Installing newer versions with conda

[GHAZAL99]

Hello,

I attempted to install the newest fastp version 0.23.2 using conda but I am facing compatibility issues:

Output in format: Requested package -> Available versions

Package libgcc-ng conflicts for:
fastp=0.23.2 -> libgcc-ng[version='>=10.3.0|>=9.4.0']
fastp=0.23.2 -> libdeflate[version='>=1.7,<1.8.0a0'] -> libgcc-ng[version='>=7.3.0']

Package _libgcc_mutex conflicts for:
fastp=0.23.2 -> libgcc-ng[version='>=10.3.0'] -> _libgcc_mutex==0.1=conda_forge
python=3.8.1 -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex[version='*|0.1',build='conda_forge|main|main']The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.27=0
  - feature:|@/linux-64::__glibc==2.27=0
  - python=3.8.1 -> libgcc-ng[version='>=7.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.27 

I was wondering if you have a conda environment available that would resolve these issues.

Additionally, I tried using version 0.19.3, and whenever I added -y for complexity filtering, I started getting Segmentation Fault (core dumped). Note: This does not occur when not using complexity filtering.

Thank you!

[mrazomej]

I was having the exact same issue and I was able to solve it by setting a conda environment with conda-forge as the priority channel. These are the steps I followed:

1. Add bioconda and conda-forge as the priority channels for the installation of packages. This will allow for the newest version of fastp . Run the following commands to add the channels:

conda config --add channels bioconda
conda config --add channels conda-forge

2. Create a new conda environment (I specified python=3.9, not sure if it is necessary)

conda create -n my_env python=3.9

3. All packages should be installed from the conda-forge channel, but just to make sure activate the environment and run

conda update --all

4. Install fastp and it should give you version 0.23.2 by simply doing

conda install fastp

Hopefully it will also work for you! This solution worked for me on my Mac running macOS Big Sur and on a Linux server.

[ezherman]

To add to this, the following was sufficient for me (without specifying a python version or updating the conda environment):

conda create -n assembly -c conda-forge -c bioconda fastp -y

[splaisan]

alternatively, specify the latest version (or your chosen) of fastp found with anaconda search like: conda install -c bioconda fastp==0.23.4

[Maria6642]

Hi everyone am facing issue in installing fast I have macOS Ventura arm64 am unable to install it through brew by using rosetta 2 and also from condo please help yesterday I installed it but now its not working and at that time it was not running the reads

[pritampanda15]

Hi, same problem here for Mac M2 arm64. I even tried to specify the version as well.

conda install -c bioconda fastp
Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed

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

  - fastp

Current channels:

  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/bioconda
  - defaults

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.

[VictorPizarroR]

Hi! Running this command worked for me:

conda config --add subdirs osx-64

Check: https://github.com/conda/conda/issues/11216