Dependency conflict when installing from bioconda along with Python 3.9

[jlumpe]

I've been unable to install FastANI from Bioconda in an environment using Python 3.9:

$ conda create -n test python=3.9 bioconda::fastani

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: | 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                                                                                                                                        

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package python conflicts for:
bioconda::fastani -> boost[version='>=1.70.0,<1.70.1.0a0'] -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']
python=3.9The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.34=0
  - bioconda::fastani -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
  - python=3.9 -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.34

The conda output doesn't make a whole lot of sense to me but I notice that it seems to be requiring the boost version be exactly 1.70.0, which seems overly restrictive.

[cjain7]

Sorry the error is unclear to me as well. I've limited experience with bioconda. Would it help to post the issue here: https://github.com/bioconda/bioconda-recipes/issues

[jlumpe]

Yeah I wasn't sure which place would be more appropriate. I'll file an issue there as well.

[rpetit3]

Hi @cjain7

Is there a specific version of boost that is needed?

[cjain7]

Can we mimic Mash bioconda recipe for FastANI? Boost can be replaced with gsl. https://bioconda.github.io/recipes/mash/README.html

[rpetit3]

I'll give it a try and see how it goes

[rpetit3]

@cjain7 mind taking a look at https://github.com/bioconda/bioconda-recipes/pull/33433 for me. I think I made the needed changes to use gsl instead of boost

Are their any significant differences in speed using one over the other?

[cjain7]

Looks ok to me. Thanks for addressing this. I don't expect a runtime difference.

[jlumpe]

It's now working with version 1.33.