start a new sos-notebook base image (mamba)

Author: gaow

docker/sos-r.yml docker/pisces-rabbit.yml

@@ -1,4 +1,4 @@
-name: sos
+name: pisces-rabbit
 channels:
   - conda-forge
   - bioconda
@@ -8,14 +8,16 @@ dependencies:
   - feather-format
   - imageio
   - jupyter_contrib_nbextensions
-  - jupyterlab =3.6.4
-  - jupyter_server
+  - jupyterlab 3.6.*
+  - jupyter_server =1.23.6
+  - jupyter_client =8.0.3
+  - jupyter-lsp
   - jupyterlab-sos
   - markdown
   - markdown-kernel
   - nbdime
   - nbformat
-  - notebook =6.5.5
+  - notebook =6.5.4
   - pillow
   - python 3.10.*
   - r-base >4
@@ -25,7 +27,6 @@ dependencies:
   - sos
   - sos-bash
   - sos-notebook
-  - sos-r
   - sos-pbs
   - sos-python
   - wand

docker/base-notebook.dockerfile docker/sos-notebook-v1.dockerfile

@@ -0,0 +1,21 @@
+FROM jupyter/base-notebook:hub-4.0.2
+
+MAINTAINER Gao Wang <wang.gao@columbia.edu>
+
+ARG CONDAENV=pisces-rabbit
+
+COPY ${CONDAENV}.yml /tmp
+RUN mamba env create -y -f /tmp/${CONDAENV}.yml && \
+    mamba activate ${CONDAENV} && \
+    mamba install -y r-dplyr r-stringr r-readr r-magrittr r-data.table r-ggplot2 r-cowplot r-remotes && \
+    mamba clean --all -f -y
+
+# https://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html
+# If you want ‘~/.Renviron’ or ‘~/.Rprofile’ to be ignored by child R processes (such as those run by R CMD check and R CMD build), set the appropriate environment variable R_ENVIRON_USER or R_PROFILE_USER to (if possible, which it is not on Windows) "" or to the name of a non-existent file.
+ENV R_ENVIRON_USER ""
+ENV R_PROFILE_USER ""
+ENV R_LIBS_USER " "
+
+## To build for multiple platforms, 
+# docker buildx create --use && docker buildx build --push --tag gaow/sos-notebook:4.0.2 --platform=linux/arm64,linux/amd64 -f sos-notebook-v4.dockerfile .
+# docker push gaow/sos-notebook:4.0.2