Update mosdepth to 0.3.8

[asp8200]

Update mosdepth to 0.3.8.

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[brentp]

Thanks for going through this. I'd prefer to stick to nim < 2 for this as I haven't tested fully on nim 2.0+. And the OSX build would be nice to have.

[asp8200]

Thanks for going through this. I'd prefer to stick to nim < 2 for this as I haven't tested fully on nim 2.0+. And the OSX build would be nice to have.

Hi @brentp. As you may have already noticed from the commit history on this PR, I did try to set nim < v2, but that seemingly forced nim to go all the way back to v1.4.8 and osx still failed. (I guess the build process went for nim v1.4.8 in that case, because v1.6 isn't available at https://anaconda.org/conda-forge/nim/files )

Do you have any suggestions as to which version of nim I should try? Cheers

[brentp]

probably the best way is to get the binaries from here: https://github.com/nim-lang/nightlies/releases/tag/latest-version-1-6 in the recipe

[asp8200]

probably the best way is to get the binaries from here: https://github.com/nim-lang/nightlies/releases/tag/latest-version-1-6 in the recipe

Tried something. From the logs from the failing osx-build:

BIOCONDA INFO (OUT) Downloading https://github.com/nim-lang/nightlies/archive/refs/tags/2024-04-24-version-1-6-b7b3f87719a201007e5dc0730bf73141fd908c6a.zip
BIOCONDA INFO (ERR) INFO:conda_build.source:Downloading https://github.com/nim-lang/nightlies/archive/refs/tags/2024-04-24-version-1-6-b7b3f87719a201007e5dc0730bf73141fd908c6a.zip
BIOCONDA INFO (OUT) Success

which looked promising, but nevertheless nimble wasn't found during the subsequent attempted build of mosdepth:

BIOCONDA INFO (ERR) /opt/mambaforge/envs/bioconda/conda-bld/mosdepth_1714289370255/work/conda_build.sh: line 10: nimble: command not found

[brentp]

is it getting unzipped and installed by some bioconda magic? I would think you'd need to unzip and then update the path to point to the bin directory.

[asp8200]

is it getting unzipped and installed by some bioconda magic? I would think you'd need to unzip and then update the path to point to the bin directory.

I'm at a loss here. Even when trying to build nim from source, the build of mosdepth under linux worked. That seems to indicate that building nim from source does work - at least under linux 🤔

I looked at the following recipes which also seem to install some dependencies from source:

https://github.com/bioconda/bioconda-recipes/blob/master/recipes/anise_basil/meta.yaml https://github.com/bioconda/bioconda-recipes/blob/master/recipes/anise_basil/build.sh

https://github.com/bioconda/bioconda-recipes/blob/master/recipes/artic-tools/meta.yaml https://github.com/bioconda/bioconda-recipes/blob/master/recipes/artic-tools/build.sh

I don't see any unzipping of the downloaded zip-files or installing, so I kind of figured that was done by some bioconda-magic.

This commit for artic-tools seemed to be intended for fixing osx-build, and it seemingly did so by simply adding url and sha256 under source: in the meta.yaml - very much like I tried doing for this PR 🤔

[asp8200]

Got the tests passing by installing osx-release of nim v1.6 in the osx-part of build.sh-file.

Seems like a pretty hacky solution 🤔 Also, I don't understand how the linux-test can pass, when I seemingly disabled the install of nim for linux? 🤔

[asp8200]

Just tested this on both linux and macOs by conda-installing:

mosdepth                0.3.8  h212548b_0  bioconda

and running:

mosdepth -n --fast-mode --by 500 sample.wgs test.paired_end.sorted.bam

It worked fine - as far as I can tell.