git clone [email protected]:morinlab/pyGAMBL.git
cd pyGAMBL
conda activate /projects/rmorin_scratch/for_kostia/pygambl
To access a running service:
./client.py
To launch your own service (asssuming you have sufficient permissions):
./api.py &
This repository currently contains two Python scripts. The api.py script will launch a Flask server on the specified port (5678). Only one instance of api.py can be run on a server and attempting to run it while the port is in use will result in an error. If the server launches successfully, you should see something like this in your terminal:
Launch the server on a gphost (within a tmux/screen shell).
./api.py &
* Debugger is active!
* Debugger PIN: 132-309-303
The client.py script provides a simple example demonstrating the functionality of the server. Run it by specifying the full name of the GAMBLR function you want to run. Because this code is in the early stages of development, currently only a few functions are supported.
Example:
To retrieve the metadata as a pandas dataframe:
./client.py get_gambl_metadata
To retrieve the full coding ssm MAF file as a pandas dataframe (default grch37/genome):
./client.py get_coding_ssm
You only really need to worry about how this script works if you are a developer or are running the api.py script. When api.py receives a recognized request, it calls the run_gamblr_function.R script to run the requested GAMBLR function with the parameters provided and it captures the output (from STDOUT) into a data frame which is returned to the client (as json). The client then converts this back to a data frame.