https://github.com/common-workflow-language/cwldep
Common Workflow Language dependency manager
https://github.com/common-workflow-language/cwldep
Last synced: 5 months ago
JSON representation
Common Workflow Language dependency manager
- Host: GitHub
- URL: https://github.com/common-workflow-language/cwldep
- Owner: common-workflow-language
- License: apache-2.0
- Created: 2018-06-29T15:38:03.000Z (almost 7 years ago)
- Default Branch: main
- Last Pushed: 2024-05-06T14:11:33.000Z (12 months ago)
- Last Synced: 2024-11-19T00:47:54.588Z (6 months ago)
- Language: Python
- Size: 31.3 KB
- Stars: 9
- Watchers: 12
- Forks: 3
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
# Common Workflow Language dependency manager
This tool helps you to import tools and workflows from other sources for use in your own workflow.
# Setup
It is highly recommended to setup virtual environment before installing `cwldep`:
```
virtualenv -p python2 venv # Create a virtual environment, can use `python3` as well
source venv/bin/activate # Activate environment before installing `cwldep`
```
Install from PyPi:
```
pip install cwldep
```
Install from source:
```
git clone https://github.com/common-workflow-language/cwldep.git # clone cwldep repo
cd cwldep # Switch to source directory
python setup.py install
cwldep -h # Check if the installation works correctly
```
# Adding file dependencies
```
cwldep add myfile.cwl https://raw.githubusercontent.com/common-workflow-language/workflows/master/tools/samtools-faidx.cwl
```
This will download the CWL file *and its dependencies* to `raw.githubusercontent.com/common-workflow-language/workflows/master/tools`
Include it in your workflow as a relative file reference:
```
steps:
step1:
in: ...
out: ...
run: raw.githubusercontent.com/common-workflow-language/workflows/master/tools/samtools-faidx.cwl
```
# Changing the install target
```
cwldep add --install-to samtools myfile.cwl https://raw.githubusercontent.com/common-workflow-language/workflows/master/tools/samtools-faidx.cwl
```
# Using archives
You can also import archives (.tar.gz, .tar.bz2, and .zip):
```
cwldep add myfile.cwl https://github.com/common-workflow-language/workflows/archive/draft2.tar.gz
```
This will download and extract to the local directory `github.com/common-workflow-language/workflows/archive`
# Using git upstream
You can also import git repositories:
```
cwldep add myfile.cwl https://github.com/common-workflow-language/workflows
```
This will clone into the local directory `github.com/common-workflow-language/workflows`
```
cwldep add --set-version=draft-2 myfile.cwl https://github.com/common-workflow-language/workflows
```
# Installing dependencies
This will install any dependencies listed in `myfile.cwl`
```
cwldep install myfile.cwl
```
# Checking if upstream dependencies have changed
This will report if the upstream dependencies listed in `myfile.cwl` have changed
```
cwldep check myfile.cwl
```
# Updating dependencies
This will install updated dependencies:
```
cwldep update myfile.cwl
```
# Deleting unreferenced dependencies
This will delete any dependencies listed in the ".dep.lock" file that are not referenced by `myfile.cwl`.
```
cwldep clean myfile.cwl
```