The Proteomics Sandbox is a platform optimized for software applications used in proteomics. The app is deployed as a virtual desktop environment.
The Initialization parameter can be used to execute a Bash script when the job starts. This is useful to set up the sandbox software environment.
Proteomics analysis tools can be installed and accessed as separate modules using EasyBuild, a build and installation framework for the deployment and management of scientific applications/tools on HPC systems. A brief introduction to EasyBuild is available here.
New software modules should be installed in a directory accessible from the default working tree, e.g.
/work/sandbox. As a result, the
sandbox software stack will be available in the UCloud workspace once the job is completed. The user should mount this folder as a data volume inside the app and make the new modules available from the command-line interface:
$ module use /work/sandbox/modules/all/
To check all available modules, use the command:
$ module avail
More commands are listed here.
Environment modules are loaded automatically when the
sandbox folder is mounted using the optional Modules path parameter.