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

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 can run the following in a terminal in either a virtual desktop started from the web portal, or through an interactive shell session through salloc or srun. The cool thing about the latter is that windows will show up on your own computer, but everything is running inside a SLURM job on a BioCloud compute node:

# create tmp folder for arb in our home folder and create the file
arbtmp="${HOME}/.tmp/arb7"
filename="names_start.dat"
file_path="${arbtmp}/${filename}"
mkdir -p "$arbtmp"
touch "${file_path}"
srun --cpus-per-task 2 --mem 4G --time 0-3:00:00 --x11 apptainer run \
  -B ${file_path}:/opt/arb/lib/nas/names_start.dat \
  -B ~/.Xauthority \
  -B /projects /shared_software/biocloud-software/arb/arb-7.0.sif

As mentioned in the job submission guide ensure you have X11 forwarding enabled for your SSH connection if you want to run things through SSH using salloc or srun.

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

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.

usearch11

usearch11 is made available on all servers by simply running usearch11 or usearch.