From 83e9e9881eb23b5ac525d1323339df5525c15747 Mon Sep 17 00:00:00 2001
From: Martin Kim <46072231+martinkim0@users.noreply.github.com>
Date: Thu, 9 Mar 2023 13:06:41 -0800
Subject: [PATCH] Update .gitignore and environment files (#15)

---
 .gitignore                          |  1 +
 allen_brain/env.yaml                | 18 ++++++++++++++++++
 fetal_immune/env.yaml               | 18 ++++++++++++++++++
 human_lung_cell_atlas/env.yaml      |  4 +---
 non_small_cell_lung_cancer/env.yaml | 18 ++++++++++++++++++
 pbmc_cite_seq/env.yaml              | 18 ++++++++++++++++++
 tabula_sapiens/env.yaml             | 18 ++++++++++++++++++
 7 files changed, 92 insertions(+), 3 deletions(-)

diff --git a/.gitignore b/.gitignore
index 031fb42..22706c8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -139,3 +139,4 @@ local/
 
 # Snakemake
 */.snakemake
+*/data/
diff --git a/allen_brain/env.yaml b/allen_brain/env.yaml
index e69de29..de0f605 100644
--- 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
index e69de29..de0f605 100644
--- 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
index bac4020..de0f605 100644
--- 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
index e69de29..de0f605 100644
--- 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
index e69de29..de0f605 100644
--- 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
index e69de29..de0f605 100644
--- 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