From 8789efd4d22f6140a3f6870f4a718f0c64d233c3 Mon Sep 17 00:00:00 2001
From: Peter Steinbach <steinbach@scionics.de>
Date: Mon, 18 May 2015 13:55:36 +0200
Subject: [PATCH] added alternative cluster submission
---
spim_registration/timelapse/README.md | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
diff --git a/spim_registration/timelapse/README.md b/spim_registration/timelapse/README.md
index f1d5499..16250b5 100644
--- a/spim_registration/timelapse/README.md
+++ b/spim_registration/timelapse/README.md
@@ -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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