Documentation under development, sorry for the inconvenience
Scipion framework plugin for the use of immunoinformatics tools comming from several sources:
- IIITD: for epitope prediction and evaluation
- Vaxign-ML: for protective antigen prediction
You will need to use 3.0.0 version of Scipion to run these protocols. To install the plugin, you have two options:
- Stable version
scipion installp -p scipion-chem-immuno
OR
- through the plugin manager GUI by launching Scipion and following Configuration >> Plugins
- Developer's version
- Download repository:
git clone https://github.com/scipion-chem/scipion-chem-immuno.git
- Switch to the desired branch (main or devel):
Scipion-chem-immuno is constantly under development. If you want a relatively older an more stable version, use main branch (default). If you want the latest changes and developments, user devel branch.
cd scipion-chem-immuno git checkout devel
- Prerequisites
- IIITD:
This package uses web browser to access the software servers online. Therefore, you need to specify which browser to use and its location. Do so editing the scipion.conf file and add the variables:
- IIITD_BROWSER = firefox/chrome/chromium (defines the browser to use, that must already be installed in your computer)
- IIITD_BROWSER_PATH = <path/to/browser> (defines the location of the binary for the browser use)
- Vaxign-ML:
This package runs using a docker image. Since docker images need special permission to be downloaded, the user needs to be included in the "docker" bash group of the machine to be able to use it. Managing these groups need sudo permissions.
To create the "docker" group: .. code-block:
sudo groupadd docker
Then add your user to the group: .. code-block:
sudo usermod -aG docker $USER
Once your user is in the docker group, the installation can proceed normally.
- Install:
scipion installp -p path_to_scipion-chem-immuno --devel
- Tests
To check the installation, simply run the following Scipion test:
Status devel version:
Status production version:
