SamStudio8
commented
2 months ago Hi @bcardus, our Docker images are not hosted on quay.io. I have not used the nf-core download command but from a cursory glance at the docs it looks like you might need to supply -l docker.io to override the registry. For any further support on the nf-core tools I would ask the nf-core community.
If you want to simply pull our images with Singularity, you should be able to accomplish this by removing the reference to quay.io:
$ singularity pull --name ontresearch-modkit-shaeedb131a939d3eea2f9bd4dbecec805c0fa20bdb.img docker://ontresearch/modkit:shaeedb131a939d3eea2f9bd4dbecec805c0fa20bdbNote the command will first pull the Docker image in order to build the Singularity image, as we do not host a registry of native Singularity images.
bcardus
Operating System
CentOS 7
Other Linux
CentOS Linux 7 (Core)
Workflow Version
v2.1.0
Workflow Execution
Command line (Cluster)
Other workflow execution
No response
EPI2ME Version
No response
CLI command run
[hzs682@rescomp2 hzs682]$ nf-core download epi2me-labs/wf-human-variation --force
? Select release / branch: v2.1.0 [release] ? Include the nf-core's default institutional configuration files into the download? Yes
In addition to the pipeline code, this tool can download software containers. ? Download software container images: singularity
If you are working on the same system where you will run Nextflow, you can amend the downloaded images to the ones in the$NXF_SINGULARITY_CACHEDIR folder, Nextflow will automatically find them.However if you will transfer the downloaded files to a different system then they should be copied to the target folder. ? Copy singularity images from $NXF_SINGULARITY_CACHEDIR to the target folder or amend new images to the cache? co py
If transferring the downloaded files to another system, it can be convenient to have everything compressed in a single file. This is not recommended when downloading Singularity images, as it can take a long time and saves very little space. ? Choose compression type: none
Workflow Execution - CLI Execution Profile
None
What happened?
I am trying to use nf-core to download the wf-human-variation workflow onto a cluster entry node so that I can run it on a compute node which does not have internet access. I input the above code and then run through the options below it to select the version, container images etc. However, when it tries to pull the singularity images, it fails and crashes. It seems that the command tries to look at an address in quay.io for the singularity image but can't find it, and when I go to that address on my browser there is nothing there either. When I run the individual command to pull the singularity image, as suggested in the error report, I get another error saying it failed to get the checksum and I am not authorised to access it. I did find docker images in different locations when searching manually e.g. at a different quay.io address and at a Docker hub address, but I don't know how to change this in the command. I am also not sure why it is pulling Docker images when I have asked for Singularity images.
Relevant log output
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
no
Other demo data information
No response