTPUT_DIR - run the test example placing the output in a user specified OUTPUT_DIR. No other options are required.
* out_dir OUTPUT_DIR - directory for the output
* outdir OUTPUT_DIR - directory for the output
** May also be specified via OUT_DIR in the configuration file
** May also be specified via OUT_DIR in the configuration file
** Required to be set either via command-line or configuration
** Required to be set either via command-line or configuration
* conf CONFIG_FILE - configuration file
* conf CONFIG_FILE - configuration file
* index_file INDEX_FILE_NAME - name of the index file
* list FASTQ_LIST_FILE_NAME - name of the fastq list file
** May also be specified via INDEX_FILE in the configuration file
** May also be specified via FASTQ_LIST in the configuration file
** Required to be set either via command-line or configuration
** Required to be set either via command-line or configuration
* ref_dir REFERENCE_DIR - value to set config key REF_DIR to, overriding other values, REF_DIR can then be used inside config files.
* ref_dir REFERENCE_DIR - value to set config key REF_DIR to, overriding other values, REF_DIR can then be used inside config files.
** May also be specified via REF_DIR in the configuration file
** May also be specified via REF_DIR in the configuration file
* fastq FASTQ_PATH - prefix path to the fastq files specified in the INDEX_FILE
* ref_prefix REFERENCE_DIR - path to prepend to non-absolute REF paths.
** May also be specified via FASTQ in the configuration file
** May also be specified via REF_PREFIX in the configuration file
* fastq_prefix FASTQ_PATH - prefix path to the fastq files specified in the FASTQ_LIST
** May also be specified via FASTQ_PREFIX in the configuration file
* base_prefix BASE_PATH - prefix path to the prepend to fastq/ref files without absolute paths
** May also be specified via BASE_PREFIX in the configuration file
* keepTmp - Do not remove the temporary files (removed by default)
* keepTmp - Do not remove the temporary files (removed by default)
** May also be specified via KEEP_TMP in the configuration file
** May also be specified via KEEP_TMP in the configuration file
* numcs N - Replace N with the number of samples that should be processed in parallel
* keepLog - Do not remove the intermediate log files (removed by default)
* numjobs N - Replace N with the number of targets in each makefile that should be run in parallel
** May also be specified via KEEP_LOG in the configuration file
* numjobs N - Replace N with the number of samples that should be processed in parallel
* threads N - Replace N with the number of targets in each makefile that should be run in parallel
* dryrun - Create the Makefile, but do not run it
* maxlocaljobs N - Replace N with the maximum number of jobs that can be run locally (no batchtype specified). Default is 10.
* batchtype TYPE - Tells GotCloud the specified batch type to send jobs to the client nodes
** May also be specified via BATCH_TYPE in the configuration file
** Can be: mosix, slurm, slurmi, pbs, sge, sgei
* batchopts OPTS - Tells GotCloud the options to pass onto the batch system
** May also be specified via BATCH_OPTS in the configuration file
* noPhoneHome - disable the phone home logic
* gotcloudroot DIR - Specifies an alternate path to other gotcloud files rather than using the path to the gotcloud/align.pl.
Note: Command-line options take priority over configuration file settings
Note: Command-line options take priority over configuration file settings
