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Critical conda bug prevents creation of environments and installing packages from file #364

@hassanfa

Description

@hassanfa

As a bioinfo person, I want to install environments in conda without any error.

Problem:
conda 4.5.xx has a bug while resolving environments: conda/conda#7780

Steps to reproduce

  1. conda env create -f my_conda_env.yaml --quite --name some_conda_env_name

Example conda_env.yaml

channels:
  - bioconda
  - conda-forge 
dependencies:
  - python=3.6
  - pip=9.0.3
  - snakemake=4.8.0
  - r-data.table=1.11.4
  - r-optparse=1.6.0
  - r-deconstructsigs=1.8.0.1
  - r-reshape2=1.4.3
  - bioconductor-bsgenome=1.48.0
  - bioconductor-bsgenome.hsapiens.ucsc.hg19=1.4.0

and this is the command: conda env create -f abovefile.yaml --quiet --name S_test_190524_HFA

Expected outcome / suggested solution:
A conda environment to be created with this name: some_conda_env_name

Questions:
Q: Does the same problem occur for tea?
A: Yes.

What needs to be done on the planning meeting:

  • Estimate storypoints
  • Remember to add label PBL Teamname

See https://github.com/Clinical-Genomics/development/blob/master/git/issue-reports.md for more!

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