Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

euk contamination hmm shouldn't be hardcoded #17

Closed
wwood opened this issue Feb 22, 2015 · 0 comments
Closed

euk contamination hmm shouldn't be hardcoded #17

wwood opened this issue Feb 22, 2015 · 0 comments

Comments

@wwood
Copy link
Collaborator

wwood commented Feb 22, 2015

Hmmer.py:            nhmmer_cmd = "nhmmer --cpu %s %s --tblout %s /srv/db/graftm/0.1/HMM/Euk.hmm " % (threads, eval, out_table)
Hmmer.py:            cmd = "nhmmer --cpu %s %s --tblout %s /srv/db/graftm/0.1/HMM/Euk.hmm %s 2>&1 > /dev/null " % (threads, eval, out_table, reads)

Maybe we need some kind of 'GRAFTM_DB' environment variable or something, where all the gpkgs live and then the user can specify them by name rather than path, and euk 18S can just be one of those. Just to make things easier. It should also be possible to specify the euk HMM directly on the cmdline though.

@geronimp geronimp closed this as completed Apr 7, 2015
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants