Add missing files for docker container building

docker/.bashrc_docker

@@ -0,0 +1,19 @@
+# Manually added .bashrc
+# Source global definitions
+if [ -f /etc/bashrc ]; then
+    . /etc/bashrc
+fi
+
+export USER=root
+export LOGNAME=root
+export HOME=/root
+export PATH=/root/.local/bin:/root/bin:/opt/python/bin:/opt/R/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+export LD_LIBRARY_PATH=/opt/R/lib/R/lib
+export SHELL=/bin/bash
+export TERM=xterm-256color
+export LANG=en_US.UTF-8
+
+alias ll='ls -lha --color=auto'
+alias jn='jupyter-notebook --no-browser --ip=0.0.0.0 --allow-root /root/host_home'
+alias jl='jupyter-lab --no-browser --ip=0.0.0.0 --allow-root /root/host_home'
+alias cx='cellxgene launch --host 0.0.0.0 --port 8888'

docker/.profile_docker

@@ -0,0 +1,10 @@
+# ~/.profile: executed by the command interpreter for login shells.
+# This file is not read by bash(1), if ~/.bash_profile or ~/.bash_login exists.
+
+# if running bash, source ~/.bashrc
+if [ -n '$BASH_VERSION' ]; then
+    # include .bashrc if it exists
+    if [ -f '/root/.bashrc' ]; then
+        . '/root/.bashrc'
+    fi
+fi

Dockerfile → docker/Dockerfile

@@ -3,7 +3,7 @@ FROM debian:10
 ENV DEBIAN_FRONTEND=noninteractive
 
 # Install system libraries required for python and R installations
-RUN apt-get update && apt-get install -y --no-install-recommends build-essential apt-utils ca-certificates zlib1g-dev gfortran locales libxml2-dev libcurl4-openssl-dev libssl-dev libzmq3-dev libreadline6-dev xorg-dev libcairo-dev libpango1.0-dev libbz2-dev liblzma-dev libffi-dev libsqlite3-dev nodejs npm
+RUN apt-get update && apt-get install -y --no-install-recommends build-essential apt-utils ca-certificates zlib1g-dev gfortran locales libxml2-dev libcurl4-openssl-dev libssl-dev libzmq3-dev libreadline6-dev xorg-dev libcairo-dev libpango1.0-dev libbz2-dev liblzma-dev libffi-dev libsqlite3-dev libopenmpi-dev libhdf5-dev libjpeg-dev libblas-dev liblapack-dev nodejs npm
 
 # Install common linux tools
 RUN apt-get update && apt-get install -y --no-install-recommends wget curl htop less nano vim emacs git
@@ -21,7 +21,7 @@ RUN tar xvfz R-3.6.3.tar.gz && rm R-3.6.3.tar.gz
 
 WORKDIR /opt/R/R-3.6.3
 RUN ./configure --enable-R-shlib --with-cairo --with-libpng --prefix=/opt/R/
-RUN make && make install
+RUN make -j 3 && make install
 
 WORKDIR /opt/R
 RUN rm -rf /opt/R/R-3.6.3
@@ -37,22 +37,22 @@ RUN Rscript -e 'writeLines(capture.output(sessionInfo()), "../package_versions_r
 
 # Download and compile python from source
 WORKDIR /opt/python
-RUN wget https://www.python.org/ftp/python/3.7.7/Python-3.7.7.tgz
-RUN tar zxfv Python-3.7.7.tgz && rm Python-3.7.7.tgz
+RUN wget https://www.python.org/ftp/python/3.8.6/Python-3.8.6.tgz
+RUN tar zxfv Python-3.8.6.tgz && rm Python-3.8.6.tgz
 
-WORKDIR /opt/python/Python-3.7.7
+WORKDIR /opt/python/Python-3.8.6
 RUN ./configure --enable-optimizations --with-lto --prefix=/opt/python/
-RUN make && make install
+RUN make -j 3 && make install
 
 WORKDIR /opt/python
-RUN rm -rf /opt/python/Python-3.7.7
+RUN rm -rf /opt/python/Python-3.8.6
 RUN ln -s /opt/python/bin/python3 /opt/python/bin/python
 RUN ln -s /opt/python/bin/pip3 /opt/python/bin/pip
 ENV PATH="/opt/python/bin:${PATH}"
 
+COPY python-packages.txt /opt/python/python-packages.txt
 RUN pip install --no-cache-dir -U pip wheel setuptools cmake
-RUN pip install --no-cache-dir -U scanpy==1.4.6 python-igraph==0.8.0 louvain==0.6.1 jupyterlab=2.1.0 cellxgene==0.15.0 rpy2==3.2.7 anndata2ri==1.0.2 leidenalg==0.7.0 fa2==0.3.5 MulticoreTSNE==0.1 scvelo==0.1.25 diffxpy==0.7.4 tables==3.5.1 ipywidgets==7.5.1 jupyter_contrib_nbextensions==0.5.1 gprofiler-official==1.0.0 scrublet==0.2.1 xlsxwriter xlrd==1.2.0 tensorflow==2.1.0 tensorflow-probability==0.9.0
-RUN pip install --no-cache-dir git+https://github.com/le-ander/epiScanpy.git
+RUN pip install --no-cache-dir -r /opt/python/python-packages.txt
 RUN jupyter contrib nbextension install --system
 RUN jupyter nbextension enable --py widgetsnbextension
 
@@ -64,3 +64,4 @@ COPY .bashrc_docker /root/.bashrc
 COPY .profile_docker /root/.profile
 
 RUN apt-get clean -y && apt-get autoremove -y
+

docker/python-packages.txt

@@ -0,0 +1,22 @@
+h5py==2.10
+scanpy[louvain]
+jupyterlab
+cellxgene
+rpy2
+anndata2ri
+leidenalg
+fa2
+MulticoreTSNE
+scvelo
+diffxpy
+ipywidgets
+jupyter_contrib_nbextensions
+gprofiler-official
+scrublet
+xlsxwriter
+xlrd
+tensorflow
+tensorflow-probability
+episcanpy
+cellrank[krylov]
+sfaira