Commit e4272556 authored by Kenzo-Hugo Hillion's avatar Kenzo-Hugo Hillion
Browse files

export venv in requirements (not working)

parent 707d6747
......@@ -8,7 +8,6 @@
## Setting up virtual environment for Toil
28/05/2019: _The following instruction will change when different PR will be merged to the main repositories_
### Initialize your virtual environment
......@@ -21,7 +20,17 @@ source your-toil-venv/bin/activate
(your-toil-venv)$ # your are now in your virtual environment
```
### Install Toil
### Install all packages
To install all packages (__This is currently not working since there is a modification of `setup.py` file of toil__):
```bash
(your-toil-venv)$ pip install -r requirements.txt
```
#### How this environment has been created
28/05/2019: _The following instructionis will change when different PR will be merged to the main repositories so it is recommanded to reproduce the environment with the `requirements.txt` file provided_
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).
......@@ -31,9 +40,7 @@ So we need to pull `Toil` repository and modify the `setup.py` prior to manual i
(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
(your-toil-venv)$ pip install .[cwl]
```
### Install cwltool and cwl-utils
......@@ -41,6 +48,14 @@ So we need to pull `Toil` repository and modify the `setup.py` prior to manual i
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
(your-toil-venv)$ pip install --upgrade -e git+https://github.com/drkennetz/cwltool.git@singularity23_fix#egg=cwltool # This will change soon
(your-toil-venv)$ pip install -e git+https://github.com/khillion/cwl-utils.git#egg=cwl_utils # This need to change to to be more stable
```
### Export requirements
Finally the list of requirements for the corresponding virtual environment is exported:
```bash
(your-toil-venv)$ pip freeze > requirements.txt
```
addict==2.2.0
alabaster==0.7.12
Babel==2.7.0
bagit==1.7.0
boltons==19.1.0
CacheControl==0.11.7
certifi==2019.3.9
chardet==3.0.4
-e git+https://github.com/khillion/cwl-utils.git@f7a2fc68d2be6108f6f31dbe4cf4b8ebc949bac7#egg=cwl_utils
-e git+https://github.com/drkennetz/cwltool.git@309919e593380c5c331c50b655d024a5400a7d2f#egg=cwltool
decorator==4.4.0
dill==0.2.7.1
docker==2.5.1
docker-pycreds==0.4.0
docutils==0.14
future==0.17.1
galaxy-lib==18.9.2
idna==2.8
imagesize==1.1.0
isodate==0.6.0
Jinja2==2.10.1
lockfile==0.12.2
lxml==4.3.3
MarkupSafe==1.1.1
mistune==0.8.4
mypy-extensions==0.4.1
networkx==2.3
packaging==19.0
pathlib2==2.3.2
prov==1.5.1
psutil==3.0.1
Pygments==2.4.2
pyparsing==2.4.0
python-dateutil==2.8.0
pytz==2019.1
PyYAML==5.1
rdflib==4.2.2
rdflib-jsonld==0.4.0
requests==2.22.0
ruamel.yaml==0.15.77
scandir==1.10.0
schema-salad==4.2.20190417121603
shellescape==3.4.1
six==1.12.0
snowballstemmer==1.2.1
Sphinx==1.7.5
sphinxcontrib-websupport==1.1.2
toil==3.21.0a1
typing-extensions==3.7.2
urllib3==1.25.3
websocket-client==0.56.0
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