Replace t_coffee with t-coffee

[amizeranschi]

In light of the recent un-blacklisting and update of t-coffee (a78d91b), it should now replace t_coffee as a dependency here.

For more info: #32576 (comment)

[nsoranzo]

Can you please fix the linting issues (bump the build number and remove the skip line)?

[0xaf1f]

I think this PR should also be marked as resolving the issue #32576. I'm excited to see it land!

[amizeranschi]

Can you please fix the linting issues (bump the build number and remove the skip line)?

OK, did I properly address what you meant?

[nsoranzo]

@amizeranschi Yes, thanks, let's see if tests pass now!

[0xaf1f]

@dpryan79, are we sure that the new t-coffee package is working now? This package is trying to switch to using it but the tests fail when trying to run t-coffee. With several errors like

15:21:37 BIOCONDA INFO (OUT) #   Failed test at t/TCoffee.t line 74.
15:21:37 BIOCONDA INFO (OUT) # died:
15:21:37 BIOCONDA INFO (OUT) # ------------- EXCEPTION -------------
15:21:37 BIOCONDA INFO (OUT) # MSG: TCoffee call crashed: 256 [command /opt/conda/conda-bld/perl-bio-tools-run-alignment-tcoffee_1669994129120/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/bin/t_coffee  -profile=wFKPu888Ma -seq=ty5F_FnXFD -matrix=blosum -method=lalign_id_pair,clustalw_pair  -ktuple=3 -outfile=/tmp/fVnlE_JMmE/Aede5VRDuk -output=clustalw -quiet]
15:21:37 BIOCONDA INFO (OUT) #

[nsoranzo]

I see similar errors with the Galaxy wrapper, it seems a recent rebuild is causing issues (it was definitely working before with the same t-coffee version).

[0xaf1f]

Yes, the t-coffee package build was not complete and that's what doomed this package's test. I described the bug and made a pull request to fully build t-coffee.

[0xaf1f]

Can we re-run the builds now that the new t-coffee package is in the archive? I tested the failing test suite command here using the new t-coffee build and can confirm it works.

[nsoranzo]

@BiocondaBot please merge

[BiocondaBot]

I will attempt to upload artifacts and merge this PR. This may take some time, please have patience.