Available in bioconda and/or Galaxy?

[Takadonet]

Is there any plan in putting BIGSI into bioconda for ease of installation and/or into Galaxy platform ?

[Phelimb]

Yes, will try to add packages to these, thanks!

[Phelimb]

If you've used docker, there's a prepacked install there https://hub.docker.com/r/phelimb/bigsi/

[Takadonet]

Unfortunately our computing cluster does not support docker yet.

[Phelimb]

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.

[Takadonet]

We are moving toward using singularity and hope to be moved in the near future!

[darwinbandoy]

Is there an update on the conda package?

[johnlees]

I would find a conda package useful too - I will try writing one for bioconda

[johnlees]

I've added this to bioconda (pending review): https://github.com/bioconda/bioconda-recipes/pull/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.

[johnlees]

(I think mccortex is already on bioconda)