Usage

Run ATSAS tools in command line

Run the ATSAS simulation directly (assuming you are in the cloned repo dir).

$ dammif examples/IgG_0152-0159s.out --prefix=test --symmetry=P1 --mode=FAST

Run ATSAS tools from Python using Dask

Start an IPython session with ipython to perform the following calculations.

Local cluster

Run 36 separate ATSAS simulations on a local Dask cluster.

from atsas_pipelines.dask import dask_client
from atsas_pipelines.run import run_with_dask

client = dask_client()
futures = run_with_dask('dammif', 'examples/IgG_0152-0159s.out',
                        n_repeats=36)
client.gather(futures)
fut = futures[0]
fut.result()
out = fut.result().stdout.decode('utf-8')
print(out)

Slurm cluster

from atsas_pipelines.dask import dask_client, dask_slurm_cluster
from atsas_pipelines.run import run_with_dask

cluster = dask_slurm_cluster()
client = dask_client(cluster)

futures = run_with_dask('dammif', 'examples/IgG_0152-0159s.out',
                        n_repeats=36)

See run_with_dask() for implementation.