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README.md

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# cwl-utils
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A collection of scripts to demonstrate the use of the [new Python classes for loading and parsing CWL v1.0 documents](https://github.com/common-workflow-language/cwl-utils/blob/master/cwl_utils/parser_v1_0.py).
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`cwl_utils/parser_v1_0.py` was created via
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`schema-salad-tool --codegen python https://github.com/common-workflow-language/common-workflow-language/raw/master/v1.0/CommonWorkflowLanguage.yml`
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A collection of scripts to demonstrate the use of the new Python classes for
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loading and parsing [CWL v1.0 ](https://github.com/common-workflow-language/cwl-utils/blob/main/cwl_utils/parser/v1_0.py),
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[CWL v1.1](https://github.com/common-workflow-language/cwl-utils/blob/main/cwl_utils/parser/v1_1.py),
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and [CWL v1.2](https://github.com/common-workflow-language/cwl-utils/blob/main/cwl_utils/parser/v1_2.py)
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documents.
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## Install
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Requires Python 3.6.x or Python 3.7
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Requires Python 3.6+
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``` bash
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git clone https://github.com/common-workflow-language/cwl-utils.git
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virtualenv -p python3.6 venv3.6
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virtualenv -p python3.6 venv3.6 # Python 3.7, 3.8, or 3.9 would also work
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source venv3.6/bin/activate
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pip install cwl-utils
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```
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or install the latest development version of `cwl-utils`
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``` bash
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git clone https://github.com/common-workflow-language/cwl-utils.git
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cd cwl-utils
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virtualenv -p python3.6 venv3.6 # Python 3.7, 3.8, or 3.9 would also work
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source venv3.6/bin/activate
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pip install .
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```
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## Usage
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### Pull the image with Docker
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### Pull the all referenced software container images
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This is the default behaviour:
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`docker_extract.py` is useful to cache or pre-pull all software container images
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referenced in a CWL CommandLineTool or CWL Workflow (including all referenced
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CommandLineTools and sub-Workflows and so on).
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The default behaviour is to use the Docker engine to download and save the software
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container images in Docker format.
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```bash
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python docker_extract.py DIRECTORY path_to_my_workflow.cwl
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```
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### Pull the image with Singularity
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Or you can use the Singularity software container engine to download and save the
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software container images and convert them to the Singularity format at the same
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time.
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```bash
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python docker_extract.py --singularity DIRECTORY path_to_my_workflow.cwl
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```
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## Regenerate
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## Development
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To regenerate install `schema_salad` package and run:
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### Regenerate parsers
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To regenerate install the `schema_salad` package and run:
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`cwl_utils/parser_v1_0.py` was created via
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`schema-salad-tool --codegen python https://github.com/common-workflow-language/common-workflow-language/raw/main/v1.0/CommonWorkflowLanguage.yml`
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`cwl_utils/parser_v1_1.py` was created via
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`schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.1/raw/main/CommonWorkflowLanguage.yml`
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`cwl_utils/parser_v1_2.py` was created via
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`schema-salad-tool --codegen python https://github.com/common-workflow-language/cwl-v1.2/raw/main/CommonWorkflowLanguage.yml`
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```
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schema-salad-tool --codegen python \
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https://raw.githubusercontent.com/common-workflow-language/common-workflow-language/master/v1.0/CommonWorkflowLanguage.yml
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```
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## Release
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### Release
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To release CWLUtils, bump the version in `cwl_utils/__meta__.py`, and tag that commit with the new version. TravisCI should release that tag.
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To release CWLUtils, bump the version in `cwl_utils/__meta__.py`, and tag that
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commit with the new version. TravisCI should release that tag.

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