update bedtools 2.31

[bgruening]

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[mjsteinbaugh]

Erroring at this step:

2023-04-30T07:11:40.4468524Z 07:11:40 BIOCONDA INFO (OUT) make: *** No rule to make target 'install'.  Stop.

[mjsteinbaugh]

Aha I think the problem is we need to cd to nested bedtools2 subdirectory before running make.

[mjsteinbaugh]

Cool yeah that fixed it -- looks good to merge

[bgruening]

Looks like osx is failing. Thanks @mjsteinbaugh for looking at it!

[mjsteinbaugh]

Ah you're right, I'll try building locally to see if I can fix this

[mjsteinbaugh]

Hmm yeah my recipe in koopa builds bedtools on macOS but conda is failing:
https://github.com/acidgenomics/koopa/blob/main/lang/shell/bash/include/install/common/shared/bedtools.sh

Not sure what difference is causing the issue

[jmarshall]

The need to add cd bedtools2 is because the new upstream tarball contains .DS_Store files and the top-level one of those has prevented conda-build's usual “move the contents up” behaviour.

I was not able to reproduce the macOS failure locally. There are other problems with the upstream tarball that may have caused this failure, and I think the upstream tarball may be going to be re-released soon (which will also correct the .DS_Store problem).

So I would suggest holding off with this until upstream have corrected or superseded their release.

[jmarshall]

The upstream tarball has now been re-released, and this PR is probably superseded by #40802. We shall see whether the macOS failure has cured itself…

[jmarshall]

For the record: the reason why the macOS build continued to fail is that on macOS .DS_Store was ignored and did not cause the ‘usual ”move the contents up” behaviour’ to be suppressed. Hence cd bedtools2 was counterproductive on macOS:

2023-05-01T12:16:08.3334030Z 12:16:08 BIOCONDA INFO (ERR) /…/conda_build.sh: line 7: cd: bedtools2: No such file or directory

The replacement PR now does this conditionally.