From da737f418f811c093faabafea60fd072a3acbd3d Mon Sep 17 00:00:00 2001
From: Andrew Butler <abutler@nygenome.org>
Date: Mon, 12 Apr 2021 10:38:28 -0400
Subject: [PATCH] add vitessce docker file

---
 .gitignore                 |  1 +
 docker/vitessce/Dockerfile | 16 ++++++++++++++++
 2 files changed, 17 insertions(+)
 create mode 100644 docker/vitessce/Dockerfile

diff --git a/.gitignore b/.gitignore
index 184c4c2..d6f620b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -16,6 +16,7 @@ src/*.dll
 **/seurat-objects/
 **/seurat_objects/
 **/vitessce/
+!docker/vitessce/
 **/.snakemake
 **/.snakemake_timestamp
 **/.wget-hsts
diff --git a/docker/vitessce/Dockerfile b/docker/vitessce/Dockerfile
new file mode 100644
index 0000000..f123987
--- /dev/null
+++ b/docker/vitessce/Dockerfile
@@ -0,0 +1,16 @@
+# Dockerfile for building references
+FROM satijalab/seurat:4.0.1
+
+# Install other R dependencies
+RUN R --no-echo --no-restore --no-save -e "install.packages('feather')"
+
+# Install Azimuth (0.3.2)
+RUN R --no-echo --no-restore --no-save -e "remotes::install_github('immunogenomics/presto')"
+RUN R --no-echo --no-restore --no-save -e "install.packages(c('DT', 'googlesheets4', 'shinyBS', 'shinydashboard', 'shinyjs'))"
+RUN R --no-echo --no-restore --no-save -e "BiocManager::install('glmGamPoi')"
+RUN R --no-echo --no-restore --no-save -e "remotes::install_github('satijalab/azimuth', ref = 'v0.3.0', dependencies = FALSE)"
+
+# Install python dependencies
+RUN pip3 install scanpy
+RUN pip3 install zarr
+