* DONE Quick Start
** Install Docker
   1. See installation instructions for [[https://docs.docker.com/installation/mac/][Mac]], [[https://docs.docker.com/installation/windows/][Windows]], [[https://docs.docker.com/installation/][etc]]
   2. On Mac and Windows, launch "Docker Quickstart Terminal".  All subsequent commands will be run in the terminal launched by "Docker Quickstart Terminal".
   *Notes:* On other operating systems, the docker daemon may run automatically after installation.  Also, on other operating systems, you may need to use the command ~sudo docker~ instead of just ~docker~.

** Download Run Script
   Download the run script [[https://raw.githubusercontent.com/granek/OrthoMCL-docker/master/run_orthomcl.sh][run_orthomcl.sh]] (e.g. right click on the link and select "Save Link As ...")
** Run the script
   Within the Docker terminal run ~bash run_orthomcl.sh~ to launch the OrthoMCL container.
   You should now have a bash shell in the OrthoMCL container that looks something like this:

#+BEGIN_SRC sh
root@a74d15695ca9:/#
#+END_SRC
** Generate OrthoMCL Configuration File
    Download the config generation script into your docker container, and run it with the following commands *within your docker container*:
#+BEGIN_SRC sh
wget https://raw.githubusercontent.com/granek/OrthoMCL-docker/master/test_run/create_config.sh
bash create_config.sh > orthomcl.config
#+END_SRC
This should generate the config file ~orthomcl.config~ in the current directory in your docker container.
** Install the schema into MySQL database
   Run it with the following command *within your docker container* to set up the database:
#+BEGIN_SRC sh
orthomclInstallSchema orthomcl.config
#+END_SRC
* OrthoMCL Docker Details
** One-time Use
   Download the run script [[https://raw.githubusercontent.com/granek/OrthoMCL-docker/master/run_orthomcl_oneshot.sh][run_orthomcl_oneshot.sh]]. Run this script within the Docker terminal run ~bash run_orthomcl_oneshot.sh~ to launch the OrthoMCL container.  This script cleans up after itself, which means that your session is completely obliterated once you exit. If you might want to resume your session, see *Multi-time Use* below.
** Multi-time Use
   If you expect to want to use OrthoMCL in several different sessions, you will want to run ~bash run_orthomcl.sh~. When you want to get out of your OrthoMCL session, but want to resume it later (technically this is detaching), use the "escape sequence" ~Ctrl-p~ + ~Ctrl-q~. This leaves the container running.  To resume your orthomcl session use the command ~docker attach orthomcl-run~ within your "Docker Quickstart Terminal". *Note* that when you attach the shell will not print a prompt right away, just hit the enter/return key to get a prompt.

   Accidentally did ~exit~ in your OrthoMCL session?  Don't worry, just run ~docker start orthomcl-run~ before ~docker attach orthomcl-run~.
# docker exec -ti orthomcl-run bash
# This is roughly equivalent to logging back into a server by ssh, after logging out.
*** Cleanup When Done
Once you are completely done with OrthoMCL, you might want to get rid of the containers:
#+BEGIN_SRC sh
docker stop orthomcl-mysql
docker rm orthomcl-run orthomcl-mysql
#+END_SRC
** Accessing files on the host computer
A Docker container is almost completely isolated from the host computer that it is running on.  This prevents the container from doing nasty things to your computer, but also makes it a bit more difficult to interact with files that are residing on your computer.  A simple way around this limitation is to mount a directory from the host computer into the Docker container.  When you run ~bash run_orthomcl.sh~, the directory that you run it from (the "working directory") will automatically be mounted within the OrthoMCL container at the mountpoint ~/host_dir~.  This means that you can read and write files that are in that directory.  Try the following within your OrthoMCL container:
#+BEGIN_SRC sh
ls /host_dir
echo "I am writing this from the future ... a docker container" > /host_dir/test_output.txt
#+END_SRC

If you want to mount a different directory, just supply this as a full path when you run the orthomcl script ~bash run_orthomcl.sh FULL_PATH_TO_DATA~, and that directory will be mounted at ~/host_dir~ instead
** OrthoMCL Configuration File
   The github repo contains a script for automatically generating an OrthoMCL configuration file.  There are two ways to generate the configuration file.
*** From repo
    If you cloned the repo from github, and started things up by running the run_orthomcl.sh (or run_orthomcl_oneshot.sh) script in the repo directory, you can generate the configuration file by running the following command *within your docker container*:
#+BEGIN_SRC sh
bash /host_dir/test_run/create_config.sh > orthomcl.config
#+END_SRC

This should generate the config file in the current directory in your docker container.  You can check this by running the following *within your docker container*:
#+BEGIN_SRC sh
cat orthomcl.config
#+END_SRC

If it worked, the second line should be the following (but probably with a different IP address):
#+BEGIN_SRC sh
dbConnectString=dbi:mysql:orthomcl:172.17.0.40:3306
#+END_SRC
*** Download script
    You can also download the config generation script into your docker container, and run it with the following commands *within your docker container*:
#+BEGIN_SRC sh
wget https://raw.githubusercontent.com/granek/OrthoMCL-docker/master/test_run/create_config.sh
bash create_config.sh > orthomcl.config
#+END_SRC
This should generate the config file in the current directory in your docker container.  You can check this by running the following *within your docker container*:
#+BEGIN_SRC sh
cat orthomcl.config
#+END_SRC

If it worked, the second line should be the following (but probably with a different IP address):
#+BEGIN_SRC sh
dbConnectString=dbi:mysql:orthomcl:172.17.0.40:3306
#+END_SRC
** OrthoMCL Image
*** Download OrthoMCL Image
    The OrthoMCL image is automatically downloaded from Docker Hub by the run_orthomcl.sh script, but you can manually download it with the command ~docker pull granek/orthomcl~.
*** Manual build of the OrthoMCL Image
If you want to build the OrthoMCL image instead of pulling it from Docker Hub, download [[https://raw.githubusercontent.com/granek/OrthoMCL-docker/master/Dockerfile][Dockerfile]] (or pull this repo), then run ~docker build -t orthomcl~ within the directory containing Dockerfile.