cannot install using environment.yml

[alxndrkalinin]

Running conda env create -f environment.yml returns PackageNotFound for dvc and dvc-s3.
If those are moved to the pip section, it complains about not finding s_gd2 that is used by phate.

Seems like it's Apple Silicon-related issues and environment.yml should be updated to address them and fix installation.

[alxndrkalinin]

Turns out some packages do not have conda binaries compiled for Apple Silicon. This can be fixed by installing them via pip: 8c42242

However, there are issues with installing packages for perturbseq preprocessing from perturbseq_processing_environment.yml
Specifically, bioconductor-biostrings and r-seurat also do not have apple silicon binaries. Installing everything else and trying to install these two directly from inside R fails as there are issues with compiling the source code.

[alxndrkalinin]

I managed to install from perturbseq_processing_environment.yml by:

• removing r-seurat and bioconductor-biostrings from yml, bumping nb_conda_kernels to 2.3.1 and installing from yml with conda
• removing MKL from conda environment as described in Issue with Seurat installation in R version 4.0.2 satijalab/seurat#3273 (comment)
• setting compiling flags as described in R on ARM Mac M1:load failed for ‘stats’ and Rlog1p error conda-forge/r-base-feedstock#163 (comment)
• finally, installing in R console:

install.packages('sctransform')
install.packages('Seurat')

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Biostrings")

[alxndrkalinin]

Bumped dependency versions for creating figure environment. Commented it out r-magick, because it does not currently have osx-arm64 binaries and was only used to read a pre-made figure panel.

[mfansler]

We now have r-seurat building for osx-arm64 on Conda Forge. But bioconductor-biostrings is a different story, since those are built by Bioconda, which has not yet set up CI for osx-arm64 builds.

[alxndrkalinin]

Thanks for letting us know @mfansler! I just tested it and it works perfectly. Turns out, we were not using bioconductor-biostrings, so everything installs fine through conda now.