Error: "bowtie2-build-s does not exist" on Windows

[ivoseverins]

First of all: thank you for making wonderful software!

When I run bowtie2-build (v2.5.3) on Windows 11 I get the error:

bowtie2-build-s does not exist, try running `[g]make bowtie2-build-s

The problem seems to be in line 118 of the bowtie2-build python script:

if not os.path.exists(build_bin_spec):

In my case it searches for bowtie2-build-s, but in the folder there is only bowtie2-build-s.exe.

Changing line 118 to

if not (os.path.exists(build_bin_spec) | os.path.exists(build_bin_spec + '.exe')):

fixes the issue for me.

Note that I did not use v2.5.4, as the Windows binaries for that version produced other errors.