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.

[ch4rr0]

I pushed a change to the bug_fixes branch that addresses this issue. The changeset will be part of the next release.

P.S. what issues are you having with v2.5.4?

[ivoseverins]

Thank you!

For v2.5.4 when running bowtie2-build (without any arguments) I get the error:

OSError: [WinError 193] %1 is not a valid Win32 application`

When running bowtie2 (without any arguments) I get the error:

(ERR): Expected bowtie2 to be in same directory with bowtie2-align:
C:/Users/user/Desktop/bowtie2-2.5.4-mingw-aarch64/
Exiting now ...

Which is a similar error as #489. Perhaps it is related to #480?