diff --git a/spim_registration/timelapse/README.md b/spim_registration/timelapse/README.md new file mode 100644 index 0000000000000000000000000000000000000000..36f3b9f7c9647e6a75a0ede5b1fdfde04acabbd2 --- /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}" +```