Note
This tool is still under active development, so there could be significant changes to its API.
This repo contains a cromwell_tools Python package and IPython notebooks for interacting with the Cromwell
Install it like this:
pip install git+git://github.com/broadinstitute/cromwell-tools.gitThis package installs a command line interface, which is used as follows:
$> cromwell-tools -h
usage: cromwell-tools [-h] {run,wait,status} ...
positional arguments:
{run,wait,status} sub-command help
run run help
wait wait help
status status help
optional arguments:
-h, --help show this help message and exitSub-commands to start, wait for completion, and determining status of jobs are exposed by this CLI:
- To start a job:
cromwell-tools run -h
usage: cromwell-tools run [-h] [-c CROMWELL_URL] [-u USERNAME] [-p PASSWORD]
[-s SECRETS_FILE] --wdl-file WDL_FILE
[--dependencies-json DEPENDENCIES_JSON]
--inputs-json INPUTS_JSON
[--inputs2-json INPUTS2_JSON]
[--options-file OPTIONS_FILE]
Run a WDL workflow on Cromwell.
optional arguments:
-h, --help show this help message and exit
-c CROMWELL_URL, --cromwell-url CROMWELL_URL
-u USERNAME, --username USERNAME
-p PASSWORD, --password PASSWORD
-s SECRETS_FILE, --secrets-file SECRETS_FILE
--wdl-file WDL_FILE
--dependencies-json DEPENDENCIES_JSON
--inputs-json INPUTS_JSON
--inputs2-json INPUTS2_JSON
--options-file OPTIONS_FILE- To wait for completion of jobs:
$> cromwell-tools wait -h
usage: cromwell-tools wait [-h] [-c CROMWELL_URL] [-u USERNAME] [-p PASSWORD]
[-s SECRETS_FILE] --workflow-ids WORKFLOW_IDS
[WORKFLOW_IDS ...]
[--timeout-minutes TIMEOUT_MINUTES]
[--poll-interval-seconds POLL_INTERVAL_SECONDS]
Wait for one or more running workflow to finish.
optional arguments:
-h, --help show this help message and exit
-c CROMWELL_URL, --cromwell-url CROMWELL_URL
-u USERNAME, --username USERNAME
-p PASSWORD, --password PASSWORD
-s SECRETS_FILE, --secrets-file SECRETS_FILE
--workflow-ids WORKFLOW_IDS [WORKFLOW_IDS ...]
--timeout-minutes TIMEOUT_MINUTES
number of minutes to wait before timeout
--poll-interval-seconds POLL_INTERVAL_SECONDS
seconds between polling cromwell for workflow status- To determine the status(es) of jobs:
cromwell-tools status -h
usage: cromwell-tools status [-h] [-c CROMWELL_URL] [-u USERNAME]
[-p PASSWORD] [-s SECRETS_FILE] --workflow-ids
WORKFLOW_IDS [WORKFLOW_IDS ...]
Get the status of one or more workflows.
optional arguments:
-h, --help show this help message and exit
-c CROMWELL_URL, --cromwell-url CROMWELL_URL
-u USERNAME, --username USERNAME
-p PASSWORD, --password PASSWORD
-s SECRETS_FILE, --secrets-file SECRETS_FILE
--workflow-ids WORKFLOW_IDS [WORKFLOW_IDS ...]The rest of the package consists of scripts that are meant to be invoked from the command line.
In Python, you can then import the package with:
from cromwell_tools import cromwell_tools
cromwell_tools.start_workflow(*args)assuming args is a list of arguments needed.
To run tests:
Create and activate a virtualenv with requirements:
virtualenv test-env
pip install -r requirements.txt -r test-requirements.txt
source test-env/bin/activateThen, from the root of the cromwell-tools repo, do:
python -m unittest discover -vThis runs all the tests in the cromwell_tools package.