bwa: update to latest master and add linux-aarch64

[martin-g]

Describe your pull request here

---

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

General instructions

• 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.

Instructions for avoiding API, ABI, and CLI breakage issues

Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes.
This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe.
If not already present in the meta.yaml, make sure to specify run_exports (see here for the rationale and comprehensive explanation).
Add a run_exports section like this:

build:
  run_exports:
    - ...

with ... being one of:

Case	run_exports statement
semantic versioning	{{ pin_subpackage("myrecipe", max_pin="x") }}
semantic versioning (0.x.x)	{{ pin_subpackage("myrecipe", max_pin="x.x") }}
known breakage in minor versions	{{ pin_subpackage("myrecipe", max_pin="x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
known breakage in patch versions	{{ pin_subpackage("myrecipe", max_pin="x.x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
calendar versioning	{{ pin_subpackage("myrecipe", max_pin=None) }}

while replacing "myrecipe" with either name if a name|lower variable is defined in your recipe or with the lowercase name of the package in quotes.

Bot commands for PR management

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.

Note that the @BiocondaBot please merge command is now depreciated. Please just squash and merge instead.

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

[martin-g]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Azure

No artifacts found on the most recent Azure build. Either the build failed, the artifacts have been removed due to age, or the recipe was blacklisted/skipped.

CircleCI

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

Arch	Package	Repodata
linux-aarch64	bwa-0.7.17-h73052cd_12.tar.bz2	repodata.json

---

You may also use conda to install these:

conda install -c https://output.circle-artifacts.com/output/job/6b5e733a-a91c-4bf0-a3a9-371defe6b010/artifacts/0/tmp/artifacts/packages <package name>

[martin-g]

mgrigorov in 🌐 euler-arm-22 in /tmp/bwa via 🅒 font-ubuntu 
❯ file bin/*                                                                                                                                                                                           (font-ubuntu) 
bin/bwa:          ELF 64-bit LSB pie executable, ARM aarch64, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, with debug_info, not stripped
bin/qualfa2fq.pl: Perl script text executable
bin/xa2multi.pl:  Perl script text executable

mgrigorov in 🌐 euler-arm-22 in /tmp/bwa via 🅒 font-ubuntu 
❯ ./bin/bwa                                                                                                                                                                                            (font-ubuntu) 

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.17-r1198-dirty
Contact: Heng Li <hli@ds.dfci.harvard.edu>

Usage:   bwa <command> [options]

Command: index         index sequences in the FASTA format
         mem           BWA-MEM algorithm
         fastmap       identify super-maximal exact matches
         pemerge       merge overlapping paired ends (EXPERIMENTAL)
         aln           gapped/ungapped alignment
         samse         generate alignment (single ended)
         sampe         generate alignment (paired ended)
         bwasw         BWA-SW for long queries (DEPRECATED)

         shm           manage indices in shared memory
         fa2pac        convert FASTA to PAC format
         pac2bwt       generate BWT from PAC
         pac2bwtgen    alternative algorithm for generating BWT
         bwtupdate     update .bwt to the new format
         bwt2sa        generate SA from BWT and Occ

Note: To use BWA, you need to first index the genome with `bwa index'.
      There are three alignment algorithms in BWA: `mem', `bwasw', and
      `aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
      first. Please `man ./bwa.1' for the manual.

[martin-g]

@jmarshall What do you think about this approach (using Git SHA) ?
I could add the other PRs you mentioned at lh3/bwa#401 (comment) as patches too !

[jmarshall]

Such a package would be lying when it claimed to be an accurate rendition of BWA 0.7.17.

Me, I would very much rather that @bioconda/core added its voice to advocate for a proper upstream BWA release.

I would regret having mentioned those PRs if doing so caused bioconda to do extra work to convert them to local patches. That would be wasted work; the effort would be better put to improving BWA upstream, and later taking advantage of that in our packaging.

[martin-g]

Converted the PR to a Draft until it is decided whether using git_url is a good idea or not.
There is no new release of bwa since 7 years ...

[bgruening]

Fwiw: I added a comment to the upstream issue.

[jmarshall]

Superseded by #47224.