Build docker from local sources

[naittaleb]

close #157

These PR includes:

• The Dockerfile uses COPY to use the local source files instead of passing a branch name as a parameter
• A minimal documentation on how to build and run the docker image
• Add a text editor in the docker image to facilitate debugging

[jlegrand62]

I am ok with the changes.

I see two changes on stuff I did to ease the work of "biologist", so I will let them argue if they still need it:

1. you removed (again) the dev approach that speeds up the test of the docker build by creating a base image (useful for debug)
2. you did not copy/transpose the 'git update' mechanism (run.sh) and we will have to rebuild the image from scratch every time (or hope that the docker build cache will save time for us)

[jlegrand62]

By what mechanism the CI server has up-to-date local copies of each required repo and know the branches to use in the build ?!

[naittaleb]

By what mechanism the CI server has up-to-date local copies of each required repo and know the branches to use in the build ?!

For each pull_request, an action checkout is performed and the right branch is synchronized.

[naittaleb]

I am ok with the changes.

I see two changes on stuff I did to ease the work of "biologist", so I will let them argue if they still need it:

1. you removed (again) the dev approach that speeds up the test of the docker build by creating a base image (useful for debug)
2. you did not copy/transpose the 'git update' mechanism (run.sh) and we will have to rebuild the image from scratch every time (or hope that the docker build cache will save time for us)

As discussed during the meeting a cache mechanism could speed up the docker build and a nightly build will be performed every time new commits are pulled from dev