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How to indicate variable node-local-storage paths to snakemake using --shadow-prefix?

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0

The FAQ state, there is no option to indicate a node-local-storage mount point to snakemake, but rather a workaround using --shadow-prefix. Our cluster uses a path / mount point per job, e.g. /localscratch/$JOBID/

Prior to a job its ID obviously is not known. Is there a known way to indicate such a path to snakemake?

Thanks a lot in advance,
Christian

snakemake

share|improve this question

asked Mar 25 at 8:40

user4278912user4278912

11

add a comment | 

0

The FAQ state, there is no option to indicate a node-local-storage mount point to snakemake, but rather a workaround using --shadow-prefix. Our cluster uses a path / mount point per job, e.g. /localscratch/$JOBID/

Prior to a job its ID obviously is not known. Is there a known way to indicate such a path to snakemake?

Thanks a lot in advance,
Christian

snakemake

share|improve this question

asked Mar 25 at 8:40

user4278912user4278912

11

add a comment | 

The FAQ state, there is no option to indicate a node-local-storage mount point to snakemake, but rather a workaround using --shadow-prefix. Our cluster uses a path / mount point per job, e.g. /localscratch/$JOBID/

Prior to a job its ID obviously is not known. Is there a known way to indicate such a path to snakemake?

Thanks a lot in advance,
Christian

snakemake

share|improve this question

asked Mar 25 at 8:40

user4278912user4278912

11

share|improve this question

asked Mar 25 at 8:40

user4278912user4278912

11

share|improve this question

asked Mar 25 at 8:40

user4278912user4278912

11

asked Mar 25 at 8:40

user4278912user4278912

11

asked Mar 25 at 8:40

user4278912user4278912

11