https://github.com/inab/vre_wfexs_executor
WfExS tool job executor for VRE (under development)
https://github.com/inab/vre_wfexs_executor
cwl nextflow ro-crate tool vre wfexs wrapper
Last synced: about 2 months ago
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WfExS tool job executor for VRE (under development)
- Host: GitHub
- URL: https://github.com/inab/vre_wfexs_executor
- Owner: inab
- License: apache-2.0
- Created: 2020-04-30T10:40:26.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2021-07-08T14:55:47.000Z (almost 4 years ago)
- Last Synced: 2025-01-06T07:25:37.432Z (4 months ago)
- Topics: cwl, nextflow, ro-crate, tool, vre, wfexs, wrapper
- Language: Python
- Homepage: https://github.com/inab/openVRE
- Size: 282 KB
- Stars: 0
- Watchers: 8
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# VRE WfExS 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_WfExS_executor.git
cd vre_container_executor
```
Create the Python environment:
```bash
python3 -m venv venv
source venv/bin/activate
pip install --upgrade wheel
pip install -r requirements.txt
```
## Run the Wrapper
First, go to [tests/basic/](https://github.com/inab/vre_WfExS_executor/tree/master/tests/basic) to change `config.json` and `in_metadata.json` files.
```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
* © 2020-2021 Barcelona Supercomputing Center (BSC), ES
Licensed under the Apache License, version 2.0 , see the file `LICENSE.txt` for details.