How to install hisat2 on Mac OS Big Sur
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Entering edit mode
5 weeks ago
Atsunop • 0

I'd like to install HISAT2 on Mac OS Big Sur ver.11.5.2. I have tried to install HISAT2 by using bioconda (Hisate2 :: Anaconda), and the installation seemed to be successful, but when I tried to start hisat2, I'm getting the following output (below). Please advise.

installation by conda:

$ conda install -c bioconda hisat2 

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: opt/anaconda3

  added / updated specs:
    - hisat2


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2019.11.28         |           py37_0         148 KB  conda-forge
    conda-4.10.3               |   py37hf985489_0         3.0 MB  conda-forge
    ------------------------------------------------------------
                                           Total:         3.2 MB

The following NEW packages will be INSTALLED:

  hisat2             bioconda/osx-64::hisat2-2.2.0-py37h6de7cb9_1
  python_abi         conda-forge/osx-64::python_abi-3.7-2_cp37m

The following packages will be SUPERSEDED by a higher-priority channel:

  certifi                                         pkgs/main --> conda-forge
  conda              pkgs/main::conda-4.10.3-py37hecd8cb5_0 --> conda-forge::conda-4.10.3-py37hf985489_0


Proceed ([y]/n)? y


Downloading and Extracting Packages
conda-4.10.3         | 3.0 MB    | ########################################################################################################### | 100% 
certifi-2019.11.28   | 148 KB    | ########################################################################################################### | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Help command:

$ hisat2 --help
(ERR): Description of arguments failed!
Exiting now ...

Start hisat2:

$ hisat2    
(ERR): Description of arguments failed!
Exiting now ...
hisat2 anaconda bioconda • 192 views
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1
Entering edit mode

strange, I got version 2.2.1 working without problem. It might have to do with missing channel set-up. Go to https://bioconda.github.io/user/install.html#set-up-channels and add the channels as shown there. Then, conda create -n hisat2 hisat2, conda activate hisat2, hisat2 --version

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0
Entering edit mode

Thank you for your help! I set up the channel again, and made a new hisat2 environment, then worked successfully! Although, I'm wondering why it doesn't work on my root environment...

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