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gitter-lab / SINGE

Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data
MIT License
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Example for High Throughput Computing #6

Open atuldeshpande opened 5 years ago

atuldeshpande commented 5 years ago

Provide example with high throughput computing. Could include specific example with broad guidelines to facilitate the adaptation on other high-throughput systems.

agitter commented 4 years ago

The generalized SINGE.sh from #43 can now support a high-throughput computing workflow. The script tests/high_throughput_test.sh gives one example of how to run the GLG and aggregate steps separately through Docker. We could also add a HTCondor example or other real example of how to run in a high-throughput setting without Docker before closing this.

agitter commented 4 years ago

The Docker command that HTCondor uses is relevant for this issue https://github.com/gitter-lab/SINGE/issues/18#issuecomment-489319432

agitter commented 4 years ago

I'd like to consider Snakemake for our high-throughput computing SINGE example. It can support HTCondor as well as other clustering queueing systems.