Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add possibility to provide empty default resources in a profile (as was possible with SnakeMake 7.x.x) #2820

Open
sven0schuierer opened this issue Apr 18, 2024 · 0 comments
Labels
enhancement New feature or request

Comments

@sven0schuierer
Copy link

sven0schuierer commented Apr 18, 2024

Is your feature request related to a problem? Please describe.
See the setup for my bug report "Using option --drmaa_logs crashes snakemake #2819" except the profile config.yaml looks now as follows:

jobs: 100
latency-wait: 120

default-resources:
    mem_mb:    1000
    h_vmem_mb: 1200
    h_rt:  14400
    additional_drmaa_options: ''
    
executor: drmaa
drmaa-args: "-V -l h_rt={resources.h_rt} -l m_mem_free={resources.mem_mb}M -l h_vmem={resources.h_vmem_mb}M -pe smp {threads} {resources.additional_drmaa_options}"
drmaa-log-dir: drmaa_logs

If I run SnakeMake as in the bug report, I get:

(snakemake-tutorial-v8+) $ snakemake --cores 1 --use-conda --profile drmaa
Using profile drmaa for setting default command line arguments.
Building DAG of jobs...
Your conda installation is not configured to use strict channel priorities. This is however crucial for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'.
Using shell: /usr/bin/bash
Provided remote nodes: 100
Job stats:
job          count
---------  -------
map_reads        1
total            1

Select jobs to execute...
InputFunctionException in rule map_reads in file <path to snakemake-tutorial>/snakemake-tutorial-v8+/snakemake-snakemake-tutorial-data-be6ae5a/Snakefile, line 1:
Error:
  WorkflowError:
    Failed to evaluate resources value ''.
        String arguments may need additional quoting. E.g.: --default-resources "tmpdir='/home/user/tmp'" or --set-resources "somerule:someresource='--nice=100'". This also holds for setting resources inside of a profile, where you might have to enclose them in single and double quotes, i.e. someresource: "'--nice=100'".
    SyntaxError: invalid syntax (<string>, line 0)
Wildcards:

Traceback:
 (rule map_reads, line 1, <path to snakemake-tutorial>/snakemake-tutorial-v8+/snakemake-snakemake-tutorial-data-be6ae5a/Snakefile)
(snakemake-tutorial-v8+) $

Describe the solution you'd like
I would like SnakeMake to accept empty default resources

Describe alternatives you've considered
Provide an option that I would specify directly in "drmaa_option", e.g. -V as an additional_drmaa_options

@sven0schuierer sven0schuierer added the enhancement New feature or request label Apr 18, 2024
@sven0schuierer sven0schuierer changed the title Add possibility to provide empty default resources in a profles (as was possible with SnakeMake 7.x.x) Add possibility to provide empty default resources in a profile (as was possible with SnakeMake 7.x.x) Apr 18, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

No branches or pull requests

1 participant