Commit 775bf846 authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

add documentation about tars-cwl-runner script

parent 9f6599cd
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## Usage
## Description
Here is a little description of what is going on in the `tars-cwl-runner.sh` script.
### Load the right environment
We need to load modules for:
* Python3
* Singularity
* node (used for `javascript` expression within CWL
Then we need to activate the `toil_venv`:
```bash
source ${toil_venv}/bin/activate
```
### Prefetch singularity images
The script is run by the head of the cluster which is the only access point to internet.
We do so to allow the automatic fetching of docker images (that are then built for singularity) and
stored/cached into the `${singularity_imgs_path} folder.
### Run toil
When `cwltool` is used with the `--singularity` option, it can find the singularity images either in ([ref](https://github.com/common-workflow-language/cwltool/pull/1113)):
* `$SINGULARITY_CACHEDIR`
* `$SINGULARITY_PULLFOLDER`
* current directory
_Please note that your image follow a certain nomenclature. For a `repo/image` docker image, the
expected name is `repo-image.img`. Every `:` and `/` are replaced by `-` and the `img` extension
is expected at the end of the image name._
---------
# Maintenance and Development
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