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Commit 8789efd4 authored by Peter Steinbach's avatar Peter Steinbach
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added alternative cluster submission

parent 56866d4c
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......@@ -22,12 +22,20 @@ Expected setup
* `tomancak.json` contains the parameters that configure the beanshell scripts found in the data directory
* `Snakefile` from this directory
* `cluster.json` that resides in the same directory as the `Snakefile`
* cluster runs LSF
Submitting Jobs
---------------
If DRMAA is supported on your cluster:
```bash
snakemake -j2 -d /path/to/data/ --cluster-config ./cluster.json --drmaa " -q {cluster.lsf_q} {cluster.lsf_extra}"
```
If not:
```bash
snakemake -j2 -d /path/to/data/ --cluster-config ./cluster.json --cluster "bsub -q {cluster.lsf_q} {cluster.lsf_extra}"
```
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