The Codes of Discworld

ℹ️ If you need some code for your science and don’t see it listed here, please discuss with the Discworld systems administration team (sbf+discworld@unsw.edu.au) and we can see how to install it.

If it’s a reasonably straightforward install, please have a go in your own /home folder

Programs at launch

• CryoSPARC [through portal.discworld.analytical.unsw.edu.au]
• Typical Cryo-EM/ET command line interface (CLI) programs
• Doppio [portal] / Relion [graphical/CLI]

Software package managers

• SBGrid (all 200+ programs in the Electron Microscopy collection, major programs from Vizualisation & Analysis)

⚠️ Check module avail sbgrid to see if an available tool run, or the error is from the framework used on top of the tool

• Scipion framework — graphical and workflow and plugin interface for major CryoEM tools

📧 Email d.luque@unsw.edu.au for expertise, support, and contact with the scipion developers for difficult use cases and debugging

• Spack – scientific program installer

⚙️ Spack provides the potential to install 8559+ total programs, and counting

Installing your own software

Feel free to give new programs a try, you can’t break other people’s /home — or ask us to install!

If there’s a program you want, walk down the list in order of preference in how to go about it

1. Load a system module: module avail to see all available modules, then module load program will give you access to the programs important enough to have been installed on the base system.

   module overview shows you just the programs without every version. Much shorter

   This includes code tools like CUDA, programming languages python, R, etc.

2. Check sbgrid:

   Check sbgrid by typing module load sbgrid/program/version into your terminal

   sbgrid is an amazing collaborative Structural Biology Grid consortium. We install all 200+ programs in the Electron Microscopy collection.
   These installs usually live under /apps/sbgrid/<program>/<version_number>/bin/<program>. The bin folder because computers use binary.
   SBGrid has good guides on how to switch software versions and even provides examples on running some programs via SBGrid.

3. Check scipion: if you start a virtual desktop the sdesktop via the Discworld portal you can load the Scipion visual interface which provides a convenient way to run workflows. We pre-load a set of CryoEM programs inside Scipion, worth checking as what’s packaged may be different.

4. Have a go installing it yourself: This is what your /home is for.

   1. In open science code, most is stored on GitHub. GitHub has many commands for software developers. Don’t worry about these, you just need a local clone of the raw code inside /home.

      To get a local copy of the raw code, run: git clone online-code-location

      For example: git clone https://github.com/ml-struct-bio/cryodrgn.git ❄️ 🐉
      However, the Installation section for cryodrgn actually recommends using a package manger (e.g. pip—the python package manager)

      # Create and activate a conda environment to install a specific program within
      (base) $ conda create --name cryodrgn python=3.12
      (base) $ conda activate cryodrgn
      (cryodrgn) $ 
      
      # install cryodrg
      (cryodrgn) $ pip install cryodrgn
      

   2. We are going to let you use the module system for your own installs. spack install program. Spack is a cool way to share code install recipes at every supercomputer around the world.

5. Follow the README this list the typing invocations to install the program are in the README if you’re luckily enough for it to ‘just work’.

   Central UNSW Research Technology Services already have a guide on installation

6. Reach out : For tricky installs, if you’re unsure of the code, or the going gets rough, drop us a line 📨

Please contact Dr Daniel Luque for expertise in the use of Scipion