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wzthu / Rbowtie2

Bioconductor package: an R wrapper for Bowtie2 and AdapterRemoval
https://www.bioconductor.org/packages/release/bioc/html/Rbowtie2.html
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Add 'simde' as a Git submodule #8

Closed martin-g closed 1 year ago

martin-g commented 1 year ago

Fixes #7

Used the following command to add the submodule:

git submodule add --name simde -b master https://github.com/simd-everywhere/simde-no-tests.git src/bowtie2-2.4.4/third_party/simde

martin-g commented 1 year ago

@wzthu Could you please update the bioconductor repo with this improvement and a version bump? Thank you!

wzthu commented 1 year ago

Done.

martin-g commented 1 year ago

Thanks, @wzthu ! I don't see it at https://code.bioconductor.org/browse/Rbowtie2/commits/master yet. Maybe the code browser needs some time to detect it. I'll check again later and let you know if it is still missing.

martin-g commented 1 year ago

I see the commits now!

hpages commented 1 year ago

Unfortunately Bioconductor doesn't support git submodules at the moment so the simde-no-tests source tree would need to be copied to Rbowtie2.

(BTW note that something seems to be wrong with how the "simde" submodule is currently registered in Rbowtie2 anyways, because git clone --recurse-submodules https://github.com/wzthu/Rbowtie2 ignores it.)

martin-g commented 1 year ago

Thank you, @hpages ! I will send a new PR that copies the simde sources instead of using Git submodules.

hpages commented 1 year ago

Sounds good. Just to be clear, the simde sources should be added to the Rbowtie2 git repo, rather than dynamically downloaded and added to the package C code at package installation time. Thx!