Other software

In rare cases, some software tools are not readily available through conda or biocontainers. Below are some guides on how to run some them.

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 is licensed to a single machine and is only available through a virtual desktop on axomamma. So ensure that you fill in the Nodelist field. You can then find CLC in the menus.

AlphaFold

AlphaFold is quite complex to install and run. It runs through containers, but through a python wrapper script. Copy the SLURM sbatch script from /shared_software/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. So submit to the appropriate partition.

To make folders available inside the container you need to bind/mount them, as described here.