Failed to pull singularity image about fetchngs HOT 2 CLOSED

From the error message it appears that singularity could not connect to the galaxy repository housing the image. If running the pull command manually (singularity shell https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3) results in the same error, then the issue is likely due to the configuration of the HPC system or its network/firewall.

Depending on the way the HPC is configured, it could be that the problem only occurs on worker nodes during job execution, but not on login nodes. In any case, I'd reach out to your HPC's help desk and ask them if they block the download of singularity images from https://depot.galaxyproject.org/singularity/.

As a workaround, you could download the image manually on your own device and upload it to the HPC yourself. You'd also need to instruct nextflow to look for the image in a specific location rather than downloading it from galaxy, as described here:

Nextflow caches those images in the singularity directory in the pipeline work directory by default. However it is suggest to provide a centralised caching directory by using either the NXF_SINGULARITY_CACHEDIR environment variable or the singularity.cacheDir setting in the Nextflow config file.

If you use the environment variable, be sure to export it or define it in your job submission script, rather than just setting it in your local shell. E.g. export NXF_SINGULARITY_CACHEDIR=/path/to/cachedir, and also ensure it is in a location that your HPC worker nodes can access.

from fetchngs.

Yep, I agree this is an infrastructure and not pipeline related issue. Will close this for now but please feel free to join the nf-core Slack Workspace for any future questions/issues. We have an #fetchngs channel where you can get more real-time help.

from fetchngs.