BaMM web server

This repository contains the source code of the BaMM web server. A bioinformatic resource for analysis of nucleotide binding proteins with higher-order Bayesian Markov Models (BaMMs).

News

• 2018/06/13- We updated the server to version 1.2, please check the Release Notes for a list of changes.
• 2018/06/01- We updated the server to version 1.1, fixed a couple of nasty bugs and give a way to visualize motif occurrences in the genome browser.
• 2018/05/06- We fixed a couple of edge cases, improved the input validation and alert the user if we suspect that refined motifs in the de-novo workflow may not be the actual motif.
• 2018/04/22- We are happy to present a massively improved version. Highlights are a drastic speed improvement, a standalone one-step denovo workflow, estimation of the motif occurrence from the data, a cleaner user interface, a list of recently submitted jobs, and much more. We would like to thank our reviewers for their helpful suggestions for improving the server.
• 2018/03/07 - We fixed a bug in the interface causing a 500 error when running the seeding stage in single-strand mode.

Setting up the webserver locally

1) Preparing the database directories on the host

All persistent data will be stored on the host. I am using the directory /var/webserver. Make sure to choose a folder in which your BaMM user account has read/write access.

WEBSERVER_DIR=/var/webserver
# create folder structure
mkdir -p $WEBSERVER_DIR/{media_db,logs,motif_db,mysql_db,redis_db,backup,tmp,test_data}

cd $WEBSERVER_DIR
git clone https://github.com/soedinglab/BaMM_webserver.git

cd  BaMM_webserver
git submodule update --init --recursive

2) Setting up the motif databases

Download the motif databases from http://wwwuser.gwdg.de/~compbiol/bamm/, extract the databases into the database directory /var/webserver/motif_db.

Here I chose gtrd_mouse_BaMMv102.zip and remap2018_human_BAMMv102.zip. The first level of motif_db now looks like this:

motif_db
├── gtrd_mouse_v1801
└── remap2018_human

3) Configuring the webserver

cd $WEBSERVER_DIR/BaMM_webserver
cp .env_template .env

Now open .env with your favorite editor and adapt the server configuration to your system.

Please make sure that

• DEFAULT_MOTIF_DB is set to a database present in /var/webserver/motif_db
• BAMM_USER_UID matches the UID of the user account that owns the webserver files. You can find your UID by typing echo $UID in the shell.

If you are done, you can double check the settings by running docker-compose config. You should not see any warnings.

4) Starting the webserver

After successfully building, the webserver can be started typing docker-compose up. In case you see errors related to mysql migrations try stopping the server by ctrl-C and let is shut down gracefully, then restart by docker-compose up. The error should be gone.

Now you should be able to access the webserver at 0.0.0.0:10080 in your favorite browser.

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Notes and caveats

General notes

• docker-compose build commands always have to be started from the root of the git repository of the webserver
• all files created by the webserver are accessible on the host in $WEBSERVER_DIR/media_db

Developer notes

• whenever you change the models, you have to restart the server. Django will create a database migration automatically. These migrations are under version control and should be committed to the git repository
• Sometimes building the migrations needs user input. In this case, use docker exec -it bammmwebserver_web_1 bash to jump into the webserver container and run the migration commands manually. You can find the migration commands in run_web.sh.

Setting up the server in production

We strongly advice against running your own publicly accessible webserver without familiarizing yourself the django documentation. Failure in doing so can lead to an insecure server.

License

The BaMMserver code can be used, distributed and modified under the GNU Affero General Public License v3.0 (GNU AGPLv3)