Question: Trouble installing Bioconda
0
gravatar for mac03pat
6 months ago by
mac03pat10
mac03pat10 wrote:

I'm trying to install bioconda so that I can run the program antiSMASH:

https://docs.antismash.secondarymetabolites.org/install/

I'm following directions from here:

http://www.ddocent.com//bioconda/

I installed miniconda, added it to my PATH, and began entering commands into my windows command line. I'm held up when entering:

conda create -n ddocent_env ddocent

Error returned:

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

  - ddocent

When searching ddocent on anaconda.org I found this code to add the ddocent package but I'm not sure if it's what I should be doing:

conda install -c bioconda ddocent

Here's my full session:

C:\Users\macstest>conda config --add channels r

C:\Users\macstest>conda config --add channels defaults
Warning: 'defaults' already in 'channels' list, moving to the top

C:\Users\macstest>conda config --add conda-forge
usage: conda-script.py config [-h] [--json] [-v] [-q]
                              [--system | --env | --file FILE]
                              [--show [SHOW [SHOW ...]] | --show-sources |
                              --validate | --describe
                              [DESCRIBE [DESCRIBE ...]] | --write-default]
                              [--get [KEY [KEY ...]] | --append KEY VALUE |
                              --prepend KEY VALUE | --set KEY VALUE | --remove
                              KEY VALUE | --remove-key KEY | --stdin]
conda-script.py config: error: argument --prepend/--add: expected 2 arguments

C:\Users\macstest>conda config --add channels defaults
Warning: 'defaults' already in 'channels' list, moving to the top

C:\Users\macstest>conda config --add channels bioconda
Warning: 'bioconda' already in 'channels' list, moving to the top

C:\Users\macstest>conda config --add channels conda-forge
Warning: 'conda-forge' already in 'channels' list, moving to the top

C:\Users\macstest>conda create -n ddocent_env ddocent
Collecting package metadata: done
Solving environment: failed

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

  - ddocent

Current channels:

  - https://conda.anaconda.org/conda-forge/win-64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/win-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/win-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/win-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/win-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/msys2/win-64
  - https://repo.anaconda.com/pkgs/msys2/noarch
  - https://conda.anaconda.org/r/win-64
  - https://conda.anaconda.org/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.



C:\Users\macstest>conda config --append channels conda-forge
Warning: 'conda-forge' already in 'channels' list, moving to the bottom

C:\Users\macstest>where conda
C:\Anaconda\Library\bin\conda.bat
C:\Anaconda\Scripts\conda.exe

C:\Users\macstest>SETX PATH "%PATH%;C:\Anaconda\Scripts;C:\Anaconda"

WARNING: The data being saved is truncated to 1024 characters.

SUCCESS: Specified value was saved.

C:\Users\macstest>conda create -n ddocent_env ddocent
Collecting package metadata: done
Solving environment: failed

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

  - ddocent

Current channels:

  - https://conda.anaconda.org/bioconda/win-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/win-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/win-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/win-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/msys2/win-64
  - https://repo.anaconda.com/pkgs/msys2/noarch
  - https://conda.anaconda.org/r/win-64
  - https://conda.anaconda.org/r/noarch
  - https://conda.anaconda.org/conda-forge/win-64
  - https://conda.anaconda.org/conda-forge/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.



C:\Users\macstest>conda create -n antismash antismash
Collecting package metadata: done
Solving environment: failed

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

  - antismash

Current channels:

  - https://conda.anaconda.org/bioconda/win-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/win-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/win-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/win-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/msys2/win-64
  - https://repo.anaconda.com/pkgs/msys2/noarch
  - https://conda.anaconda.org/r/win-64
  - https://conda.anaconda.org/r/noarch
  - https://conda.anaconda.org/conda-forge/win-64
  - https://conda.anaconda.org/conda-forge/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.



C:\Users\macstest>conda config --add channels bioconda
Warning: 'bioconda' already in 'channels' list, moving to the top

C:\Users\macstest>conda install -c bioconda antismash
Collecting package metadata: done
Solving environment: failed

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

  - antismash

Current channels:

  - https://conda.anaconda.org/bioconda/win-64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/win-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/win-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/win-64
  - https://repo.anaconda.com/pkgs/r/noarch
  - https://repo.anaconda.com/pkgs/msys2/win-64
  - https://repo.anaconda.com/pkgs/msys2/noarch
  - https://conda.anaconda.org/r/win-64
  - https://conda.anaconda.org/r/noarch
  - https://conda.anaconda.org/conda-forge/win-64
  - https://conda.anaconda.org/conda-forge/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.
bioconda • 562 views
ADD COMMENTlink written 6 months ago by mac03pat10

Bioconda appears to be installed correctly. ddocent is only available on linux and macOS.
Same with antismash.

If you are using windows 10 then consider installing Windows subsystem for Linux ( https://docs.microsoft.com/en-us/windows/wsl/install-win10 ) and install/use things you need there.

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax75k
1

Thanks for the tip! I successfully set up a Debian 9 VM and was able to get ddocent and antismash working.

ADD REPLYlink written 6 months ago by mac03pat10
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