augustus: fix bug in proteinprofile on macOS

[gaberoo]

• Have you followed the guidelines for contributing?
• Have you checked that there aren't other open pull requests for the same formula update/change?
• Have you built your formula locally with brew install --build-from-source <formula>, where <formula> is the name of the formula you're submitting?
• Is your test running fine brew test <formula>, where <formula> is the name of the formula you're submitting?
• Does your build pass brew audit --strict <formula> (after doing brew install <formula>)?

---

There is a bug in augustus when built on macOS with Clang that has been reported to upstream as far back as 2016 (see nextgenusfs/funannotate#3). I ran into this when revising a formula on brewsci/bio (brewsci/homebrew-bio#642).

 ❯ augustus --species=human --proteinprofile=profile/HsDHC.prfl example.fa
# This output was generated with AUGUSTUS (version 3.3.2).
# AUGUSTUS is a gene prediction tool written by M. Stanke ([email protected]),
# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters using config directory /usr/local/Cellar/augustus/3.3.2/config/ ...

/usr/local/Cellar/augustus/3.3.2/libexec/bin/augustus: ERROR
	PP::Profile: Error parsing pattern file"profile/HsDHC.prfl", line 9.

As suggested by @nextgenusfs, this can be resolved by comping augustus with gcc on macOS.

I've also added an explicit test for this to the formula. The bug can be recreated by removing with_env. fails_with :clang cannot be used because of dependencies on boost in the auxprogs, which aren't interoperable between clang and gcc.

With the patch,

 ❯ brew test augustus
Testing augustus
==> /usr/local/Cellar/augustus/3.3.2/bin/augustus --species=human test.fasta
==> /usr/local/Cellar/augustus/3.3.2/bin/augustus --species=human --proteinprofile=HsDHC.prfl example.fa 2> /dev/null

I've also removed the run-time dependency on boost:

 ❯ brew linkage augustus
System libraries:
  /usr/lib/libSystem.B.dylib
  /usr/lib/libc++.1.dylib
  /usr/lib/libz.1.dylib
Homebrew libraries:
  /usr/local/lib/gcc/9/libgcc_s.1.dylib (gcc)
  /usr/local/opt/gcc/lib/gcc/9/libstdc++.6.dylib (gcc)
Dependencies with no linkage:
  boost

[sjackman]

Some minor nits, but otherwise looks good to me. Thanks for this fix, Gabriel.

[gaberoo]

@sjackman, am I still missing some changes?

[sjackman]

Looks good to me. Thanks, Gabriel. Note that force pushing oddly doesn't trigger a notification, so you need to bump the issue with a comment (like you did) to get my attention for another review.

[sjackman]

Merged. Thanks again for your contribution to Homebrew/core, Gabriel! 🌟