Other software

In rare cases, some software tools are not readily available through conda or biocontainers, or they are problematic to get to run properly. Below are some guides on how to run some them. Most are installed under /software/lib/biocloud-software.

ARB 7

ARB version 6.0 can be installed through conda from the bioconda channel, however it is not maintained anymore, and the latest version 7.0 is not available. To run version 7.0 on BioCloud, you need to run a wrapper script that runs ARB 7.0 from a custom built container image. You can do that through either a virtual desktop started from the web portal, or through an interactive shell session using salloc from a login node. ARB 7 is then available by simply typing arb7 in the terminal.

CLC

CLC Genomics Workbench version 25 is currently only installed on (and licensed to) the bio-node11 node, which is not in the interactive partition. To use CLC include --constraint=clc in the "Additional job options" field when starting a virtual desktop which ensures the job is only assigned to the bio-node11 node. You should then be able to find CLC in the menus.

AlphaFold

AlphaFold is quite complex to install and run. It runs within a container, but it must be started using a python wrapper script. It has been bundled up under /software/lib/biocloud-software/alphafold_singularity/. Just Copy the SLURM sbatch script from /software/lib/biocloud-software/alphafold_singularity/sbatch_example.sh and adjust to suit your needs. AlphaFold benefits from GPU-accelerated servers, but can also run on regular CPUs depending on the size of the input data.

ESMFold

ESMFold can be run through a custom-built container by simply typing esm-fold.