Available in bioconda and/or Galaxy?
Opened this issue · 9 comments
Is there any plan in putting BIGSI into bioconda for ease of installation and/or into Galaxy platform ?
Yes, will try to add packages to these, thanks!
If you've used docker, there's a prepacked install there https://hub.docker.com/r/phelimb/bigsi/
Unfortunately our computing cluster does not support docker yet.
Have you come across singularity http://singularity.lbl.gov/user-guide? I think they have better support for clusters and also support docker containers.
I'll also make a conda package as I know containers aren't widely supported.
We are moving toward using singularity and hope to be moved in the near future!
Is there an update on the conda package?
I would find a conda package useful too - I will try writing one for bioconda
I've added this to bioconda (pending review):
bioconda/bioconda-recipes#13969
Only requirement was to add a package for mmh3 in conda-forge
The test only checks that the bigsi imports work, and that the command line can work, so if there is an issue with berkeley-db that is called later I don't know if that gets picked up, so might be worth testing locally too.
I didn't add rocks-db support, as the conda-forge package for that is in limbo.
(I think mccortex is already on bioconda)