make a useable docker image as the starting point for Shilpa's pipeline

[cschin]

see notes/NoteToShlipa.txt and the diff to understand how to handle various setup for running the pipeline smoothly.

1. using the python code (pipeline.py) to call subprocess shell may messup shell environment, at least DV docker won't run proper in my test
2. As Shilpa code have many hard-coded relative paths to the excutables, please follow the following exactly

   mkdir -p /wd/dipasm/
   git clone https://github.com/shilpagarg/DipAsm.git
   # swith to a proper brach in nessary
   cd /wd/dipasm/DipAsm/docker
   docker build -t dipasm .
   cd /wd/dipasm/DipAsm
   docker run -it --rm -v  /wd/dipasm/DipAsm:/wd/dipasm/DipAsm/ -v /var/run/docker.sock:/var/run/docker.sock dipasm:latest /bin/bash

   note the mount point setting "-v /wd/dipasm/DipAsm:/wd/dipasm/DipAsm/" and "-v /var/run/docker.sock:/var/^Cn/docker.sock".

Both should be followed exactly as-is. The second one make it possible to call another docker container (in this case DV) inside the docker container. The first is also important to DV. When one excutate docker container insider a docker container, the new container actually see the host file system not the contatiner file system

2. test run with docker In the container:

cd /wd/dipasm/DipAsm bash test.sh | bash

[lh3]

Thanks so much, @cschin. I guess by -v /var/run/docker.sock:/var/^Cn/docker.sock you mean -v /var/run/docker.sock:/var/run/docker.sock.

[cschin]

Thanks so much, @cschin. I guess by -v /var/run/docker.sock:/var/^Cn/docker.sock you mean -v /var/run/docker.sock:/var/run/docker.sock.

yes, your right. working on different OS/keyboard... can't type it right