Unable to install Bioconda packages in Conda environments

Question

I am trying to install some packages from the Bioconda channel with Conda but even though the channel is added, I get to following error:

C:\Users\matti>conda install -c bioconda pybedtools
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - pybedtools

Current channels:

  - https://conda.anaconda.org/bioconda/win-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/conda-forge/win-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.continuum.io/pkgs/main/win-64
  - https://repo.continuum.io/pkgs/main/noarch
  - https://repo.continuum.io/pkgs/free/win-64
  - https://repo.continuum.io/pkgs/free/noarch
  - https://repo.continuum.io/pkgs/r/win-64
  - https://repo.continuum.io/pkgs/r/noarch
  - https://repo.continuum.io/pkgs/pro/win-64
  - https://repo.continuum.io/pkgs/pro/noarch
  - https://repo.continuum.io/pkgs/msys2/win-64
  - https://repo.continuum.io/pkgs/msys2/noarch
  - https://conda.anaconda.org/daler/win-64
  - https://conda.anaconda.org/daler/noarch
  - https://conda.anaconda.org/anaconda-fusion/win-64
  - https://conda.anaconda.org/anaconda-fusion/noarch

This also happens for other Bioconda packages like bowtie2. I have tried regular pip install and easy_install but those do not work either. Any ideas?

Additional Info

• OS: Windows
• Anaconda base

Answer 1

From your command line it appears you are on windows. There are several veresions of pybedtools on bioconda, however, if I grep through them, they are all for the linux platform.

If you're on Windows 10, you could consider setting up the 'windows subsystem for linux' (and possibly Xming), installing conda, and then installing pybedtools. This is obviously a long-winded approach, but would open up many bioconda packages to you

Answer 2

Bioconda does not have a Windows channel, only Linux and Intel macOS, so you can't install bioconda packages natively.

Your options are:

• Install "Windows Subsystem for Linux", install conda in that subsystem which is basically Linux
• Set up docker and then install the environment in a container