Timelapse based workflow
Expected setup
- a data directory e.g. looks like this
/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.jsoncontains the parameters that configure the beanshell scripts found in the data directory -
Snakefilefrom this directory -
cluster.jsonthat resides in the same directory as theSnakefile - cluster runs LSF
Submitting Jobs
If DRMAA is supported on your cluster:
snakemake -j2 -d /path/to/data/ --cluster-config ./cluster.json --drmaa " -q {cluster.lsf_q} {cluster.lsf_extra}"If not:
snakemake -j2 -d /path/to/data/ --cluster-config ./cluster.json --cluster "bsub -q {cluster.lsf_q} {cluster.lsf_extra}"