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− | | + | === Required Options === |
| {| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" | | {| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" |
| ! Command-line Flag !! Configuration Key !! Value Description !! Default Value | | ! Command-line Flag !! Configuration Key !! Value Description !! Default Value |
| |- | | |- |
− | | --help || || print help information || | + | | --outdir ''path'' || OUT_DIR || output directory || |
| |- | | |- |
− | | --test ''path'' || || run the snpcall/ldrefine test and write output to the specified path|| | + | | --list/--bam_list/--bamlist ''file'' || BAM_LIST || path to the [[#BAM List File|BAM List File]] || $(OUT_DIR)/bam.list |
− | |-
| |
− | | --conf ''file'' || || configuration file to use ||
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| |- | | |- |
| | --numjobs ''#'' || || number of jobs to run in parallel || 0 (generate Makefile of steps, but do not run) | | | --numjobs ''#'' || || number of jobs to run in parallel || 0 (generate Makefile of steps, but do not run) |
| + | |} |
| + | |
| + | === Common Options === |
| + | {| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" |
| + | ! colspan="4" | Common Options |
| |- | | |- |
− | | --maxlocaljobs ''#'' || || maximum # of jobs that can run if batchtype is local (to prevent accidentally starting jobs locally that were meant to be on a cluster) || 10
| + | ! Command-line Flag !! Configuration Key !! Value Description !! Default Value |
− | |-
| |
− | | --outdir ''path'' || OUT_DIR || output directory ||
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− | |-
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− | | --list/--bam_list/--bamlist ''file'' || BAM_LIST || path to the [[#BAM List File|BAM List File]] || $(OUT_DIR)/bam.list
| |
| |- | | |- |
| + | | --conf ''file'' || || configuration file to use || |
| + | |} |
| + | |
| + | === Analysis Region Options === |
| + | {| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" |
| + | ! Command-line Flag !! Configuration Key !! Value Description !! Default Value |
| | --chrs ''# #'' || CHRS || pace separated list of chromosomes to process || 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X | | | --chrs ''# #'' || CHRS || pace separated list of chromosomes to process || 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X |
| |- | | |- |
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| format (-end is optional): chr:start-end | | format (-end is optional): chr:start-end |
| | | | | |
| + | |} |
| + | |
| + | === Cluster Options === |
| + | {| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" |
| + | ! Command-line Flag !! Configuration Key !! Value Description !! Default Value |
| + | | --batchtype ''type'' || BATCH_TYPE || name of cluster type || local |
| + | |- |
| + | | --batchopts ''opts'' || BATCH_OPTS || options to pass to the cluster command || |
| + | |- |
| + | | --copyglf ''path'' || COPY_GLF || path to copy glfs to before processing them (path local to remote nodes, maybe in /tmp) || |
| + | |- |
| + | |} |
| + | |
| + | === Test/Debug Options === |
| + | {| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" |
| + | |- |
| + | ! Command-line Flag !! Configuration Key !! Value Description !! Default Value |
| + | |- |
| + | | --help || || print help information || |
| + | |- |
| + | | --test ''path'' || || run the snpcall/ldrefine test and write output to the specified path|| |
| |- | | |- |
− | | --makebasename ''name'' || MAKE_BASE_NAME || basename of the Makefile generated by GotCloud || umake | + | | --verbose || || Add additional messages when reading configuration || |
| + | |} |
| + | |
| + | === Path Options === |
| + | {| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" |
| |- | | |- |
− | | --batchtype ''type'' || BATCH_TYPE || name of cluster type || local
| + | ! Command-line Flag !! Configuration Key !! Value Description !! Default Value |
| |- | | |- |
− | | --batchopts ''opts'' || BATCH_OPTS || options to pass to the cluster command || | + | | --makebasename ''name'' || MAKE_BASE_NAME || basename of the Makefile generated by GotCloud || umake |
| |- | | |- |
| | --bamprefix ''prefix'' || BAM_PREFIX || path to prepend to relative BAM file paths in the BAM list || | | | --bamprefix ''prefix'' || BAM_PREFIX || path to prepend to relative BAM file paths in the BAM list || |
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| | --refdir ''path'' || REF_DIR || value to use for REF_DIR key || $(GOTCLOUD_ROOT)/gotcloud.ref | | | --refdir ''path'' || REF_DIR || value to use for REF_DIR key || $(GOTCLOUD_ROOT)/gotcloud.ref |
| |- | | |- |
− | | --verbose || || Add additional messages when reading configuration || | + | | --gotcloudroot ''path'' || GOTCLOUD_ROOT || specify to use a different directory for finding GotCloud bins/scripts || based on the location of the gotcloud/umake.pl script |
| + | |- |
| + | |} |
| + | |
| + | === Validation Adjustment Options === |
| + | {| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" |
| + | |- |
| + | ! Command-line Flag !! Configuration Key !! Value Description !! Default Value |
| |- | | |- |
− | | --copyglf ''path'' || COPY_GLF || path to copy glfs to before processing them (path local to remote nodes, maybe in /tmp) || | + | | --maxlocaljobs ''#'' || || maximum # of jobs that can run if batchtype is local (to prevent accidentally starting jobs locally that were meant to be on a cluster) || 10 |
| |- | | |- |
| | --ignoresmcheck || IGNORE_SM_CHECK || disable the validation that the Sample name in the BAM file matches the one in the BAM list file || | | | --ignoresmcheck || IGNORE_SM_CHECK || disable the validation that the Sample name in the BAM file matches the one in the BAM list file || |
| |- | | |- |
− | | --gotcloudroot ''path'' || GOTCLOUD_ROOT || specify to use a different directory for finding GotCloud bins/scripts || based on the location of the gotcloud/umake.pl script | + | |} |
| + | |
| + | === Miscellaneous Options === |
| + | {| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1" |
| + | |- |
| + | ! Command-line Flag !! Configuration Key !! Value Description !! Default Value |
| |- | | |- |
| | --nophonehome || || disable phonehome in GotCloud and the tools it calls || | | | --nophonehome || || disable phonehome in GotCloud and the tools it calls || |
| |- | | |- |
| |} | | |} |