Commit 74bd744f authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

update README for venv setup

parent 54f34562
......@@ -10,13 +10,37 @@
28/05/2019: _The following instruction will change when different PR will be merged to the main repositories_
### Initialize your virtual environment
To set up and environment for Toil on Tars, follow the the following instructions:
```bash
module load Python/3.7.2
python3 -m venv your-toil-venv
source your-toil-venv/bin/activate
(your-toil-venv)$ pip install toil
(your-toil-venv)$ # your are now in your virtual environment
```
### Install Toil
We want to install a specific version of `cwltool` and `Toil` has its requirements refered to specific version number
(we do the same for galaxy-lib which is used by `Toil` for the dependency resolver).
So we need to pull `Toil` repository and modify the `setup.py` prior to manual install:
```
(your-toil-venv)$ git clone https://github.com/DataBiosphere/toil.git
(your-toil-venv)$ cd toil
(your-toil-venv)$ sed -i 's/cwltool==/cwltool>=/g' setup.py
(your-toil-venv)$ sed -i 's/galaxy-lib==/galaxy-lib>=/g' setup.py
(your-toil-venv)$ pip install .
(your-toil-venv)$ pip install galaxy-lib
```
### Install cwltool and cwl-utils
Since we want specific versions of `cwltool` and `cwl-utils` for the moment, we refer to github repository directly:
```bash
(your-toil-venv)$ pip install git+https://github.com/drkennetz/cwltool.git@singularity23_fix # This will change soon
(your-toil-venv)$ pip install git+https://github.com/khillion/cwl-utils.git # This need to change to to be more stable
```
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