Update .gitignore and environment files (#15)

YosefLab · Mar 9, 2023 · 83e9e98 · 83e9e98
1 parent 5adebf4
commit 83e9e98
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Showing 7 changed files with 92 additions and 3 deletions.
diff --git a/.gitignore b/.gitignore
@@ -139,3 +139,4 @@ local/
 
 # Snakemake
 */.snakemake
+*/data/
diff --git a/allen_brain/env.yaml b/allen_brain/env.yaml
@@ -0,0 +1,18 @@
+name: run-models
+channels:
+  - conda-forge
+  - bioconda
+  - pytorch
+  - nvidia
+  - defaults
+dependencies:
+  - python=3.10
+  - scvi-tools==0.20.1
+  - anndata>=0.8.0
+  - scanpy>=1.9.0
+  - pytorch
+  - torchvision
+  - torchaudio
+  - jax
+  - jaxlib
+  - pooch
diff --git a/fetal_immune/env.yaml b/fetal_immune/env.yaml
@@ -0,0 +1,18 @@
+name: run-models
+channels:
+  - conda-forge
+  - bioconda
+  - pytorch
+  - nvidia
+  - defaults
+dependencies:
+  - python=3.10
+  - scvi-tools==0.20.1
+  - anndata>=0.8.0
+  - scanpy>=1.9.0
+  - pytorch
+  - torchvision
+  - torchaudio
+  - jax
+  - jaxlib
+  - pooch
diff --git a/human_lung_cell_atlas/env.yaml b/human_lung_cell_atlas/env.yaml
@@ -7,6 +7,7 @@ channels:
   - defaults
 dependencies:
   - python=3.10
+  - scvi-tools==0.20.1
   - anndata>=0.8.0
   - scanpy>=1.9.0
   - pytorch
@@ -15,6 +16,3 @@ dependencies:
   - jax
   - jaxlib
   - pooch
-  - pip
-  - pip:
-      - scvi-tools[hub]==0.20.0b1
diff --git a/non_small_cell_lung_cancer/env.yaml b/non_small_cell_lung_cancer/env.yaml
@@ -0,0 +1,18 @@
+name: run-models
+channels:
+  - conda-forge
+  - bioconda
+  - pytorch
+  - nvidia
+  - defaults
+dependencies:
+  - python=3.10
+  - scvi-tools==0.20.1
+  - anndata>=0.8.0
+  - scanpy>=1.9.0
+  - pytorch
+  - torchvision
+  - torchaudio
+  - jax
+  - jaxlib
+  - pooch
diff --git a/pbmc_cite_seq/env.yaml b/pbmc_cite_seq/env.yaml
@@ -0,0 +1,18 @@
+name: run-models
+channels:
+  - conda-forge
+  - bioconda
+  - pytorch
+  - nvidia
+  - defaults
+dependencies:
+  - python=3.10
+  - scvi-tools==0.20.1
+  - anndata>=0.8.0
+  - scanpy>=1.9.0
+  - pytorch
+  - torchvision
+  - torchaudio
+  - jax
+  - jaxlib
+  - pooch
diff --git a/tabula_sapiens/env.yaml b/tabula_sapiens/env.yaml
@@ -0,0 +1,18 @@
+name: run-models
+channels:
+  - conda-forge
+  - bioconda
+  - pytorch
+  - nvidia
+  - defaults
+dependencies:
+  - python=3.10
+  - scvi-tools==0.20.1
+  - anndata>=0.8.0
+  - scanpy>=1.9.0
+  - pytorch
+  - torchvision
+  - torchaudio
+  - jax
+  - jaxlib
+  - pooch
Original file line number	Diff line number	Diff line change
Expand Up		@@ -139,3 +139,4 @@ local/

		# Snakemake
		*/.snakemake
		*/data/