update version for cwltool after merged PR for singularity

README.md

@@ -44,7 +44,6 @@ is expected at the end of the image name._
 
 ## Setting up virtual environment for Toil
 
-
 ### Initialize your virtual environment
 
 To set up and environment for Toil on Tars, follow the the following instructions:
@@ -84,7 +83,7 @@ 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 --upgrade -e git+https://github.com/drkennetz/cwltool.git@singularity23_fix#egg=cwltool  # This will change soon
+(your-toil-venv)$ pip install --upgrade cwltool==1.0.20190603140227
 (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
 ```
 

requirements.txt

@@ -7,7 +7,7 @@ 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
+cwltool==1.0.20190603140227
 decorator==4.4.0
 dill==0.2.7.1
 docker==2.5.1