conda create PackagesNotFoundError

Question

[raquel]

Hello everyone

I ran:

 conda create -n scinkd meryl snakemake pigz r r-dplyr r-ggplot2 samtools`

The output was

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: failed

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

  - snakemake
  - samtools
  - meryl

Current channels:

  - https://repo.anaconda.com/pkgs/main/linux-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/linux-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

I understand this means it cannot find the packages I want in my environment. Is it because they have a different name? Or should I install them before hand? Not all gave me that issue, what is wrong with it? I'm trying to follow the SCINKD pipeline but I've been having trouble installing it

Also, what does the "solving environment: failed" mean? Is it failed because it could not find the packages or is that a different error?

Thanks

Answer 1

[cfos4698]

You should explicitly name the channels from which the packages are to be installed, as the error suggests (PackagesNotFoundError: The following packages are not available from current channels).

Add the -c bioconda channel to your command.

conda create -n scinkd -c conda-forge -c bioconda r-base r-dplyr r-ggplot2 snakemake meryl pigz samtools