install bwa 0.7.17 in alpine docker image

[cmccabe0728]

I am trying to install bwa 0.7.17 in alpine:3.15.4. I am reading issue PR275 which if I am reading correctly I need to replace the makefile in the install directory with the makefile from github? Or is there something else? Thank you :).

 https://github.com/lh3/bwa/issues/275

/usr/lib/gcc/x86_64-alpine-linux-musl/10.3.1/../../../../x86_64-alpine-linux-musl/bin/ld: ./libbwa.a(rope.o):/home/ec2
-user/bwa-0.7.17/rle.h:33: multiple definition of `rle_auxtab'; ./libbwa.a(bwtindex.o):/home/ec2-user/bwa-0.7.17/rle.h
:33: first defined here
/usr/lib/gcc/x86_64-alpine-linux-musl/10.3.1/../../../../x86_64-alpine-linux-musl/bin/ld: ./libbwa.a(rle.o):/home/ec2-
user/bwa-0.7.17/rle.h:33: multiple definition of `rle_auxtab'; ./libbwa.a(bwtindex.o):/home/ec2-user/bwa-0.7.17/rle.h:
33: first defined here
collect2: error: ld returned 1 exit status
make: *** [Makefile:30: bwa] Error 1

Post also suggest adding two lines to the docker might help:

sed -i 's/a\/rle.h//' makefile
sed -i 's/b\/rle.h//' makefile

[jmarshall]

Crossposted to biostars.

You need to apply 2a1ae7b from #267. And BWA needs a new release that actually compiles with current compilers, but several outstanding PRs should be merged before a new release is made: see the commentary in my biostars answer.