Update UCSC recipes

[siebrenf]

The UCSC tools occasionally throw errors that should have been fixed ages ago (example1, example2). So I thought I'd try to update the recipes first.

breakdown:

• updated ucsc_config.yaml
• updated create-ucsc-packages.py
  • several packages have been fixed on UCSC's side and can now use the default build system
  • extended summary_program checking code
• updated the UCSC patch
  • use shared libssl and libcrypto libraries
  • fixed straw compilation
• updated all (template) recipes
  • added build dependency make as added manually in previous Bulk PRs
  • added build dependencies for straw (cxx + binutils to export Conda's ld command) as it is built for every package
  • left in the OSX build skip
  • removed unused run_test.sh scripts

The skeletons should now be up to date again. Errors are likely due to individual recipes breaking.

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[siebrenf]

@bioconda/core, I'm pinging you directly because of the size of this PR (it might have to point to the bulk branch).

This PR should now be in a decent state (I tested a handful of recipes using the standard build system, plus one recipe of each custom build systems, with bioconda-utils build locally).

[mbargull]

@siebrenf, thanks a bunch!

• ... manually in previous Bulk PRs

Haha, yeah I remember, in 2020 I fixed some hundreds recipes semi-automatically and the UCSC ones were a part of it -- guess during that busywork I never got to modify the templates accordingly 🤦 . Thanks for rectifying that! :).

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I'd like to review this, but will probably not get to it in the next two weeks or so. After the review e should then build this on bulk. But the bulk branch will also be busy with the upcoming Bioconductor update during that time frame, so hopefully my pending review will not delay this too much.

Thanks again for working on this and also for detailing your changes.

[mbargull]

Hi @siebrenf, I'll be reviewing this today/tomorrow so we can proceed and build all of v439 probably this week.

[aliciaaevans]

Closing in favor of #50325 which has been merged and used to bulk update. If you think there are any improvements to the scripts that are on this branch that the other one missed, please let me know and/or open a fresh PR without recipe changes.

Sorry this never ended up getting approved, I am just finding it now when searching for old UCSC PRs.