Name: BaMM_webserver
Owner: Söding Lab
Description: Webserver for Motif discovery with higher-order Bayesian Markov Models (BaMMs)
Created: 2017-02-14 10:03:10.0
Updated: 2018-05-15 11:12:39.0
Pushed: 2018-05-15 11:12:36.0
Homepage: https://bammmotif.mpibpc.mpg.de
Size: 68752
Language: HTML
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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).
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.
ERVER_DIR=/var/webserver
eate folder structure
r -p $WEBSERVER_DIR/{media_db,logs,motif_db,mysql_db,redis_db}
WEBSERVER_DIR
clone https://github.com/soedinglab/BaMM_webserver.git
BaMM_webserver
submodule update --init --recursive
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:
f_db
gtrd_mouse_v1801
remap2018_human
WEBSERVER_DIR/BaMM_webserver
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.
Now you can build the webserver by running docker-compose build
from the root of $WEBSERVER_DIR/BaMM_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.
$WEBSERVER_DIR/media_db
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
.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.
The BaMMserver code can be used, distributed and modified under the GNU Affero General Public License v3.0 (GNU AGPLv3)