add modbam2bed

[EliseCoopman]

Describe your pull request here

add PR of modbam2bed .

Please read the guidelines for Bioconda recipes before opening a pull request (PR).

• If this PR adds or updates a recipe, use "Add" or "Update" appropriately as the first word in its title.
• New recipes not directly relevant to the biological sciences need to be submitted to the conda-forge channel instead of Bioconda.
• PRs require reviews prior to being merged. Once your PR is passing tests and ready to be merged, please issue the @BiocondaBot please add label command.
• Please post questions on Gitter or ping @bioconda/core in a comment.

Please use the following BiocondaBot commands:

Everyone has access to the following BiocondaBot commands, which can be given in a comment:

@BiocondaBot please update	Merge the master branch into a PR.
@BiocondaBot please add label	Add the please review & merge label.
@BiocondaBot please fetch artifacts	Post links to CI-built packages/containers. You can use this to test packages locally.

For members of the Bioconda project, the following command is also available:

@BiocondaBot please merge

Upload built packages/containers and merge a PR. Someone must approve a PR first! This reduces CI build time by reusing built artifacts.

Also, the bot watches for comments from non-members that include @bioconda/<team> and will automatically re-post them to notify the addressed <team>.

[bgruening]

I don't think this is a python only package, we need a compiler and probably a build.sh.

@cjw85 do you have interest to look at this?

[cjw85]

Hi @bgruening,

In short no. We have somewhat given up with bioconda for packaging for various reasons including:

1. we make manylinux wheels for all our Python packages and publish these to PyPI (and mostly have mac wheels also), so conda builds are largely redundant.
2. waiting for bioconda builds slows our own internal build and deployment workflows, so we have switched to building our own conda packages and use our own channel, making bioconda redundant for out content.
3. The ragtag nature by which anyone can approve merge request to the pacakges we are listed as maintainers leads to issues for us. (see Require review by listed maintainers bioconda-actions#19, Update medaka to 1.7.2 #37063, ...)

In the current case the code is open source and you are of course free to do what you want with it, but any derivatives must be clearly labelled as such and not the work of Oxford Nanopore Technologies Plc. The modbampy Python package is available from PyPI and the modbam2bed program from epi2melabs/modbam2bed hosted by anaconda.

[wdecoster]

Hi @cjw85,

Let me clarify why we are trying to add modbam2bed to bioconda. @EliseCoopman developed methylmap, a tool for population-scale visualization of methylation frequencies in a heatmap format, which depends on modbam2bed to get modifications from BAM/CRAM files. But since modbam2bed is not in bioconda, it seems we could not create a bioconda recipe for methylmap (as all dependencies should come from conda-forge, bioconda, or the default anaconda channel).

If you don't object we will try to get the modbam2bed recipe right here, and in case we get stuck any insights are highly appreciated.

Wouter