{"id":41552761,"url":"https://github.com/ohsu-comp-bio/cwl-tes","last_synced_at":"2026-01-24T04:46:17.263Z","repository":{"id":21482091,"uuid":"93053940","full_name":"ohsu-comp-bio/cwl-tes","owner":"ohsu-comp-bio","description":"cwl-tes submits your tasks to a TES server. 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Task submission is parallelized when possible.\n\n[Funnel](https://ohsu-comp-bio.github.io/funnel) is an implementation of the [GA4GH task execution API](https://github.com/ga4gh/task-execution-schemas). It runs your dockerized tasks on slurm, htcondor, google compute engine, aws batch, etc.\n\n\n## Requirements\n\n* Python 2.7 / 3.5 / 3.6\n\n* [Docker](https://docs.docker.com/)\n\n* [Funnel](https://ohsu-comp-bio.github.io/funnel)\n\n## Quickstart\n\n* Start the task server\n\n```\nfunnel server run\n```\n\n* Run your CWL tool/workflow\n\n```\ncwl-tes --tes http://localhost:8000 tests/hashsplitter-workflow.cwl.yml --input tests/resources/test.txt\n```\n\n## Install\n\nI strongly recommend using a [virtualenv](https://virtualenv.pypa.io/en/stable/#) for installation since _cwl-tes_\ndepends on a specific version of _cwltool_.\n\nInstall from pip:\n\n```\npip install cwl-tes\n```\n\n\nInstall from source:\n\n```\npython setup.py install\n```\n\n\n## Run the v1.0 conformance tests\n\nTo start a funnel server instance automatically and run all of the tests, install [tox](https://github.com/tox-dev/tox/) and run it\n\n```\n$ pip install tox\n$ tox\n```\n\nFor running only the conformance tests in python 2.7:\n\n```\n$ tox -e py27-unit\n```\n\nIn a similar way they can be run on any supported python interpreter.\n\n_A more manual approach:_\n\nDownload the conformance tests:\n\n```\ngit submodule update --init --recursive\n```\n\nStart the funnel server.\n\n```\nfunnel server --config /path/to/config.yaml\n```\n\nMake sure that TMPDIR is specified in the AllowedDirs of your Local storage configuration.\n\nTo run all the tests:\n\n```\n./tests/run_conformance.sh\n```\n\nTo run a specifc test:\n\n```\n./tests/run_conformance.sh 10\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fohsu-comp-bio%2Fcwl-tes","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fohsu-comp-bio%2Fcwl-tes","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fohsu-comp-bio%2Fcwl-tes/lists"}