Running Common Workflow Language (CWL) workflows on Arvados » History » Version 4
Peter Amstutz, 03/03/2016 07:04 PM
1 | 1 | Peter Amstutz | h1. Running Common Workflow Language (CWL) workflows on Arvados |
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3 | "Common Workflow Language (CWL)":http://commonwl.org is an emerging standard for describing portable, cross-platform workflows. The Arvados project has been involved in this effort from the very beginning, and is pleased to offer preliminary support for running CWL in Arvados. |
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5 | 2 | Peter Amstutz | The Arvados CWL runner is located at "arvados/sdk/cwl" in the Arvados source tree. The Python package is called "arvados-cwl-runner". You can also install from PyPi: |
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7 | <pre> |
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8 | $ pip install arvados-cwl-runner |
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9 | </pre> |
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11 | 4 | Peter Amstutz | If you are using a shell account on a Curoverse-hosted cluster, your environment is already set up. Otherwise, first "set up your environment":http://doc.arvados.org/user/reference/api-tokens.html (see also [[Arvswitch]] to help manage your Arvados credentials.) |
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13 | If a pipeline inputs refer to local files, they will be uploaded before running the pipeline. You can also reference files already in Keep by prefixing "keep:" for example "keep:d341a6f1db391a780d694e240e95e475+3805/lobstr_v3.0.2_hg19_ref/lobSTR_ref.fasta". |
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15 | 3 | Peter Amstutz | See the "lobSTR":https://github.com/common-workflow-language/workflows/blob/master/workflows/lobSTR/ pipeline for an example. |