Add new recipe mantis-msi2

[nh13]

This is a fork of mantis-msi, as the latter version is no longer being maintained.

mantis-msi2 includes fixes.

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[nh13]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built on Azure are ready for inspection:

Arch	Package	Zip File
linux-64	mantis-msi2-2.0.0-h9f5acd7_0.tar.bz2	LinuxArtifacts
osx-64	mantis-msi2-2.0.0-hcd10b59_0.tar.bz2	OSXArtifacts

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You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c packages <package name>

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Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package	Tag	Install with docker
mantis-msi2	2.0.0--h9f5acd7_0	show gzip -dc LinuxArtifacts/images/mantis-msi2:2.0.0--h9f5acd7_0.tar.gz | docker load

[nh13]

@BiocondaBot please add label

[nh13]

Verified the OSX artifacts works for me locally

[daler]

@nh13 is upstream just not taking PRs or something? Or have the original authors documented that they will not maintain? The reason I as is that the changes in the fork seem pretty minor such that they could easily be incorporated to the original, which would save a little maintenance burden in bioconda and would be less confusing to users.

[nh13]

@daler The original authors have not documented that they will not maintain. However, the upstream hasn't accepted a PR since Jan 23 2020, with the last response on a comment since Nov 6 2020. The person who merged that PR and made that last comment (rbonneville) hasn't had any activity on github since April 16 2021, and I haven't seen any other activity elsewhere on other sites.

The changes in the fork are required for a clinical organization, who uses conda/bioconda as part of a reproducible build system. I have another clinical client that uses it as well (and is lucky to have chr prefixes; see below). Furthermore, I am re-implementing the software (from Python/C++ into rust, see first PR). This includes unit tests (none in the original) that have already found bugs/issues.

Yes, forks are not ideal, but in this case, the fact that bugs like this one make the original software unusable for genomes that have no chr prefix. I am totally open to forks not being accepted as easily as new software, but in this case I don't see an alternative versus having to maintain and install the software separately from bioconda. Thoughts?

[dpryan79]

@BiocondaBot please merge

[BiocondaBot]

I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.

[daler]

@nh13 thanks for all the context. Fully agreed with your position, and definitely sounds like the tool (and reimplementation) is in the right hands now!

[nh13]

@daler thank-you!