Not able to install on Mac book M1

[ranijames]

I am trying to install fastp tool on my Mac M1. So far, I have tried all these options download osx-64_fastp-0.23.4-h5712c04_2.tar.bz2 then, conda install osx-64_fastp-0.23.4-h5712c04_2.tar.bz2 The fastp file is not showing the directory. Alternatively, I have also install via conda directly,

conda install bioconda::fastp
conda install bioconda/label/cf201901::fastp

which however threw the following error PackagesNotFoundError: The following packages are not available from current channels:

• bioconda::fastp

[KimBioInfoStudio]

we have NOT got a Apple Silicon for test, but we believe that our code could run on it, could you try but the binary from source code? here is the documents for build it from soure https://github.com/OpenGene/fastp?tab=readme-ov-file#or-compile-from-source

[annajbott]

Might be a different problem but I was having the same error message with conda trying to install fastp. I ran:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority flexible

And this seemed to fix the problem I was having.

conda create -n fastp_test -c bioconda fastp=0.23.4 and conda create -n fastp_test bioconda::fastp=0.23.4 worked and installed fastp successfully

[ranijames]

@annajbott Thanks for sharing the steps. Unfortunately, none of these steps worked for me. After running all config add, I then tried this one liner to install fastp:

conda create -n fastp_test -c bioconda fastp=0.23.4

which threw me the old error,

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:

  - fastp=0.23.4

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.

[ranijames]

@KimBioInfoStudio Sorry for the delayed response,

I have tried the step 1, step 2, step 3. Those steps did not work for me from step 1 onwards. For example, this is the error for step 1:

autogen.sh: line 3: autoreconf: command not found
clang: error: unsupported option '-print-multi-os-directory'
clang: error: no input files

----------------------------------------------------------------
Initialized build system. For a common configuration please run:
----------------------------------------------------------------

./configure --prefix=/usr --libdir=/usr/lib