OC-manual-page.rst

Manual Page

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

oc run | Run a job

Positional argument: input - Input file(s). One or more variant files in a supported format.

Optional arguments: |Option|Description| |--------|---------------------------------| | -h, --help | show 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|

report | Generate a report from a job

oc report is used to generate output reports

Positional argument: dbpath - Path to aggregator output

Optional arguments: |Option|Description| |--------|---------------------------------| | -h, --help | show 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|

gui | Start the GUI

Positional argument: result - Path to a CRAVAT result SQLite file

Optional arguments: |Option|Description| |--------|---------------------------------| | -h, --help show this 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|

module | Change installed modules

View, install, inspect, and uninstall modules

Commands: |Command|Description| |--------|---------------------------------| | ls | List modules| | install | Install modules| | uninstall | Uninstall modules| | update | Update modules| | info | Module details| | install-base | Install base modules|

config | Configuration settings

View and change configuration settings

Commands: |Command|Description| |--------|---------------------------------| | md | Change modules directory| | system | Show system config| | cravat | Show cravat config|

new | Create new modules

Create new annotator, and generate an example input file.

Commands: |Command|Description| |--------|---------------------------------| | example-input | Make example input file| | annotator | Create new annotator|

store | Publish modules to the store

Publish modules to the store

Commands: |Command|Description| |--------|---------------------------------| |publish|Publish a module| |new-account|Create an account| |change-pw|Change password| |reset-pw|Request password reset| |verify-email|Request email verification| |check-login|Check login credentials|

util | Utilities

Utilities to test modules, update results databases, and send command line jobs to the GUI.

Commands: |Command|Description| |--------|---------------------------------| | test| Test installed modules| | update-result| Update old result database to newer format| | send-gui| Copy a command line job into the GUI submission list|

version | Show version

oc version displays the currently installed version of OpenCRAVAT

feedback | Send feedback to the developers

oc feedback opens the GitHub issues tracker at https://github.com/KarchinLab/open-cravat/issues.