WIP: Auto start mindcontrol from a singularity container

.circleci/config.yml

@@ -0,0 +1,10 @@
+version: 2
+jobs:
+  build:
+    machine: true
+    steps:
+      - checkout
+      - run: docker login -u $DOCKER_USER -p $DOCKER_PASS
+      - run: cd imports/docker && docker build -t shotgunosine/mindcontrol:$CIRCLE_BUILD_NUM-${CIRCLE_SHA1:0:6} -f Dockerfile_services .
+      - run: docker tag shotgunosine/mindcontrol:$CIRCLE_BUILD_NUM-${CIRCLE_SHA1:0:6} shotgunosine/mindcontrol:latest
+      - run: docker push shotgunosine/mindcontrol

.gitignore

@@ -1,2 +1,5 @@
 node_modules/
 .meteor/dev_bundle
+.mindcontrol/
+imports/docker/log/
+imports/docker/temp_for_nginx/

README.md

@@ -1,3 +1,6 @@
+[![CircleCI](https://circleci.com/gh/Shotgunosine/mindcontrol/tree/master.svg?style=svg)](https://circleci.com/gh/Shotgunosine/mindcontrol/tree/master)
+[![https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg](https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg)](https://singularity-hub.org/collections/1293)
+
 # mindcontrol
 MindControl is an app for quality control of neuroimaging pipeline outputs. 
 
@@ -34,6 +37,44 @@ Create a database json file similar to [http://dxugxjm290185.cloudfront.net/hbn/
 * Host your database json file on a server and copy/paste its url into the "startup_json" value on `settings.dev.json`
 * Define each module in `settings.dev.json` to point to your `entry_type`, and define the module's `staticURL`
 
+## Bulid and deploy with singularity
+Connect to the system where you'd like to host mindcontrol with a  port forwarded:
+```
+ssh -L 3000:localhost:3000 server
+```
+Clone mindcontrol to a directory where you've got ~ 10 GB of free space.
+```
+git clone https://github.com/Shotgunosine/mindcontrol
+cd mindcontrol
+```
+You'll need to have a python 3 environment with access to nipype, pybids, freesurfer, and singularity.
+Run start_singularity_mindcontrol.py. You can see its documentation with `python start_singularity_mindcontrol.py -h`. The script is now set up to take the name of a linux group as it's first argument. Any member of this group will be able to run the mindcontrol instance and access the mindcontrol files. 
+
+```
+python start_singularity_mindcontrol.py [name of the group you want to own mindcontrol files] [name you want to give container] —freesurfer_dir [path to directory containing subdirectories for all the subjects] --sing_out_dir [path where mindcontrol can output files] --freesurfer
+```
+
+This command does a number of things:
+1) Prompt you to create users and passwords. I would just create one user for your lab and a password that you don’t mind sharing with others in the lab.creates folders with all the settings files that need to be loaded.  
+2) Runs mriconvert to convert .mgz to .nii.gz for T1, aparc+aseg, ribbion, and wm. Right now I’m just dropping those converted niftis in the directory beside the .mgzs, let me know if that’s a problem though.  
+3) Pulls the singularity image.  
+4) Starts an instance of the singularity image running with everything mounted appropriately.  
+
+Inside the image, there’s a fair bit of file copying that has to get done. It takes a while, potentially quite a while if you are on a system with a slow filesystem.  
+You can check the progress with `cat log/simg_out/out`.  
+Once that says `Starting mindcontrol and nginx`, you can `cat log/simg_out/mindcontrol.out` to see what mindcontrol is doing.  
+Once that says `App running at: http://localhost:2998/`, mindcontrol is all set up and running (but ignore that port number, it’s running on port 3000).
+
+Anyone who wants to see mindcontrol can then `ssh -L 3000:localhost:3000` to the server and browse to http://localhost:3000 in their browser. They’ll be prompted to login with the username and password you created way back in step 1.
+
+Once you're done running mindcontrol you can stop it with `/bin/bash stop_mindcontrol.sh`. This command dumps the databse to log/simg_out/mindcontrol.out and compresses any previous database dump if finds there. It also fixes permissions on all of the files in the mindcontrol directory, so it may take a while to run. Killing the script before it finishes may prevent another user from being able to run your mindcontrol instance.
+
+The next time a user in the appropriate group would like to start it, they should just run `/bin/bash start_mindcontrol.sh`. This will start the instance and restore the database from the previously dumped data.
+
+Don't use the `singularity instance.start` and `singularity instance.stop` commands, as the additional permissions fixing and database restoring or dumping won't run.
+
+The startscript should write `my_readme.md` to the output directory you specify with instructions on running and connecting to the mindcontrol instance you've created with all of the appropriate paths and port numbers filled in. 
+
 ## Demo
 
 Check out the [demo](http://mindcontrol.herokuapp.com/). [This data is from the 1000 Functional Connectomes Project](http://fcon_1000.projects.nitrc.org/fcpClassic/FcpTable.html)