Snakemake-Profiles lsf issues

Snakemake-Profiles / lsf

Snakemake profile for running jobs on an LSF cluster

MIT License

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issues

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Support Snakemake 8

#64 royjacobson opened 2 days ago
2
BsubInvocation Error

#63 suhridbuddha closed 3 months ago
2
Does not work with Snakemake v8

#62 levlitichev closed 5 months ago
3
docs: make mamba suggested install tool; recommend isolated cookiecutter env

#61 dlaehnemann closed 11 months ago
1
Make queue configurable per rule and attempt

#60 leoisl closed 2 months ago
8
Wait for jobscript

#59 mbhall88 closed 1 year ago
1
Error submitting jobscript, bsub returns exit code 255

#58 W-L closed 2 months ago
10
New maintainers needed

#57 mbhall88 opened 2 years ago
6
Change cluster cancel to a script

#56 mbhall88 closed 2 years ago
2
Cluster cancel doesn't work with current job ID

#55 mbhall88 closed 2 years ago
0
Error with Line 207 on lsf_status.py

#54 shalabhsuman closed 2 years ago
1
Implement cluster sidecar

#53 leoisl opened 2 years ago
3
Implement --cluster-cancel and --cluster-cancel-nargs

#52 leoisl closed 2 years ago
0
Add "mem_mb is per job or per thread?" to cookie-cutter

#51 leoisl opened 2 years ago
0
Add default mem_mb, disk_mb, tmpdir

#50 leoisl opened 2 years ago
2
Remove `default_mem_mb` from the cookie-cutter

#49 leoisl closed 2 years ago
2
Change `max_status_checks` to number >1

#48 kpj closed 2 years ago
8
Support quoted jobid from snakemake v7.1.1

#47 mbhall88 closed 2 years ago
4
update jobid/log splitting for snakemake v7.1.1

#46 ASLeonard closed 2 years ago
4
LSF profile is broken for newest 7.1.1 (2022-03-07) snakemake version

#45 leoisl closed 2 years ago
4
rule-specific config parsed as a dict, not as a list

#44 nickp60 closed 2 years ago
3
Add default project and remove default threads

#43 BEFH closed 2 years ago
7
`lsf.yaml` settings for specific rules are not used

#42 mfansler closed 2 years ago
1
resources: mem_mb= specification doesn't change memory requirement for LSF job submission

#41 ipstone opened 3 years ago
6
Complex shell quote escaping fails

#40 bricoletc closed 3 years ago
3
Complex shell quote escaping fails

#39 bricoletc closed 2 years ago
0
runtime resource added

#38 NBMueller closed 3 years ago
11
Dereplicate rule-specific parameters

#37 mbhall88 closed 3 years ago
1
Order of bsub non-standard arguments from lsf.yaml file

#36 NBMueller closed 3 years ago
4
🐛 Fix bug for legacy LSF system (v8.3)

#35 haizi-zh opened 3 years ago
3
Better handling of bjobs-related errors

#34 mbhall88 closed 3 years ago
1
Make UNKWN job always return running

#33 mbhall88 closed 3 years ago
0
Snakemake write wrong error to output file, jobs fail for no reason

#32 openpaul closed 3 years ago
4
How to submit each wildcard item as a job

#31 liutiming closed 3 years ago
2
Use workflow file name in log directory names

#30 bricoletc closed 3 years ago
10
Better handling of unknown and zombie jobs

#29 mbhall88 closed 3 years ago
0
Handling UNKWN and ZOMBI status

#28 leoisl closed 3 years ago
5
Unable to set queue per rule

#27 amakunin closed 3 years ago
2
job was done but no log was created and no bjobs show up when the job is running

#26 liutiming closed 3 years ago
15
Specifying non-standard rule-specific cluster resource settings

#25 kpj opened 4 years ago
6
Set up GitHub Actions

#24 mbhall88 closed 4 years ago
0
Better handling of group jobs

#23 mbhall88 closed 4 years ago
0
update changlog with robust memory handling

#22 mbhall88 closed 4 years ago
0
Add end-to-end tests with a LSF container?

#21 leoisl opened 4 years ago
3
Robust memory unit handling

#20 mbhall88 closed 4 years ago
0
Group job ids are (now?) uuids

#19 funnell closed 4 years ago
6
Explicitly specifying memory units breaks the profile in older versions of LSF

#18 leoisl closed 4 years ago
4
Set up continuous integration

#17 mbhall88 closed 4 years ago
0
Robust status handling and per-rule config

#16 mbhall88 closed 4 years ago
0
Add per-rule configuration capability

#15 mbhall88 closed 4 years ago
2