from traitlets.config.manager import BaseJSONConfigManager
path = "/Users/camille/.jupyter/nbconfig/"
cm = BaseJSONConfigManager(config_dir=path)
cm.update('livereveal', {
'theme': 'beige',
'transition': 'zoom',
'start_slideshow_at': 'selected',
'scroll': True,
'width': 1800,
'height': 1080,
})
{'height': 1080, 'scroll': True, 'start_slideshow_at': 'selected', 'theme': 'beige', 'transition': 'zoom', 'width': 1800}
dammit is a simple de novo transcriptome annotator. It was born out of the observations that annotation is mundane and annoying, all the individual pieces of the process exist already, and the existing solutions are overly complicated or rely on crappy non-free software.
Science shouldn't suck for the sake of sucking, so dammit attempts to make this sucky part of the process suck a little less.
Thoughts from 2015...
and of course,
dammit annotate test.fa --sshloginfile <name_of_loginfile>
The gnu-parallel docs have more on the format for this file (and I have an example kicking around somewhere, I think in the docs).
There are now three pipeline options:
lastal
against uniref90--quick
: basic stats, BUSCO, TransDecoder, and user provided databases (drops HMMER, Infernal, OrthoDB)--full
: All the things.WIP: Plugin support. Basic outline is sketched. For now, it's at least easier to add new tasks.
Several rather vexing errors ended up being caused by database downloads and/or preparations being interrupted. Databases are now MD5-checked after download.
Downsides: this makes database status check a bit slower (not too bad though)
config.json
at the CLI with --config-file
dammit dependencies
subcommandDependentTask
, which exposes an interface to check for existence of command line tools[discussion]
How should it be maintained?
How to improve community involvement
How to make third-party reqs more future-proof?
[discussion]