bowtie2 installed with Conda but failed to run due to "command not found"

[santataRU]

Dear bowtie2 developers,

I can install bowtie2 with Conda, but I could not run it in the terminal (macOS 12.7.3). If I run bowtie2 -h in a newly opened terminal window, an error message of "zsh: command not found: bowtie2" appears.

I wonder if you have any input.

Thanks,

Xiao

Conda command attached:

(base) xiaolei@Xiaos-MacBook-Pro-3 ~ % conda install bioconda/label/broken::bowtie2 Collecting package metadata (current_repodata.json): | WARNING conda.models.version:get_matcher(556): Using . with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1., but conda is ignoring the .* and treating it as 1.7.1 done Solving environment: done

==> WARNING: A newer version of conda exists. <== current version: 23.9.0 latest version: 24.1.2

Please update conda by running

$ conda update -n base -c conda-forge conda

Or to minimize the number of packages updated during conda update use

 conda install conda=24.1.2

Package Plan

environment location: /Users/xiaolei/opt/anaconda3

added / updated specs:

• bioconda/label/broken::bowtie2

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
bowtie2-2.2.5              |                0        10.8 MB  bioconda/label/broken
ca-certificates-2024.2.2   |       h8857fd0_0         152 KB  conda-forge
certifi-2024.2.2           |     pyhd8ed1ab_0         157 KB  conda-forge
------------------------------------------------------------
                                       Total:        11.1 MB

The following NEW packages will be INSTALLED:

bowtie2 bioconda/label/broken/osx-64::bowtie2-2.2.5-0

The following packages will be UPDATED:

ca-certificates 2023.7.22-h8857fd0_0 --> 2024.2.2-h8857fd0_0 certifi 2023.7.22-pyhd8ed1ab_0 --> 2024.2.2-pyhd8ed1ab_0

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

[santataRU]

In my case, this is a conda problem, not a bowtie2 problem. On my macOS (12.7.3) laptop, I tried conda update -n base -c conda-forge conda to update conda to the most recent version. I then tried conda install bioconda::bowtie2, this worked well, and the problem was solved. I noticed that conda install bioconda::bowtie2 failed to work (super-long waiting time without job complete) before the conda update, it only worked after the conda update.

On my macOS (12.7.3) desktop, the situation is a bit more complicated. I tried conda update -n base -c conda-forge conda, but this failed to update my conda to the most recent version, I then tried conda install conda=24.1.2, this again failed with messages that "Warning: 8 possible package resolutions only showing differing packages anaconda ...", I noticed that most of the differing packages contain a base name "perl-common-sense" and I solved this with conda update perl-common-sense. I then tried conda install conda=24.1.2, and this went through. However, after I tried conda install bioconda::bowtie2, I failed with a message "Reason: tried: /Users/bieniaszlab/opt/miniconda3/lib/libarchive.19.dylib (no such file)". I then transferred the "libarchive.19.dylib" file from my laptop and into the path (/Users/bieniaszlab/opt/miniconda3/lib/) on my desktop. I then succeeded with conda install bioconda::bowtie2, problem was solved.