[Nextalign] Consider packaging and uploading to different package managers and container repos

[ivan-aksamentov]

Despite Nextalign being a single-file download, we might also consider packaging it for even simpler installation.

We might package for:

• Conda
• Homebrew
• Various Linux distros with deb and rpm
• Possibly various scientific package managers
• Chocolatey, when Windows native binaries are available

What is your favorite package manager? Let us know.

We welcome community contributions in this area!

Related: #422

[cjw85]

Hi, I'm just considering creating a package for conda to go in bioconda.

I'll let you know how I get on.

[rneher]

@cjw85 We'd love to have this in bioconda!

[cjw85]

I've put nextalign for linux there using your binaries on the Github release page. This seems to be acceptable given the number of bioconda packages create with static binaries. There's a bit more work to do it for the macOS binaries.

[ivan-aksamentov]

@cjw85 Thanks!

Further we could use selectors to download files for different platforms (in conda terms that will be linux64, osx and arm64) and to use destination directory and filename to keep the build.sh script platform-independent.

P.S. The package recipe is here if someone wants to try to add other platforms: https://github.com/bioconda/bioconda-recipes/tree/master/recipes/nextalign

[huddlej]

Thank you @cjw85 and @ivan-aksamentov! I've added support for x86 OS X in a PR. If this goes through, I'll add support for arm64 OS X, too.

[Batsi-2015]

@ivan-aksamentov and @cjw85 is it possible to also have Nextclade on bioconda?

[cjw85]

For the time being we've (Oxford Nanopore Technologies) have added the nextclade node CLI to a custom conda channel:

https://anaconda.org/epi2melabs/nextclade-cli

[ivan-aksamentov]

Nextclade and Nextalign are now semi-automatically released on bioconda (they still require manual approval for PRs).

This is additional to the main venues: GitHub Releases and Docker, as described in the documentation.

We will unlikely have resources to implement and maintain any additional packaging. But if someone in community wants to add other packaging automation to our CI, then we are happy to review your pull requests.

Feel free to comment, open issues and PRs as you see fit.