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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
Cornelius Roemer
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Matthijs van Kesteren
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2 Answers2

4

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

Russ Hyde
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    Oh man, I should have thought of that... Now atleast I can stop trying to make it work, thanks for the info – Matthijs van Kesteren Jan 25 '18 at 12:12
  • I'd like to start linking this out as duplicate for many of the "can't install X Bioconda package on Windows". Would you mind reworking it to be more "canonical"? E.g., [Bioconda docs](https://bioconda.github.io) clearly state only OSX and Linux 64-bit are supported, so that can just be asserted; there are two main options, WSL or containers (all Bioconda packages have correspond Biocontainers). – merv Jul 06 '22 at 16:45
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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
Cornelius Roemer
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