Unable to install bioconda and bowtie

Question

[n.anuragsharma]

➜  ~ conda install -c "bioconda/label/cf201901" bowtie

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

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

  - bowtie

Current channels:

  - https://conda.anaconda.org/bioconda/label/cf201901/osx-arm64
  - https://conda.anaconda.org/bioconda/label/cf201901/noarch
  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://conda.anaconda.org/bioconda/osx-arm64
  - https://conda.anaconda.org/bioconda/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - 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.

Based on this Github post, I simply tried replacing conda with mamba in conda install -c "bioconda/label/cf201901" bowtie and I get nothing provides requested bowtie.

I think I've tried just about everything. The Bioconda homepage says, "So easy, your grandfather could do this..." At this point, I wish he could.

I'm on a Macbook M1. Just setting it up. I had all of this set up on my old laptop. I have no idea how I did it back then.

[Michael]

Where did you get the command from that includes this channel: -c "bioconda/label/cf201901"? The standard way would be conda install -c bioconda bowtie or better configure the channels permanently as directed on the BioConda website. Mamba won't help you if conda doesn't find a package, it just makes some things faster. Maybe some packages are not available for M1 macs but try the default way first.

[n.anuragsharma]

I found the command on the Anaconda webpage.

I tried all the methods, including the one you suggested, with identical results:

Last login: Sun Sep 25 13:46:23 on ttys001
(base) ➜  ~ conda install -c bioconda bowtie
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.

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

  - bowtie

Current channels:

  - https://conda.anaconda.org/bioconda/osx-arm64
  - https://conda.anaconda.org/bioconda/noarch
  - https://conda.anaconda.org/conda-forge/osx-arm64
  - https://conda.anaconda.org/conda-forge/noarch
  - https://repo.anaconda.com/pkgs/main/osx-arm64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/r/osx-arm64
  - 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.

[Marco Pannone]

I have a MacBook M1 and it works perfectly. Just properly create a conda environment and install bowtie in the default way.

[n.anuragsharma]

Hello, please see above for my response.

[Marco Pannone]

Try this:

conda deactivate
conda activate path/to/conda/environment
conda install -c bioconda bowtie

However, is there a reason why you want to use Bowtie over Bowtie2? Otherwise, try installing Bowtie2 and see if it works.

[n.anuragsharma]

Same result.

I've tried the instructions exactly as mentioned here, but to no avail.

[Marco Pannone]

Which python version are you running for your conda environment?

[lvl2111]

Hello, I am having the same issue. I am trying to install Bowtie2 into a mamba environment on my M2 Mac, and am getting the same error:

Could not solve for environment specs
The following package could not be installed
 --- bowtie2   does not exist (perhaps a typo or a missing channel).

I am doing exactly as described above, activating my mamba environment and installing

mamba activate path/to/conda/environment
mamba install -c bioconda bowtie2

The strange thing, is when I do this exact same process on my lab's linux server, it works perfectly fine and installs Bowtie2 into my mamba environment. This makes me think there is some incompatibility with my Mac M2.

Has anyone found a solution for installing Bowtie2 into a mamba environment on a Mac M1 or M2?

I am using python 3.10.

Thank you, much appreciated

[rpolicastro]

It doesn't have osx-arm64 available on conda, probably because to my knowledge bioconda doesn't support apple silicon yet.

mamba repoquery search -p osx-arm64 -c conda-forge -c bioconda bowtie2

The bowtie2 github includes instructions on how to install it manually if you wish.

Alternatively you can run it via Rosetta2 by switching to x86-64 compatibility and installing the osx-64 version through bioconda.