https://github.com/inab/vre_cwl_executor
Generic CWL tool job executor for VRE
https://github.com/inab/vre_cwl_executor
cwl-workflows cwltool ro-crate tool vre wrapper
Last synced: 11 months ago
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Generic CWL tool job executor for VRE
- Host: GitHub
- URL: https://github.com/inab/vre_cwl_executor
- Owner: inab
- License: apache-2.0
- Created: 2020-01-03T13:38:24.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2022-08-31T10:39:35.000Z (almost 4 years ago)
- Last Synced: 2025-04-12T12:42:43.941Z (about 1 year ago)
- Topics: cwl-workflows, cwltool, ro-crate, tool, vre, wrapper
- Language: Python
- Homepage: https://github.com/inab/openVRE
- Size: 4.04 MB
- Stars: 0
- Watchers: 9
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
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README
# VRE CWL Tool Executor
## Requirements
- Python 3.6 or later
- [git](https://git-scm.com/downloads)
- [singularity](https://sylabs.io/singularity/)
```bash
sudo apt update
sudo apt install python3
sudo apt install git
```
In order to install the Python dependencies you need `pip` and `venv` modules.
```bash
sudo apt install python3-pip python3-venv
```
## Installation
Directly from GitHub:
```bash
cd $HOME
git clone https://github.com/inab/vre_cwl_executor.git
cd vre_cwl_executor
```
Create the Python environment:
```bash
python3 -m venv venv
source venv/bin/activate
pip install --upgrade pip wheel
pip install -r requirements.txt
```
## Run the Wrapper
```bash
./VRE_RUNNER --config tests/basic/config.json --in_metadata tests/basic/in_metadata.json --out_metadata out_metadata.json --log_file VRE_RUNNER.log
```
## License
* © 2020-2022 Barcelona Supercomputing Center (BSC), ES
Licensed under the Apache License [Version 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file `LICENSE` for details.