Ilya Shlyakhter

navi-mode is certainly useful, but doesn't replace Org's ability to drill down to just one part of the outline, and to move around using 2-3 uniform commands without switching buffers....

It folds plain lists (see doc of org-cycle-include-plain-lists for details). It also folds drawers and code blocks (though the end of those is simpler to find that the end of...

What about just using navi-keywords? It's not much work to define a regexp that matches class/function headlines in a given major mode. You then OR that regexp with the current...

it's like this: mfa_code = sys.argv[1] mfa_device_id = 'arn:aws:iam::AWS_ACCT_NUMBER:mfa/IAM_USER_NAME' def get_session_info(): sts_client = boto3.client('sts') sts_response = sts_client.get_session_token( DurationSeconds=900, SerialNumber=mfa_device_id, TokenCode=mfa_code ) creds = sts_response.pop('Credentials') print(sts_response) return dict(aws_access_key_id=creds['AccessKeyId'], aws_secret_access_key=creds['SecretAccessKey'], aws_session_token=creds['SessionToken']) session_info...

https://boto3.readthedocs.io/en/latest/reference/services/sts.html#STS.Client.get_session_token

https://docs.aws.amazon.com/IAM/latest/UserGuide/id_credentials_mfa_sample-policies.html

A branch adding metaspades is https://github.com/broadinstitute/viral-ngs/tree/is-add-metaspades

I've added bbmap on an old branch ( https://github.com/broadinstitute/viral-ngs/tree/is-1808081312-add-bbmap ); I'll update it and make a PR.

So which workflow would this be in? Right now metagenomics analysis and reference-assisted assembly are different workflows. For the latter we'd blast against a small db of just the taxon...

I was thinking assembly. For metagenomics, it doesn't necessarily matter where a contig blasts to, only that it does? In assembly, a misassembled contig might not align well to a...