The tensorflow image (which is the base image for our container) https://github.com/tensorflow/tensorflow/blob/master/tensorflow/tools/dockerfiles/dockerfiles/gpu.Dockerfile already contains python 3 https://github.com/tensorflow/tensorflow/blob/e0c681c5c738d8898fd698fc9d27e31c1471b993/tensorflow/tools/dockerfiles/dockerfiles/gpu.Dockerfile#L78 and tensorflow https://github.com/tensorflow/tensorflow/blob/e0c681c5c738d8898fd698fc9d27e31c1471b993/tensorflow/tools/dockerfiles/dockerfiles/gpu.Dockerfile#L98 In our docker file we install python3 https://github.com/yigbt/deepFPlearn/blob/e8f60c4251a4e2252ec094be948742f5523b4224/singularity_container/environment.yml#L7 and tensorflow https://github.com/yigbt/deepFPlearn/blob/e8f60c4251a4e2252ec094be948742f5523b4224/singularity_container/environment.yml#L12 including all their dependencies. We should avoid this. I guess easiest would be use pip instead of conda to get the additional dependencies. For instance by defining the requirements in https://github.com/yigbt/deepFPlearn/blob/master/setup.py and just pip install deepFPlearn.
The tensorflow image (which is the base image for our container) https://github.com/tensorflow/tensorflow/blob/master/tensorflow/tools/dockerfiles/dockerfiles/gpu.Dockerfile already contains python 3 https://github.com/tensorflow/tensorflow/blob/e0c681c5c738d8898fd698fc9d27e31c1471b993/tensorflow/tools/dockerfiles/dockerfiles/gpu.Dockerfile#L78 and tensorflow
https://github.com/tensorflow/tensorflow/blob/e0c681c5c738d8898fd698fc9d27e31c1471b993/tensorflow/tools/dockerfiles/dockerfiles/gpu.Dockerfile#L98
In our docker file we install python3
deepFPlearn/singularity_container/environment.yml
Line 7 in e8f60c4
deepFPlearn/singularity_container/environment.yml
Line 12 in e8f60c4
We should avoid this.
I guess easiest would be use pip instead of conda to get the additional dependencies. For instance by defining the requirements in https://github.com/yigbt/deepFPlearn/blob/master/setup.py and just pip install deepFPlearn.