Update falco to 1.2.5

[BiocondaBot]

Update falco: 1.2.4 → 1.2.5

Info	Link or Description
Recipe	recipes/falco (click to view/edit other files)
Summary	falco is a drop-in C++ implementation of FastQC to assess the quality of sequence reads.
Home	https://github.com/smithlabcode/falco
Releases
Recipe Maintainer(s)	@andrewdavidsmith, @guilhermesena1
Author	@smithlabcode

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[pdimens]

@andrewdavidsmith can you identify why the macOS build isn't working?

[andrewdavidsmith]

Will do. Can you confirm it's x86 that's the issue? That's the only macOS I have access to rn.

[pdimens]

@andrewdavidsmith IIUC, it's x86: https://github.com/bioconda/bioconda-recipes/actions/runs/11964515768/job/33357256284?pr=52297#step:7:728

[andrewdavidsmith]

Got it. Hopefully next few hours.

[andrewdavidsmith]

@pdimens Might take some time. I assumed it was the make check step, which fails for me due to different cli for the md5sum command, which I use to validate test output files. But what I'm seeing in the workflow file has drifted a bit from what I originally had and the logs aren't telling me much. There will be some trial-and-error here unless someone else has some insights. If there's anything I need to open up to allow others modify parts of this PR, I'm happy to do that and happy for anyone's help.

[andrewdavidsmith]

@mencian Thanks for this, but it didn't work. I only have gcc and llvm-clang (not darwin-clang) on my mac. I can see that the darwin-clang is used to try and compile, but I can't really debug that. I would try to switch it to gcc. My approach to getting it to work with htslib isn't the same as was put into the meta.yml file, so this is drifting a bit away from what I know. Is it possible to pull in gcc and build with CXX=g++? Thanks for any help -- I'll try to look at other recipes.

[andrewdavidsmith]

In case it helps, this is how I configure to compile falco on my Mac and it should indicate lots about my env:

../configure CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib" CC="gcc-14" CXX="g++-14" --prefix=${HOME}

I think I got all dependencies from Homebrew (zlib, htslib and gcc).

[andrewdavidsmith]

A bit of an update: I can get a build on macos with the native darwin clang (also aliased as gcc for some reason when installed with xcode I think), but if I do that I can only get it to link with htslib when htslib is installed using Homebrew or from sources. Using the various environment variables that are currently in the build.sh script seems to make a tradeoff between what is seen at compiler or link time, at least in my hands, so some of them might be working against me in my environment. But even without those I'm not yet successful at using the darwin compiler when htslib is installed through conda.

[pdimens]

@andrewdavidsmith is this related? #52553

[andrewdavidsmith]

@pdimens I'm not sure. I can't see all details in the logs. I wish the logs were more detailed. I can't replicate the exact problem on my end. I can replicate several issues when I use the native darwin compiler, but if I get some of the dependencies through homebrew I can make it work. If I need to get everything through conda, something breaks. Unfortunately I don't think the environment variables used in the runners here are the same as I can see on my x86 macbook. I did not yet go through all the other recipes to see which ones might be most similar to falco and try to replicate theirs. I think someone else likely already has that expertise, and it would take a long time for me to go through it. I'm willing to attempt it, but likely it won't be until late next week. Sorry for the delay. If there's any other way I can help you setup the software, let me know.