missing container tag 2.7.2.GRCm38 for sareksnpeff

[intawat]

2. See error: <!-- [Pulling Singularity image docker://nfcore/sareksnpeff:2.7.2.GRCm38 [cache /fullpath/NBres/work/singularity/nfcore-sareksnpeff-2.7.2.GRCm38.img]
   Pulling Singularity image docker://nfcore/sarekvep:2.7.2.GRCm38 [cache /fullpath/Jhx_data/NBres/work/singularity/nfcore-sarekvep-2.7.2.GRCm38.img]
   WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /storage/Intawat/Jhx_data/NBres/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location
   Error executing process > 'VEP (NB - TIDDIT - TIDDIT_NB.vcf.gz)'

Caused by:
Failed to pull singularity image
command: singularity pull --name nfcore-sarekvep-2.7.2.GRCm38.img.pulling.1657483696643 docker://nfcore/sarekvep:2.7.2.GRCm38 > /dev/null
status : 255
message:
time="2022-07-10T15:08:16-05:00" level=warning msg=""/run/user/1692700009" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /run/user/1692700009: no such file or directory: Trying to pull image in the event that it is a public image."
FATAL: While making image from oci registry: failed to get checksum for docker://nfcore/sarekvep:2.7.2.GRCm38: Error reading manifest 2.7.2.GRCm38 in docker.io/nfcore/sarekvep: manifest unknown: manifest unknown

-[nf-core/sarek] Pipeline completed with errors-
WARN: Killing running tasks (1)] -->

[intawat]

Please guide me how to fix the error.

[maxulysse]

@intawat we're simply missing this tag for this container.
I probably find some time to build it and push it during the week.
Otherwise, you have two options:

• use the sarek 2.7.1 version, with which the corresponding containers are there
• Build the container locally

[intawat]

I did try 2.7.2 it said "No such variable: ch_software_versions_yaml"
Another problem. I should wait, I think.

[maxulysse]

Containers is now built and pushed to dockerhub. You should not have issue with that anymore.

[intawat]

Thank you, I got the error below. The image failed to pull. Could you please check ? what's happened. Pulling Singularity image docker://nfcore/sareksnpeff:2.7.2.GRCm38 [cache /storage/Intawat/Jhx_data/NBres/work/singularity/nfcore-sareksnpeff-2.7.2.GRCm38.img] Pulling Singularity image docker://nfcore/sarekvep:2.7.2.GRCm38 [cache /storage/Intawat/Jhx_data/NBres/work/singularity/nfcore-sarekvep-2.7.2.GRCm38.img] WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /storage/Intawat/Jhx_data/NBres/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location Error executing process > 'Snpeff (NB - TIDDIT - TIDDIT_NB.vcf.gz)' Caused by: Failed to pull singularity image command: singularity pull --name nfcore-sareksnpeff-2.7.2.GRCm38.img.pulling.1657725784767 docker://nfcore/sareksnpeff:2.7.2.GRCm38 > /dev/null status : 255 message: time="2022-07-13T10:23:04-05:00" level=warning msg="\"/tmp/1692700009\" directory set by $XDG_RUNTIME_DIR does not exist. Either create the directory or unset $XDG_RUNTIME_DIR.: stat /tmp/1692700009: no such file or directory: Trying to pull image in the event that it is a public image." FATAL: While making image from oci registry: failed to get checksum for docker://nfcore/sareksnpeff:2.7.2.GRCm38: Error reading manifest 2.7.2.GRCm38 in docker.io/nfcore/sareksnpeff: manifest unknown: manifest unknown

…

On Wed, Jul 13, 2022 at 4:28 AM Maxime U. Garcia ***@***.***> wrote: Containers is now built and pushed to dockerhub. You should not have issue with that anymore. — Reply to this email directly, view it on GitHub <#627 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4VBHS6XKHEYIKXIUVO72TVT2D2BANCNFSM53G6L7CA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[maxulysse]

This container is big, so I'd recommend setting up a NXF_SINGULARITY_CACHEDIR ENV on your system, and downloading this image there.

[intawat]

I set NXF_SINGULARITY_CACHEDIR and the image was downloaded however, error is still present as below.

Pulling Singularity image docker://nfcore/sarekvep:2.7.2.GRCm38 [cache /storage/Intawat/Jhx_data/forDocker/nfcore-sarekvep-2.7.2.GRCm38.img]
Pulling Singularity image docker://nfcore/sareksnpeff:2.7.2.GRCm38 [cache /storage/Intawat/Jhx_data/forDocker/nfcore-sareksnpeff-2.7.2.GRCm38.img]
Error executing process > 'Snpeff (NB - TIDDIT - TIDDIT_NB.vcf.gz)'

Caused by:
Failed to pull singularity image
command: singularity pull --name nfcore-sareksnpeff-2.7.2.GRCm38.img.pulling.1658363013340 docker://nfcore/sareksnpeff:2.7.2.GRCm38 > /dev/null
status : 255
message:
[31mFATAL: While making image from oci registry: failed to get checksum for docker://nfcore/sareksnpeff:2.7.2.GRCm38: Error reading manifest 2.7.2.GRCm38 in docker.io/nfcore/sareksnpeff: manifest unknown: manifest unknown

[maxulysse]

My bad, I pushed 2.7.2.GRcm38 and not 2.7.2.GRCm38.
Fixing that right now.
Should be ok in 1 hour or 2