Jupyter single cell based on galaxy-jupyter

galaxy-jupyter-single-cell/image_tag

@@ -0,0 +1 @@
+pseq-galaxy-jupyter-single-cell:0.1

galaxy-jupyter-single-cell/pre_install_dockerfile

@@ -0,0 +1,8 @@
+# uses the same image as the original interactive environment in Galaxy
+FROM quay.io/bgruening/docker-jupyter-notebook:2021-03-05
+
+# install micromamba
+RUN "${SHELL}" <(curl -L micro.mamba.pm/install.sh)
+COPY templated-conda-env.yaml /tmp/env.yaml
+RUN /home/jovyan/.local/bin/micromamba install -y -n base -f /tmp/env.yaml && \
+    /home/jovyan/.local/bin/micromamba clean --all --yes

galaxy-jupyter-single-cell/templated-conda-env.yaml

@@ -0,0 +1,20 @@
+name: single-cell
+channels:
+  - defaults
+  - conda-forge
+  - bioconda
+dependencies:
+  - scanpy==1.9.3
+  - r-seurat==4.3.0
+  # - r-seuratdisk - conflicts with newer r-base required for Seurat.
+  - r-monocle3
+  # - r-sceasy - conflicts with newer Scanpy and Seurat
+  - r-ggplot2
+  - r-data.table
+  - r-stringr
+  - r-pheatmap
+  - bioconductor-deseq2
+  - bioconductor-fgsea
+  - r-complexupset
+  # - scvi-tools -- makes github actions VM run out of disk space.
+  - decoupler

miniconda_template/create_dockerfile.sh

@@ -1,6 +1,10 @@
 #!/usr/bin/env bash
 
-cat miniconda_template/Dockerfile > $1/Dockerfile
+dockerfile=miniconda_template/Dockerfile
+if [ -f "$1/pre_install_dockerfile" ]; then
+    dockerfile=$1/pre_install_dockerfile
+fi
+cat $dockerfile > $1/Dockerfile
 
 if [ -f "$1/post_install_dockerfile" ]; then
   cat $1/post_install_dockerfile >> $1/Dockerfile