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snakemake / snakemake-executor-plugin-slurm

A Snakemake executor plugin for submitting jobs to a SLURM cluster
MIT License
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slurm job name could be more informative #154

Closed dgordon562 closed 4 weeks ago

dgordon562 commented 1 month ago

Per Johannes' suggestion, I am submitting this:

job grouping is great! E.g., snakemake --groups blast_on_fugu_file=blastg --group-components blastg=16

However, I am finding that all of my slurm that are all named like: wgac-GROUP-batch=10 so I can't tell which rule (which job group) is currently running. Is there a way to get the slurm jobs named by the name of the job group or the name of the rule (in the case in which the job group has a single rule)?

Thanks! David

dgordon562 commented 1 month ago

Per Johannes, please assign this request to Christian Meesters and Johannes.

cmeesters commented 1 month ago

This is not a current part of the roadmap. But the roadmap is blurry anyway, and we can take your request into consideration. Please do not consider this a high priority for us, there are more pressing things, little time, and everything needs to be thoroughly checked.

As a reminder, I will leave this issue open.

dgordon562 commented 1 month ago

Thanks, Christian! Anything you can do would be appreciated. Right now what I have to do is to parse the log file to see which rule it is using. That's a pain in the a**.

johanneskoester commented 4 weeks ago

Note that the Snakemake output also lists the slurm log for each job or group when submitting and upon error.

johanneskoester commented 4 weeks ago

This should solve the issue: https://github.com/snakemake/snakemake/pull/3168

dgordon562 commented 4 weeks ago

thank you so much, Johannes! Do you have a page somewhere with instructions for how to get these new features? The instructions would need to assume many of us don't know much about git (except "git clone"). Such instructions would be good for everyone who is interested in getting any new feature. Maybe you already have such instructions somewhere...

Thanks again! Best wishes, David

On Thu, Oct 24, 2024 at 3:49 AM Johannes Köster @.***> wrote:

Closed #154 https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/154 as completed via snakemake/snakemake#3168 https://github.com/snakemake/snakemake/pull/3168.

— Reply to this email directly, view it on GitHub https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/154#event-14848664971, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACX6XC2KHD35AXFD6X3BKETZ5DGEHAVCNFSM6AAAAABPMEOP72VHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJUHA2DQNRWGQ4TOMI . You are receiving this because you authored the thread.Message ID: <snakemake/snakemake-executor-plugin-slurm/issue/154/issue_event/14848664971 @github.com>

cmeesters commented 4 weeks ago

The new features are always part of the next Snakemake release. Any Snakemake release (and every plugin release) is automatically published on pypi and bioconda (and of course, here on GitHub, as a code bundle, too).

dgordon562 commented 4 weeks ago

Thank you, Christian.

Another stupid question: to see if there is a new snakemake release, do I go to: https://github.com/snakemake/snakemake and check here (see snapshot below)? So whenever that version changes, this new feature will be in it and then I can get it via bioconda?

[image: image.png]

On Thu, Oct 24, 2024 at 7:45 AM Christian Meesters @.***> wrote:

The new features are always part of the next Snakemake release. Any Snakemake release (and every plugin release) is automatically published on pypi and bioconda (and of course, here on GitHub, as a code bundle, too).

— Reply to this email directly, view it on GitHub https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/154#issuecomment-2435501916, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACX6XC5HU3P7WRMSEDJKMTLZ5EBXNAVCNFSM6AAAAABPMEOP72VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMZVGUYDCOJRGY . You are receiving this because you authored the thread.Message ID: @.*** com>

johanneskoester commented 4 weeks ago

It takes some 1-3 hours for the release to appear on bioconda. If you want to be sure whether a new release is already in bioconda, check here: https://anaconda.org/bioconda/snakemake/files

dgordon562 commented 4 weeks ago

thanks, Johannes! (and, of course, thanks for all your years of work on this very useful product)

On Thu, Oct 24, 2024 at 9:58 AM Johannes Köster @.***> wrote:

It takes some 1-3 hours for the release to appear on bioconda. If you want to be sure whether a new release is already in bioconda, check here: https://anaconda.org/bioconda/snakemake/files

— Reply to this email directly, view it on GitHub https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/154#issuecomment-2435795636, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACX6XC6TNWCQEFRVBFC7DQLZ5ERMXAVCNFSM6AAAAABPMEOP72VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMZVG44TKNRTGY . You are receiving this because you authored the thread.Message ID: @.*** com>