Common questions

Discussion group

If you have suggestions or inquiries, our Slack workspace is the best place to reach out. You will receive an invitation once your username and password are send to you.

For long-running analyses, please notify the #jobs-on-servers channel so other users can prepare accordingly.

Keep in mind that the Slack workspace is public, so refrain from sharing any sensitive data.

On GitHub, we have established an organization called IBL-bioinfo. If you have any suggestions regarding this documentation, please create a new issue on the issues page of this repository. For research code repositories, the university GitLab at gitlab.services.universiteitleiden.nl is also available and is preferred for projects related to personal data, but it does not support sharing repositories externally.

Remember, there are no dedicated administrators for the IBL bioinformatics atelier, so leaving a message in the mentioned places is more effective than trying to find someone in person.

Home directory quota

Every user have a disk space quota of 20 GB for their home directory. Home directory quota explained

Do not analyse large dataset in your home directory

Program fail when HOME is full

Micromamba or Conda

We use micromamba instead of conda to manage software environments. Explanation of why

Shared storage

Our servers do not share a unified storage system. Each server provides its own dedicated storage. Typically, system and home directories reside on the same SSD, while data is stored on the server’s HDD or extra SSD, which are available on mounts such as /vol/local/ or /vol/local1/. Learn more

Server configurations

Shared environments

On servers with Micromamba setup, shared environments should be stored in /vol/local/conda_envs. It is in a shared location so every user can use it but cannot modify it. To modify, the user that last modified the environment should set the permission correctly

We recommend using a ~/.mambarc file (~/.condarc on ALICE) to configure the behaviour of micromamba (conda on ALICE). The most important setting is pkgs_dirs:; it controls where to store the cache file when downloading packages, which could easily eat up all your home directory quota if not set. The specific location /vol/local/.conda_cache/[USERNAME] ensures easy cleaning up.