ResolvePackageNotFound issue with pplacer

WatsonLab / MAGpy

Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)

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ResolvePackageNotFound issue with pplacer #2

Closed bstamps closed 5 years ago

bstamps commented 6 years ago

Hello,

Having some trouble in the install- running the below

conda env create -f MAGpy/envs/MAGpy-3.5.yaml

Produces the below error-

Solving environment: failed

ResolvePackageNotFound: 
  - pplacer==1.1.alpha17=0

Is this a conda issue, or something up with the .yaml file?

mw55309 commented 6 years ago

Hmmm, it works for me...

pplacer is in bioconda (https://anaconda.org/bioconda/pplacer) and bioconda is listed as a source in the yaml

Maybe remove the "==1.1.alpha17=0" in MAGpy-3.5.yaml and see if that works?

mw55309 commented 6 years ago

It does seem that other have had problems with that conda recipe:

https://github.com/matsen/pplacer/issues/360

Does:

conda install -c bioconda pplacer

Work for you?

Otherwise, I recommend installing pplacer outside of conda, making sure it is in the $PATH of all users who will run the jobs and on all the cluster nodes, removing pplacer from the YAML and go from there...

bstamps commented 6 years ago

This appears to be a more general issue with MacOS and pplacer- a precompiled binary won't run on a fresh MacOS install, or one with gsl installed... and there isn't currently a MacOS pplacer recipe on Conda. for now I would say close this issue - I'm going to move my install to Ubuntu or CentOS to minimize issues.