pixi.toml

# See https://pixi.sh/latest/ on how to get started with Pixi to create your enviroment

[project]
name = "polygloty"
version = "0.1.0"
description = "Workshop code for Polyglot programming for single-cell analysis"
authors = [
    "Benjamin Rombaut <benjamin.rombaut@gmail.com>",
    "Louise Deconinck <louise.deconinck@gmail.com>",
    "Robrecht Cannoodt <robrecht@cannoodt.dev>",
]
channels = ["conda-forge", "bioconda"]
platforms = ["linux-64", "linux-aarch64"]

# Environments
[environments]
bash = { features = ["bash"] }
scverse = { features = ["scverse"] }
rverse = { features = ["rverse"] }

# These are Conda dependencies and will be installed by Pixi
[dependencies]
hdf5 = ">=1.14.3,<2"

[tasks]
pipeline = { depends-on = ["load_data", "compute_pseudobulk", "analysis_de"] }

[feature.scverse.dependencies]
anndata = "0.10.9"
pandas = "*"
[feature.scverse.tasks]
compute_pseudobulk = "python book/disk_based/scripts/2_compute_pseudobulk.py"

[feature.bash.dependencies]
awscli = "*"
[feature.bash.tasks]
load_data = "bash book/disk_based/scripts/1_load_data.sh"

[feature.rverse]
activation = {scripts = ["book/disk_based/scripts/setup.sh"]} # Custom install script to also support ARM macOS
tasks = { analysis_de = "Rscript --no-init-file book/disk_based/scripts/3_analysis_de.R" } # avoid loading the .Rprofile file
[feature.rverse.dependencies]
r = ">=4.1,<5"
r-devtools = ">=2.4.5,<3"
r-biocmanager = ">=1.30.25,<2"
r-dplyr = ">=1.1.4,<2"
r-anndata = ">=0.7.5.4,<0.8"
bioconductor-deseq2 = ">=1.32.0,<2"