I cannot easily create an environment with conda containing the NGS tools I want. I reinstalled conda to get a fresh start since I had many python packages in the base env. I also took the occasion to install the full anaconda3 instead of miniconda I had before now I have way enough space.
Although all the packages are available via bioconda the only 2 i can add to my env are fastqc and multiqc. Before that I could install sra-tools and fastqc in the base env with miniconda3.
Config: MacOS Monterey 12.1 M1 chip. migration from my old macbook air with the lastest time machine bkp. I uninstalled miniconda with the anaconda-clean procedure and after that I also removed a python 3.9.5 I had in the apps folder I had initially installed to start learning 1yr ago before knowing about conda.
Also to be mentioned in case it may help: anaconda-navigator was not installed by the Anaconda3-2022.05-MacOSX-arm64.pkg (sha256 integrity check was ok) in following the check installation/navigator troubleshooting on anaconda website I came across an error upon launching spyder:
```(ModuleNotFoundError: No module named 'PyQt5.QtWebEngineWidgets')```
Does somebody know where this unability to find the packages comes?
Thank you for your help! best, Daniel
Env creation command and console output:
(base) mymac:~ D________$ conda create --name ngstools fastqc multiqc sra-tools samtools bowtie2 hisat2 subread -c conda-forge -c bioconda -c bioconda/label/cf201901
Terminal output:
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:
Current channels:
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.
That is not a configuration I would recommend to bioinformatics users with M1 machines at the moment. There is no support yet for osx-arm64 in Bioconda. I expect one would find the least configuration issues by having everything in emulation (osx-64) from the base. Or you can continue with the osx-arm64 base (as you have now), but create new environments with the subdir setting. The answer below shows steps in this direction.
Also, I would very much avoid Anaconda/Miniconda. Miniforge base is what I recommend to all bioinformaticians. And set the Bioconda channels globally.
Lastly, only advanced users should use channel labels (e.g., bioconda/label/cf201901). I realize they automatically show up on Anaconda Cloud, but they are only ever applicable in specialized circumstances, which most users will never encounter.
If you want to keep the osx-arm64 base, then you'll need to create a osx-64 environment for the NGS tools. I recommend the following protocol for best practice:
## create empty environment
conda create -n ngstools
## activate environment
conda activate ngstools
## configure architecture
conda config --env --set subdir osx-64
## configure channels for Bioconda
conda config --env --add channels defaults
conda config --env --add channels bioconda
conda config --env --add channels conda-forge
## install packages
conda install fastqc multiqc sra-tools samtools bowtie2 hisat2 subread
It's convoluted and, until osx-arm64 sees full support, you'd have to do this for every environment that requires emulation and Bioconda. Hence, why I recommend instead that you reinstall a osx-64 base (Miniforge), which would just work.