name: gastrulation_multiome_10x_rna_snakemake

channels:

  - conda-forge

  - bioconda

dependencies:

  # - python=3.9.10

  - python=3.8

  - cython

  - ipython

  # - jupyter 

  - ipywidgets

  - bioconductor-scater

  - bioconductor-scran

  - bioconductor-singlecellexperiment

  - bioconductor-batchelor

  - bioconductor-scds

  - bioconductor-edger

  - bioconductor-deseq2

  # - bioconductor-destiny = 3.4 # THIS IS DEPRECIATED, DEPENDS ON bioconductor-singlecellexperiment 1.12

  # - r-xml2 =1.3.2

  - r-r.utils

  - r-matrix

  - r-future

  - r-argparse

  - r-ggpubr

  - r-data.table

  - r-purrr

  - r-furrr

  - r-argparse

  - r-seurat=4.1.0

  - r-pheatmap

  - r-ggrastr

  - scanpy=1.8.2

  - loompy=3.0.6

  - velocyto.py

  # - h5py=2.10.0

  - python-igraph

  - louvain>=0.6,!=0.6.2

  - fa2

  - leidenalg

  - harmonypy

  - scanorama

  - seaborn

  - samtools=1.15

  - snakemake

  - pip

  - pip:

    - dfply

    - scvelo

    - git+https://github.com/settylab/Palantir@removeTSNE

    - git+https://github.com/dpeerlab/SEACells

# conda create -n gastrulation_multiome_10x_rna_snakemake python==3.9 --yes 

# conda activate gastrulation_multiome_10x_rna_snakemake

# conda install mamba --yes

# mamba env update -n gastrulation_multiome_10x_rna_snakemake --file environment.yaml