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theislab / zellkonverter

Conversion between scRNA-seq objects
https://theislab.github.io/zellkonverter/
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The first time calling writeH5AD installs more dependencies #54

Closed hisplan closed 3 years ago

hisplan commented 3 years ago

Hi,

I've installed the package via BiocManager::install("zellkonverter"), but then the first time when I tried to call the writeH5AD function, it actually started to install more dependencies such as miniconda, h5py, scipy, and etc. My end goal is including zellkonverter inside a docker image. It would be great if there is a way to install everything via BiocManager::install("zellkonverter") including all the necessary runtime dependencies. Or I'm looking for any solution that allows me to avoid additional download/installation during the "runtime".

Based on the console output, it looks like it is trying to install everything under this conda environment: /root/.cache/R/basilisk/1.4.0/zellkonverter/1.2.0/zellkonverterAnnDataEnv, even if I specified a specific python/environment to use in the beginning as shown below:

use_condaenv(
  condaenv = "/opt/conda/envs/workspace",
  conda = "/opt/conda/bin/python",
  required = TRUE
)

Any solution? Thanks!

LTLA commented 3 years ago

Have a look at BASILISK_USE_SYSTEM_DIR in the basilisk vignette.

hisplan commented 3 years ago

Thank you! This is exactly what I was looking for. Closing this.