The root command oc is used in combination with several keywords to
run OpenCRAVAT on the terminal.
| Option | Description |
|---|---|
| -h | Shows help message. |
| run | Run a job |
| report | Generate a report from a job |
| gui | Start the GUI |
| module | Change installed modules |
| config | View and change configuration settings |
| new | Create new modules |
| store | Publish modules to the store |
| util | Utilities |
| version | Show version |
| feedback | Send feedback to the developers |
Positional argument: input - Input file(s). One or more variant files in a supported format.
this help message and exit| | -a ANNOTATORS [ANNOTATORS ...]. | annotators to run| | -e EXCLUDES [EXCLUDES ...] | annotators to exclude| | -n RUN_NAME | name of cravat run| | -d OUTPUT_DIR | directory for output files| | --startat [STAGE] | starts at given stage {converter,mapper,annotator,aggregator,postaggregator,reporter}| | --repeat [STAGE] | forces re-running of given stage if it is in the run chain. {converter,mapper,annotator,aggregator,postaggregator,reporter}| | --endat [STARGE] | ends after given stage.{converter,mapper,annotator,aggregator,postaggregator,reporter}| --skip [STAGE] | Skips given stage(s). {converter,mapper,annotator,aggregator,postaggregator,reporter}| | -c CONF | path to a conf file| | --cs CONFS | configuration string| | -v | verbose| | -t {excel,tsv,vcf,text,csv} | [{excel,tsv,vcf,text,csv} ...] report types. If omitted, default one in cravat.yml is used.| | -l {hg38,hg19,hg18} | reference genome of input. CRAVAT will lift over to hg38 if needed.| | -x | deletes the existing result database and creates a new one.| | --newlog | deletes the existing log file and creates a new one.| | --note NOTE | note will be written to the run status file | | --mp MP | number of processes to use to run annotators | | -i {cravat,vcf,oldcravat}, | --input-format {cravat,vcf,oldcravat} Force input format| | --temp-files | Leave temporary files after run is complete.| | --writeadmindb | Write job information to admin db after job completion| | --jobid JOBID | Job ID for server version| | --version | Shows open-cravat version.| | --separatesample | Separate variant results by sample|
oc report is used to generate output reports
Positional argument: dbpath - Path to aggregator output
this help message and exit| | -t [FORMAT] | report types, {excel,csv,tsv,text,vcf}| | -f FILTERPATH | Path to filter file| | -F FILTERNAME | Name of filter (stored in aggregator output)| | -s SAVEPATH | Path to save file| | -c CONFPATH | path to a conf file| | --module-name MODULE_NAME | report module name| | --nogenelevelonvariantlevel | Use this option to prevent gene level result from being added to variant level result.| | --confs CONFS | Configuration string| | --inputfiles INPUTFILES [INPUTFILES ...] | Original input file path| | --separatesample | Write each variant-sample pair on a separate line| | -d OUTPUT_DIR | directory for output files|
Positional argument: result - Path to a CRAVAT result SQLite file
help message and exit| | --multiuser | Runs in multiuser mode| | --headless | do not open the cravat web page| | --http-only | Force not to accept https connection| | --debug | Console echoes exceptions written to log file|
View, install, inspect, and uninstall modules
update | Update modules| | info | Module details| | install-base | Install base modules|
View and change configuration settings
directory| | system | Show system config| | cravat | Show cravat config|
Create new annotator, and generate an example input file.
example input file| | annotator | Create new annotator|
Publish modules to the store
Utilities to test modules, update results databases, and send command line jobs to the GUI.
oc version displays the currently installed version of OpenCRAVAT
oc feedback opens the GitHub issues tracker at
https://github.com/KarchinLab/open-cravat/issues.
OpenCRAVAT 1.7.0 introduced a single command tree, oc, which
centralizes functions that previously were spread across possible
through multiple command line tools: cravat, wcravat,
cravat-admin, cravat-report, cravat-test, and
cravat-util. The table below maps old commands to the oc tree.
Users are encouraged to shift to using oc. Old root commands will be
deprecated in a later version.
| Old Program | Command | New Command |
|---|---|---|
| cravat | oc run | |
| wcravat | oc gui | |
| cravat-view | oc gui job.sqlite | |
| cravat-report | oc report | |
| cravat-admin | md | oc config md |
| install-base | oc module install-base | |
| install | oc module install | |
| update | oc module update | |
| uninstall | oc module uninstall | |
| info | oc module info | |
| publish | oc store publish | |
| create-account | oc store new-account | |
| reset-password | oc store reset-pw | |
| verify-email | oc store verify-email | |
| check-login | oc store check-login | |
| make-example-input | oc new example-input | |
| new-annotator | oc new annotator | |
| report-issue | oc feedback | |
| show-system-conf | oc config system | |
| show-cravat-conf | oc config cravat | |
| version | oc version | |
| cravat-test | oc util test | |
| cravat-util | migrate-result |