--- a
+++ b/rna/snakemake/environment.yaml
@@ -0,0 +1,57 @@
+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 
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