update bwa-0.7.17: enable linux-aarch64 build

[guozhicong]

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[jmarshall]

BWA 0.7.17 contains x86 SIMD code, so does not compile on ARM:

07:40:22 BIOCONDA INFO (OUT) ksw.c:29:10: fatal error: emmintrin.h: No such file or directory

An ARM port of this code (lh3/bwa#359) was merged 18 months ago but has not yet appeared in a bwa release.

In order to feasibly produce a linux-aarch64 package of BWA, @bioconda/core must lobby upstream for a new release.

[martin-g]

Here is an issue asking for a new release - lh3/bwa#401

I have seen some recipes using Git SHA as a version. A proper upstream release would be better but maybe this is an option too ?!

[BiocondaBot]

Reposting for @guozhicong to enable pings (courtesy of the BiocondaBot):

BWA 0.7.17 contains x86 SIMD code, so does not compile on ARM:

07:40:22 BIOCONDA INFO (OUT) ksw.c:29:10: fatal error: emmintrin.h: No such file or directory

An ARM port of this code (lh3/bwa#359) was merged 18 months ago but has not yet appeared in a bwa release.

In order to feasibly produce a linux-aarch64 package of BWA, @bioconda/core must lobby upstream for a new release.

BWA 0.7.17 包含 x86 SIMD 代码，因此无法在 ARM 上编译：

07:40:22 BIOCONDA INFO (OUT) ksw.c:29:10: fatal error: emmintrin.h: No such file or directory

此代码的 ARM 移植版 ( lh3/bwa#359 ) 已于 18 个月前合并，但尚未出现在 bwa 版本中。

为了切实可行地生成 BWA 的 linux-aarch64 包，@bioconda/core 必须游说上游发布新版本。

[guozhicong]

@jmarshall @martin-g Can I fix this problem by replacing the header file emmintrin.h with sse2neon.h as this README describes.

[martin-g]

From lh3/bwa#359 :

| There are already BWA PRs lh3/bwa#283 and lh3/bwa#344, which port the SIMD code to other platforms using SIMDe and sse2neon respectively

You can read the PR descriptions for all the history.

[jmarshall]

No. It would not be appropriate for bioconda to take on the maintenance burden of porting bwa to sse2neon. Moreover the work has already been done; and PR lh3/bwa#359 explains why that PR's approach is superior to a naive sse2neon port.

The appropriate approach for bioconda is to lobby for a new upstream release, as that is of benefit to the wider community. The other (inferior) approach open to bioconda IMHO is to apply that PR as a patch. Any other approach is not a feasible burden for bioconda IMHO.

[guozhicong]

@jmarshall @martin-g Thanks!!! It's impossible for BWA to release a new version in the near future. I'll apply that PR lh3/bwa#359 as a patch to fix this problem.

[martin-g]

It's impossible for BWA to release a new version in the near future

Do you know that from the maintainer ?
Or you meant to say "if it is impossible ..." ?

[jmarshall]

Whether to take on the burden of patching this is also a question for @bioconda/core. IMHO we should not, as this is an excellent opportunity to encourage a long-overdue new release.

[guozhicong]

@martin-g Sorry ... I mean to say "if it is impossible ..."