Proteomics Sandbox

type access

  • Operating System:

  • Terminal:

  • Shell:

  • Editor:

  • Package Manager:

  • Programming Language:

  • Database:

  • Utility:


The Proteomics Sandbox is a platform optimized for software applications used in proteomics. The app is deployed as a virtual desktop environment.

Initialization script

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.

Additional tools

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.

Note

Environment modules are loaded automatically when the sandbox folder is mounted using the optional Modules path parameter.