sos
sos copied to clipboard
vatlab
SoS workflow system for daily data analysis
Hello Bo, thanks again for providing this excellent tool. I have a workflow where I build a custom database for `kraken` and then have a subsequent step that uses `kraken`...
This looks like a reasonable feature, but there are a few problems. First as described in #1496, nested workflows can cause problems: ``` [a] output: something sos_run('b') [b] output: something...
Kubernetes is a powerful and full-features task queue system for containers. It can easily be run locally, on a local cluster, or in the cloud. It supports GPUs, resource selectors,...
Test `test_signature_of_remote_target`, if I remove the `os.remove("result.txt")` from line 309, the step will not be executed, not updating the local file with the correct answer. The original test was without...
SoS went very far in allowing multiple tasks to be executed on the same process. Mixing it with zmq made the executor very complicated. In essence, we divde the execution...
Not sure why option `trunk_size` was chosen but it should be `chunk_size` or `batch_size`, I think.
@BoPeng we are recently looking into UKB data for some traits we analyze, https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/guide-to-analyzing-large-sample-sets the new UKB release is only available through this platform (!!). As you can see, the...
Right now our tests uses unittest, and have things such as ``` class TestActions(unittest.TestCase): def setUp(self): env.reset() self.temp_files = [] def tearDown(self): for f in self.temp_files: if file_target(f).exists(): file_target(f).unlink() ```...
Saw an error message ``` Failed to connect to franklin: Failed to check remote connection franklin.dldcc.bcm.edu:22: Failed to interpolate ssh franklin.dldcc.bcm.edu -i '{'aws': '/home/bpeng/.ssh/pcluster-bopeng.pem'}' -p 22 true: Invalid format specifier...