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.

Sign up for GitHub

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

Jump to bottom

Drop pysam dependency #3

Closed
standage opened this issue Dec 1, 2016 · 4 comments
Closed

Drop pysam dependency #3

standage opened this issue Dec 1, 2016 · 4 comments

Comments

@standage
Copy link
Collaborator

standage commented Dec 1, 2016

It's heavy and kludgy for CI (which means it's probably a pain on a lot of HPC as well). Need Python-side support for BAM parsing, but something in Pure python would be preferred.
@standage
Copy link
Collaborator Author

standage commented Dec 1, 2016

https://github.com/mdshw5/simplesam?

@standage
Copy link
Collaborator Author

standage commented Dec 7, 2016

Moved to pip install from github for now, after next release should be easier to pip install from PyPI. See pysam-developers/pysam#379.

@standage
Copy link
Collaborator Author

The groundwork has been laid for introducing BAM support in khmer.

@standage
Copy link
Collaborator Author

standage commented Apr 14, 2017 •
edited
Loading

The pysam library is now a soft dependency (as of #65). Kevlar will run fine without it, and kevlar dump will handle it gracefully with a useful error message if it is invoked without pysam installed.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@standage