Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

QUAST 5.0.0: build number to 1 for forced rebuild #10596

Closed
wants to merge 1 commit into from

Conversation

alexeigurevich
Copy link
Contributor

  • 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).

@alexeigurevich
Copy link
Contributor Author

Hi @bgruening and bioconda team! Could you assist us with this update? Quast now can use Circos to build additional plots, so we added it to the dependency list, however, this causes an issue on macOS which we don't know how to solve properly. You may see in the log:

conda.exceptions.UnsatisfiableError: The following specifications were found to be in conflict:

  • circos -> perl=5.22.0
  • perl=5.26

Quast requires Perl and by default bioconda assigns Perl 5.26 while Circos requires some Perl modules which are compiled on macOS only using deprecated 5.22.0 (see #10100 for more details).

Few notes:

  • If we don't specify circos in dependencies, Quast recipe passes all the tests and installation conda package is created. However, when a macOS user will try to install Circos after installing Quast 5.0.0, he/she gets an error (UnsatisfiableError) or gets a downgrade to Quast 4.6.3.
  • If we specify circos in dependencies and upload Quast package to our own conda channel, everything seems to be working fine (Quast is associated with Perl 5.22 as Circos). Probably Perl 5.26 is somehow implicitly required by the bioconda channel.

P.S. Sorry, I've created a new alexeigurevich-patch-1 branch on bioconda/bioconda-recipes -- should create such branch in my own repo next time to prevent messing of the bioconda repo.

@bgruening
Copy link
Member

It seems that circos needs to be rebuild against this newer perl version, at least on OSX. Can you try this?

@alexeigurevich
Copy link
Contributor Author

It looks like the circos package was rebuild a month ago on both OSX and Linux (see https://anaconda.org/bioconda/circos/files). Do you think a newer rebuild can help?

Just clarifying: am I right that for rebuilding circos I simply need to create a pull request with the incremented build number in meta.yaml?

@druvus
Copy link
Member

druvus commented Aug 28, 2018

Fixed in #10722

@druvus druvus closed this Aug 28, 2018
@bgruening bgruening deleted the alexeigurevich-patch-1 branch September 1, 2018 12:28
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants