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:
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 `` prior to manual install:
(your-toil-venv)$ git clone
(your-toil-venv)$ cd toil
(your-toil-venv)$ sed -i 's/cwltool==/cwltool>=/g'
(your-toil-venv)$ sed -i 's/galaxy-lib==/galaxy-lib>=/g'
(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:
(your-toil-venv)$ pip install git+ # This will change soon
(your-toil-venv)$ pip install git+ # This need to change to to be more stable
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment