Update bedtools to 2.31.0

[jmarshall]

Update checksum (again) to reflect the re-released upstream tarball. Remove run dependencies, which will be detected automatically.

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[jmarshall]

Ugh, this time the upstream tarball is full of AppleDouble files, which have again foiled the tarball content hoisting:

2023-05-04T23:54:48.2071461Z 23:54:37 �[32mBIOCONDA INFO�[0m (OUT) .
2023-05-04T23:54:48.2072063Z 23:54:37 �[32mBIOCONDA INFO�[0m (OUT) ..
2023-05-04T23:54:48.2072381Z 23:54:37 �[32mBIOCONDA INFO�[0m (OUT) ._bedtools2    # <--
2023-05-04T23:54:48.2072613Z 23:54:37 �[32mBIOCONDA INFO�[0m (OUT) bedtools2

So it may need to be regenerated once again.

[jmarshall]

Not only might the AppleDouble droppings issue be fixed in future bedtools release tarballs, but it has different effects on Linux and macOS: on macOS the extra files do not prevent conda-build's hoisting behaviour. Thus the Hoisting prevented message appears in the Linux build log but not the macOS build log.

Hence with the current upstream tarball (which upstream has not yet regenerated again, so we may wish to work around the problem rather than wait), the cd bedtools2 is required on Linux and required not to be done on macOS — so the if condition is required.

[jmarshall]

What is the @bioconda/core policy on stripping executables?

Bedtools is a C++ executable. In the macOS build, bedtools is 2.2 MB and after stripping is 1.6 MB. In the Linux build, bedtools is 50 MB and after stripping drops to 2 MB.

This has been the case for a while: see the Anaconda bedtools file listing in which Linux packages are ~15 MB while macOS ones are ~1 MB. So Linux downloads and installations are arguably unnecessarily bloated.

In fact, it appears to have started with bedtools 2.28 — so perhaps there is a Makefile setting that changed then that we can change back.

[BiocondaBot]

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

Arch	Package	Zip File
linux-64	bedtools-2.31.0-h468198e_0.tar.bz2	LinuxArtifacts
osx-64	bedtools-2.31.0-h61647ba_0.tar.bz2	OSXArtifacts

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You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c ./packages <package name>

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Docker image(s) built (images are in the LinuxArtifacts zip file above):

Package	Tag	Install with docker
bedtools	2.31.0--h468198e_0	show gzip -dc LinuxArtifacts/images/bedtools:2.31.0--h468198e_0.tar.gz | docker load

[bgruening]

Thanks @jmarshall!

[dpryan79]

Regarding stripping executables, there's no real policy there. We kind of assume there's a good reason that debug information is included if it's in there so we generally don't strip it out.

[jmarshall]

@dpryan79: Thanks. In this case, the Makefile change adding -g to release builds appears to have been accidentally committed along with something else, so I had no real qualms about removing it and will suggest to upstream that they revert that accidental change too.