t-coffee-12.00.7fb08c2 (build 1)

[pditommaso]

• I have read the guidelines for bioconda recipes.
• This PR adds a new recipe.
• AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
• This PR updates an existing recipe.
• This PR does something else (explain below).

[SchwarzMarek]

Hi,
may I ask why to fix viennarna to 2.1.9 ?

Also tmalign should now be in bioconda, and kalign was merged today and should be in bioconda after successful nightly build. So you can add them as deps.

[pditommaso]

may I ask why to fix viennarna to 2.1.9 ?

because it's the version used by tcoffeee (see here)

Also tmalign should now be in bioconda, and kalign was merged today and should be in bioconda after successful nightly build. So you can add them as deps.

Excellent! If you add tmaling remove the one compiled in the build script and the deps on the fortran compiler.

[SchwarzMarek]

Well I don't exactly know how the t-coffee access RNAplfold, but there are at least 2 bug-fixes in RNAplfold (2.2.9 and 2.3.2). And the behavior seems to be consistent up to 2.3.4 (which introduced colored output). here

[pditommaso]

Well I don't exactly know how the t-coffee access RNAplfold, but there are at least 2 bug-fixes in RNAplfold (2.2.9 and 2.3.2)

Yes, but this recipe should use the same package versions used in the upstream tcoffee build for the sake of reproducibility.

[druvus]

@pditommaso I restarted testing after the rebuilding of problematic dependencies and it seems to work now.

[pditommaso]

Excellent! I've pushed another commit to fix the pre-link hook script.

[pditommaso]

Not sure to understand why the linting is failing

From ssh://github.com/bioconda/bioconda-recipes
 * [new branch]          master     -> __upstream__rZ0o3h9oMI/master
Your bioconda-recipes CI configuration is out of date.
Please update it to the latest version of the upstream master branch.
You can do this, e.g., by running:
  git fetch https://github.com/bioconda/bioconda-recipes.git master
  git merge FETCH_HEAD
Exited with code 1

[druvus]

A modification of circleci config got merged in #12662. So you need to merge master into your branch to restart the testing.

[pditommaso]

Oops, it should better now.

[pditommaso]

No way, now it's failing the pre-link

Command '['bash', '-x', '/opt/conda/pkgs/t-coffee-12.00.7fb08c2-h26a2512_1/bin/.t-coffee-pre-link.sh']' returned non-zero exit status 1.

[pditommaso]

Nice, all green! Please merge at your convenience.