A web application for visualizing and exploring the results of pathway enrichment analysis.
You can host DecoPath locally using Docker by following the steps below.
In order to host DecoPath, make sure you have Docker and Docker Compose installed on your system (see how to install Docker and/or how to install Docker Compose).
- Clone and download DecoPath from GitHub.
$ git clone https://github.com/decopath/decopath.git
$ cd decopath- Generate a SECRET_KEY for password encryption using the code below and add the generated text to the settings file on line 23.
$ python3.7 generate_secret_key.py-
If you are not using a domain name, remove the string domain.com from line 29 of the settings file and line 45 of the docker-compose file.
Additionally, you can choose to update the admin email address in the docker-compose file on line 14. Note the default admin password: admin.
-
Build the DecoPath image using Docker.
$ docker image build -t decopath:latest .- Start the docker image using docker-compose.
$ docker-compose up -d-
If you are not using a domain name, navigate to the local host (e.g., localhost:8000) from your browser an 993A d login with the following credentials (note this step may take some time, and you may need to refresh the page):
- username: user@domain.com
- password: admin
Alternatively, if you changed the admin email address, login with your chosen username and the default password (admin).
At this point, you should be all set to host DecoPath locally.
Optional:
- You can obtain a domain name in case you are installing DecoPath for your entire institution
- If you wish to host DecoPath using your own domain, you might need to change the ports in the docker-compose file to reflect your port-forwarding configuration (See Networking in Docker).
- You must then change "domain.com" with your domain name in the settings file and the docker-compose file.
DecoPath, out of the box, is installed in development mode. In order to deploy it, you can change the "DEBUG" variable in the settings file from "True" to "False" and serve static files along with the website using a web server of your choosing, such as nginx.
DecoPath is provided as a Python 3.7 package that you can customize and edit the functionality of. You can clone the repository from GitHub and set up the website following the commands below:
$ git clone https://github.com/decopath/decopath.git
$ cd decopath
$ python3.7 -m pip install -r requirements.txt
$ python3.7 manage.py makemigrations
$ python3.7 manage.py migrate
$ python3.7 manage.py load_db
$ python3.7 manage.py init_user --superuser "user@domain.com"
$ python3.7 manage.py runserverLogin credentials:
- username: user@domain.com
- password: admin
Note: You can use replace "user@domain.com" with your own administrator Email ID (default admin password: admin).
In a separate terminal, RabbitMQ & Celery can be setup using:
$ docker run -d --name rabbitmq -e RABBITMQ_DEFAULT_USER=user -e RABBITMQ_DEFAULT_PASS=password -e RABBITMQ_DEFAULT_VHOST=vhost -p 8080:15672 -p 5672:5672 rabbitmq:management
$ pip install celery
$ celery -A DecoPath worker -l infoNote: To obtain fold changes, the DESeq2 package must first be installed. To do so, start R and enter:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")To speed up a GSEA run with large gene sets, you can clone this branch to enable multi-processing. Then, alter the number of processes here.
If you have difficulties using DecoPath, please open an issue at our bug-tracker on GitHub.
If you have found DecoPath useful in your work, please consider citing:
Mubeen S., Bharadhwaj, V.S., Gadiya Y., Hofmann-Apitius M., T Kodamullil A.T., & Domingo-Fernández D. (2021). DecoPath: a web application for decoding pathway enrichment analysis. NAR Genomics and Bioinformatics, 3(3). https://doi.org/10.1093/nargab/lqab087
DecoPath is a scientific web application that has been developed in an academic capacity and thus comes with no warranty or guarantee of maintenance, support, or back-up of data.