Open yingchen69 opened 1 year ago
Hello @yingchen69,
I hope you are having a great day! I just have a really quick question.
Are you running this pipeline on the NIH's Biowulf cluster?
Are you running this pipeline on a SLURM cluster?
I am just wondering because if you are running the pipeline on Biowulf, you will not need to cache any of the references/software containers? Also, at the current moment, this pipeline is set up to run on a cluster-- specifically a SLURM cluster. Other job schedulers can/will be added in the future on a per-need basis, but this is the current backend for execution.
Please let me know what you think.
Hi Skyler,
I am not with NIH. Justin leads me to the OpenOmics and I am trying to set it here at Rutgers to run it on our cluster Amarel. My guess is that the dockers images are on your local srever's /data.
Thanks,
Ying
From: Skyler Kuhn @.> Sent: Monday, March 27, 2023 1:42 PM To: OpenOmics/genome-seek @.> Cc: yingchen69 @.>; Mention @.> Subject: Re: [OpenOmics/genome-seek] genome-seek cache error (Issue #14)
Hello @yingchen69https://github.com/yingchen69,
I hope you are having a great day! I just have a really quick question.
Are you running this pipeline on the NIH's Biowulf cluster?
Are you running this pipeline on a SLURM cluster?
I am just wondering because if you are running the pipeline on Biowulf, you will not need to cache any of the references/software containers? Also, at the current moment, this pipeline is set up to run on a cluster-- specifically a SLURM cluster. Other job schedulers can/will be added in the future on a per-need basis, but this is the current backend for execution.
Please let me know what you think.
— Reply to this email directly, view it on GitHubhttps://github.com/OpenOmics/genome-seek/issues/14#issuecomment-1485565554, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABQ767Q3OPMEDGHR6NPM5PDW6HGRDANCNFSM6AAAAAAWIVJSPU. You are receiving this because you were mentioned.Message ID: @.***>
Hi Skyler,
Yes we use slurm on Amarel.
Thanks,
Ying
Hey @yingchen69,
I would need to make a few changes on my side if you would like to run this outside the NIH. Right now, it is pointing to local SIFs, but I can update that to use DockerHub URIs. There is also a pretty large resource bundle that you will need to download too to run the pipeline. I was planning on adding those changes with the next major release, but I haven't had time. This pipeline is still a WIP, but I will set aside some time later this week and next week to make those updates and a few other updates that have been proposed.
I will reach out to you when everything is completed.
Best, @skchronicles
Hi Skyler,
Thanks a lot!
Ying
From: Skyler Kuhn @.> Sent: Monday, March 27, 2023 6:05 PM To: OpenOmics/genome-seek @.> Cc: yingchen69 @.>; Mention @.> Subject: Re: [OpenOmics/genome-seek] genome-seek cache error (Issue #14)
Hey @yingchen69https://github.com/yingchen69,
I would need to make a few changes on my side if you would like to run this outside the NIH. Right now, it is pointing to local SIFs, but I can update that to use DockerHub URIs. There is also a pretty large resource bundle that you will need to download too to run the pipeline. I was planning on adding those changes with the next major release, but I haven't had time. This pipeline is still a WIP, but I will set aside some time later this week and next week to make those updates and a few other updates that have been proposed.
I will reach out to you when everything is completed.
Best, @yingchen69https://github.com/yingchen69
— Reply to this email directly, view it on GitHubhttps://github.com/OpenOmics/genome-seek/issues/14#issuecomment-1485920244, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ABQ767UDPZGWQQBJWQOHMBTW6IFLHANCNFSM6AAAAAAWIVJSPU. You are receiving this because you were mentioned.Message ID: @.***>
Hi Skyler,
Sorry to bother you. Is there any update?
Thanks,
Ying
Hi,
I installed genome-seek through conda:
But when I tried to run: /genome-seek/genome-seek cache --sif-cache /sif-cache, I got the following error:
It seems that the image sif files are missing and the SLURM_JOB_ID in cache.sh is not defined. Is there a way to get around?
Thanks a lot!
Ying