Update READMEs and update figure for docs

README.rst

@@ -1,4 +1,4 @@
-|Build_Status| |License| |Documentation|
+|Build_Status| |License| |Documentation| |Docker|
 
 COBRAme
 =======
@@ -9,6 +9,12 @@ For more information on ME-models and the COBRAme ME-model architecture, see the
 
 If using COBRAme or iJL1678b-ME in a publication, please cite: `doi:10.1101/106559 <https://doi.org/10.1101/106559>`_. Note that the model may be edited and updated until it is peer-reviewed and published.
 
+COBRAme with Docker
+-------------------
+Docker images are available on DockerHub_ which contain pre-installed versions COBRAme, the solvers, all dependencies using Python 3.6. Dockerfiles_ are also available to build Docker containers locally.
+
+The DockerHub images contain a precompiled version the qMINOS solver and SoPlex can additionally be installed if a Docker container is build locally.
+
 Installation
 ------------
 
@@ -73,9 +79,13 @@ COBRAme and its extensions require:
 .. _soplex_cython: https://github.com/SBRG/soplex_cython
 .. _solvemepy: https://github.com/SBRG/solvemepy
 .. _COBRApy: https://github.com/opencobra/cobrapy
+.. _DockerFiles: https://github.com/SBRG/cobrame/tree/master/docker
+.. _DockerHub: https://hub.docker.com/r/sbrg/cobrame/
 .. |Build_Status| image:: https://travis-ci.org/SBRG/cobrame.svg?branch=master
     :target: https://travis-ci.org/SBRG/cobrame
-.. |License| image:: https://img.shields.io/github/license/mashape/apistatus.svg
+.. |License| image:: https://img.shields.io/github/license/sbrg/cobrame.svg
     :target: https://github.com/SBRG/cobrame/blob/master/LICENSE
 .. |Documentation| image:: https://readthedocs.org/projects/cobrame/badge/?version=master
     :target: http://cobrame.readthedocs.io/en/master/?badge=master
+.. |Docker| image:: https://img.shields.io/docker/build/sbrg/cobrame.svg
+    :target: https://hub.docker.com/r/sbrg/cobrame/builds/

docker/Dockerfile

@@ -49,7 +49,6 @@ RUN echo \
 	&& if [[ -e /source/soplex-$SOPLEX_VERSION.tgz ]]; then \
         git clone https://github.com/SBRG/soplex_cython.git; \
         cd /source/soplex_cython; \
-        git checkout devel_windows; \
         mv /source/soplex-$SOPLEX_VERSION.tgz  /source/soplex_cython/ ;\
         pip install . ;\
         fi \

docker/README.rst

@@ -11,7 +11,7 @@ Installation
 To run a Docker container with everything required to build and solve the iJL1678b model of *E. coli* K-12 MG1655 using qMINOS:
 
 1. Install Docker (https://docs.docker.com/install/)
-2. In the command line, run ``docker run --rm -i -v $(pwd):/home/meuser/ -t sbrg/cobrame:everything bash``.
+2. In the command line, run ``docker run --rm -i -v $(pwd):/home/meuser/ -t sbrg/cobrame:master bash``.
 
 This will initiate a Docker container (virtual machine) and copy everything in the directory where the command was run into the docker container at ``/workdir/``