Tools
List of tools for common tasks such as editing files, software development and configuration, simple post-processing. Please not that while these tools are often run on the login node, if you are processing large files or running jobs that take more than a few minutes to run, please run these tools via the batch queue. This can easily be done with a simple jobscript. Long running post-processing jobs may be killed if they are affecting the performance of the login node.
Instructions only shown to logged-in users
The tables shown here are auto-populated. When editing a Tools page, ensure the page’s custom field values RI_Summary is set to a short description and RI_Cat is set to tool.
Tools and Utilities
| PACKAGE | NOTES |
|---|---|
| cmake | Cross-platform, open-source build system |
| dcm2niix | DICOM to the NIfTI file converter |
| gedit - a simple text editor | A simple text editor, similar to notepad |
| git & git-lfs | Version Control |
| Gnuplot | A command-line driven graphing utility. |
| Grace / xmgrace | 2D interactive plotting tool |
| ninja | Software build system |
| p7zip | 7z archive compression and decompression |
| pigz and unpigz | Parallel gzip file compression/decompression |
| Proxy (for web downloads) | Envronment setup to give name of proxy server |
| PyCharm | Python IDE |
| SCons | Software configuration tool |
| SQLite browser (DB4S) | Graphical browser for sqlite files |
| Subversion (svn) | Version Control |
| UKBioBank Helper Modulefile | Environment variables to help access UK BioBank full-release datasets. |
| unzip | Extract files from zip archives |
| VSCode | A popular source-code editor by Microsoft. |
| zstd | fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios |