From 4ca8d4a1185e7d1cea34e393ace6844b7054310d Mon Sep 17 00:00:00 2001
From: Peter Steinbach <steinbach@scionics.de>
Date: Mon, 18 May 2015 13:49:53 +0200
Subject: [PATCH] added readme with instructions

---
 spim_registration/timelapse/README.md | 33 +++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 spim_registration/timelapse/README.md

diff --git a/spim_registration/timelapse/README.md b/spim_registration/timelapse/README.md
new file mode 100644
index 0000000..36f3b9f
--- /dev/null
+++ b/spim_registration/timelapse/README.md
@@ -0,0 +1,33 @@
+Timelapse based workflow
+========================
+
+Expected setup
+--------------
+
+* a data directory e.g. looks like this
+```bash
+/path/to/data
+├── deconvolution_CPU.bsh	# copied/symlinked from this repo
+├── deconvolution_GPU.bsh	# copied/symlinked from this repo
+├── hdf5_test_unicore-00-00.h5
+├── hdf5_test_unicore-01-00.h5
+├── hdf5_test_unicore.h5
+├── hdf5_test_unicore.xml
+├── registration.bsh 		# copied/symlinked from this repo
+├── tomancak.json	 		# copied/symlinked from this repo
+├── transform.bsh	 		# copied/symlinked from this repo
+└── xml_merge.bsh	 		# copied/symlinked from this repo
+```
+
+* `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 than the `Snakefile`
+
+
+
+Submitting Jobs
+---------------
+
+```bash
+snakemake -j2 -d /projects/hpcsupport/steinbac/unicore/snakemake-sandbox/ --cluster-config ./cluster.json --drmaa " -q {cluster.lsf_q} {cluster.lsf_extra}"
+```
-- 
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