add R studio support to Biology

deployments/biology/image/Dockerfile

@@ -0,0 +1,189 @@
+FROM buildpack-deps:focal-scm
+
+ENV LC_ALL en_US.UTF-8
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US.UTF-8
+ENV DEBIAN_FRONTEND=noninteractive
+ENV NB_USER jovyan
+ENV NB_UID 1000
+
+ENV CONDA_DIR /opt/conda
+ENV R_LIBS_USER /opt/r
+
+# Explicitly add littler to PATH
+# See https://github.com/conda-forge/r-littler-feedstock/issues/6
+ENV PATH ${CONDA_DIR}/lib/R/library/littler/bin:${CONDA_DIR}/bin:$PATH
+
+RUN adduser --disabled-password --gecos "Default Jupyter user" ${NB_USER}
+
+# Create user owned R libs dir
+# This lets users temporarily install packages
+RUN mkdir -p ${R_LIBS_USER} && chown ${NB_USER}:${NB_USER} ${R_LIBS_USER}
+
+# Install these without 'recommended' packages to keep image smaller.
+# Useful utils that folks sort of take for granted
+RUN apt-get update -qq --yes && \
+    apt-get install --yes --no-install-recommends -qq \
+        htop \
+        less \
+        man \
+        nano \
+        screen \
+        tar \
+        tmux \
+        wget \
+        vim \
+        locales > /dev/null
+
+RUN echo "${LC_ALL} UTF-8" > /etc/locale.gen && \
+    locale-gen
+
+RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
+RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/" > /etc/apt/sources.list.d/cran.list
+
+# Install R packages
+# Our pre-built R packages from rspm are built against system libs in focal
+# rstan takes forever to compile from source, and needs libnodejs
+# So we install older (10.x) nodejs from apt rather than newer from conda
+RUN apt-get update -qq --yes > /dev/null && \
+    apt-get install --yes -qq \
+    r-base \
+    r-base-dev \
+    r-recommended \
+    r-cran-littler \
+    nodejs
+
+# Install desktop packages
+RUN apt-get update -qq --yes > /dev/null && \
+    apt-get install --yes -qq \
+        dbus-x11 \
+        firefox \
+        xfce4 \
+        xfce4-panel \
+        xfce4-terminal \
+        xfce4-session \
+        xfce4-settings \
+        xorg \
+        xubuntu-icon-theme > /dev/null
+
+# for nbconvert & notebook-to-pdf
+RUN apt-get update -qq --yes && \
+    apt-get install --yes -qq \
+        pandoc \
+        texlive-xetex \
+        texlive-fonts-recommended \
+        libx11-xcb1 \
+        libxtst6 \
+        libxrandr2 \
+        libasound2 \
+        libpangocairo-1.0-0 \
+        libatk1.0-0 \
+        libatk-bridge2.0-0 \
+        libgtk-3-0 \
+        libnss3 \
+        libxss1 \
+        > /dev/null
+
+WORKDIR /home/jovyan
+
+COPY install-miniforge.bash /tmp/install-miniforge.bash
+RUN chmod 777 /tmp/install-miniforge.bash
+RUN /tmp/install-miniforge.bash
+
+# Needed by RStudio
+RUN apt-get update -qq --yes && \
+    apt-get install --yes --no-install-recommends -qq \
+        psmisc \
+        sudo \
+        libapparmor1 \
+        lsb-release \
+        libclang-dev  > /dev/null
+
+# Set path where R packages are installed
+# Download and install rstudio manually
+# Newer one has bug that doesn't work with jupyter-rsession-proxy
+ENV RSTUDIO_URL https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.2.5042-amd64.deb
+RUN curl --silent --location --fail ${RSTUDIO_URL} > /tmp/rstudio.deb && \
+    dpkg -i /tmp/rstudio.deb && \
+    rm /tmp/rstudio.deb
+
+# Needed by many R libraries
+# Picked up from https://github.com/rocker-org/rocker/blob/9dc3e458d4e92a8f41ccd75687cd7e316e657cc0/r-rspm/focal/Dockerfile
+RUN apt-get update && \
+	apt-get install -y --no-install-recommends \
+                   libgdal26 \
+                   libgeos-3.8.0 \
+                   libproj15 \
+                   libudunits2-0 \
+                   libxml2 > /dev/null
+# R_LIBS_USER is set by default in /etc/R/Renviron, which RStudio loads.
+# We uncomment the default, and set what we wanna - so it picks up
+# the packages we install. Without this, RStudio doesn't see the packages
+# that R does.
+# Stolen from https://github.com/jupyterhub/repo2docker/blob/6a07a48b2df48168685bb0f993d2a12bd86e23bf/repo2docker/buildpacks/r.py
+RUN sed -i -e '/^R_LIBS_USER=/s/^/#/' /etc/R/Renviron && \
+    echo "R_LIBS_USER=${R_LIBS_USER}" >> /etc/R/Renviron
+
+USER ${NB_USER}
+
+COPY environment.yml /tmp/
+COPY requirements.txt /tmp/
+COPY infra-requirements.txt /tmp/
+
+RUN conda env update -p ${CONDA_DIR} -f /tmp/environment.yml
+
+# Set CRAN mirror to rspm before we install anything
+COPY Rprofile.site /usr/lib/R/etc/Rprofile.site
+# RStudio needs its own config
+COPY rsession.conf /etc/rstudio/rsession.conf
+
+#install rsession proxy
+RUN pip install --no-cache-dir \
+        jupyter-rsession-proxy==1.2 
+
+# Install IRKernel
+RUN r -e "install.packages('IRkernel', version='1.1.1')" && \
+    r -e "IRkernel::installspec(prefix='${CONDA_DIR}')"
+
+# Install R packages, cleanup temp package download location
+COPY install.R /tmp/install.R
+RUN r /tmp/install.R && \
+ 	rm -rf /tmp/downloaded_packages/ /tmp/*.rds
+
+# Set bash as shell in terminado.
+ADD jupyter_notebook_config.py  ${CONDA_PREFIX}/etc/jupyter/
+# Disable history.
+ADD ipython_config.py ${CONDA_PREFIX}/etc/ipython/
+
+# Install PAUP* for BIO 1B
+# https://github.com/berkeley-dsep-infra/datahub/issues/1699
+RUN wget http://phylosolutions.com/paup-test/paup4a168_ubuntu64.gz -O ${CONDA_DIR}/bin/paup.gz
+RUN gunzip ${CONDA_DIR}/bin/paup.gz
+RUN chmod +x ${CONDA_DIR}/bin/paup
+
+############################
+# Install packages for IB134L
+############################
+#LOCAL_BIN=${REPO_DIR}/.local/bin
+#mkdir -p ${LOCAL_BIN}
+#
+## mitoZ installation
+#
+#wget https://raw.githubusercontent.com/linzhi2013/MitoZ/master/version_2.4-alpha/release_MitoZ_v2.4-alpha.tar.bz2 -O ${REPO_DIR}/release_MitoZ_v2.4-alpha.tar.bz2
+#pushd ${REPO_DIR}
+#tar -jxvf release_MitoZ_v2.4-alpha.tar.bz2
+#rm release_MitoZ_v2.4-alpha.tar.bz2
+#cd release_MitoZ_v2.4-alpha
+#wget https://raw.githubusercontent.com/linzhi2013/MitoZ/master/version_2.4-alpha/mitozEnv.yaml
+#cd ..
+#
+### create mitoZ env
+#conda env create -n mitozEnv -f release_MitoZ_v2.4-alpha/mitozEnv.yaml # worked after reinstallation of conda
+#
+### patch ncbiquery.py
+#cp patches/ncbiquery.py /srv/conda/envs/mitozEnv/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py
+#
+### download annotations
+##source activate mitozEnv
+##python3 mitozEnv_config.py
+##source deactivate

deployments/biology/image/Rprofile.site

@@ -0,0 +1,6 @@
+local({
+    r <- getOption("repos")
+    r["CRAN"] <- "https://packagemanager.rstudio.com/all/__linux__/focal/latest"
+    options(repos = r)
+    options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))
+})

deployments/biology/image/environment.yml

@@ -5,13 +5,16 @@ dependencies:
 - python=3.8.*
 - pip=20.*
 
+# nodejs
+- nodejs
+
 # Packages from bioconda for IB134L
 - bwa=0.7.12 
 - samtools=1.3.1 
 - mafft=7.471
 - emboss=6.6.0
 - augustus=3.3.3
-- repeatmasker=4.0.9
+  #- repeatmasker=4.0.9
 
 # Packages from bioconda for BIO1B
 - raxml=8.2.*

deployments/biology/image/install-miniforge.bash

@@ -0,0 +1,42 @@
+#!/bin/bash
+# This downloads and installs a pinned version of miniconda
+set -ex
+
+cd $(dirname $0)
+MINIFORGE_VERSION=4.8.3-5
+
+URL="https://github.com/conda-forge/miniforge/releases/download/4.8.3-5/Miniforge3-${MINIFORGE_VERSION}-Linux-x86_64.sh"
+INSTALLER_PATH=/tmp/miniforge-installer.sh
+
+# make sure we don't do anything funky with user's $HOME
+# since this is run as root
+unset HOME
+
+wget --quiet $URL -O ${INSTALLER_PATH}
+chmod +x ${INSTALLER_PATH}
+
+bash ${INSTALLER_PATH} -b -p ${CONDA_DIR}
+export PATH="${CONDA_DIR}/bin:$PATH"
+
+# Do not attempt to auto update conda or dependencies
+conda config --system --set auto_update_conda false
+conda config --system --set show_channel_urls true
+
+# empty conda history file,
+# which seems to result in some effective pinning of packages in the initial env,
+# which we don't intend.
+# this file must not be *removed*, however
+echo '' > ${CONDA_DIR}/conda-meta/history
+
+# Clean things out!
+conda clean --all -f -y
+
+# Remove the big installer so we don't increase docker image size too much
+rm ${INSTALLER_PATH}
+
+# Remove the pip cache created as part of installing miniconda
+rm -rf /root/.cache
+
+chown -R $NB_USER:$NB_USER ${CONDA_DIR}
+
+conda list -n root

deployments/biology/image/install.R

@@ -0,0 +1,47 @@
+#!/usr/bin/env r
+
+# Install devtools, so we can install versioned packages
+install.packages("devtools")
+
+# Install a bunch of R packages
+# This doesn't do any dependency resolution or anything,
+# so refer to `installed.packages()` for authoritative list
+cran_packages <- c(
+  "tidyverse", "1.3.0"
+  #"learnr", "0.10.1",
+  #"knitr", "1.29"
+  #"rmarkdown", "2.3",
+  #"Rcpp", "1.0.5"
+  #"reticulate", "1.16",
+  #"openintro", "2.0.0",
+  #"gridExtra", "2.3",
+  #"BHH2", "2016.05.31",
+  #"nycflights13", "1.0.1",
+  #"tinytex", "0.25",
+  #"spdep", "1.1-5",
+  #"shiny", "1.5.0",
+  #"rstan", "2.21.2",
+  #"ggforce", "0.3.2",
+  #"ggthemes", "4.2.0"
+)
+
+#github_packages <- c(
+#  # https://github.com/utoronto-2i2c/jupyterhub-deploy/issues/31
+#  #"cutterkom/generativeart", "56ce6beed0433748b4372bfffba0e1c9f2740f9b",
+#  #"djnavarro/flametree", "0999530f758d074c214c068726e68786bb4698f6"
+#)
+#
+for (i in seq(1, length(cran_packages), 2)) {
+  devtools::install_version(
+    cran_packages[i],
+    version = cran_packages[i + 1]
+  )
+}
+#
+#
+#for (i in seq(1, length(github_packages), 2)) {
+#  devtools::install_github(
+#    github_packages[i],
+#    ref = github_packages[i + 1]
+#  )
+#}

deployments/biology/image/jupyter_notebook_config.py

@@ -0,0 +1,12 @@
+# This is sh (dash) by default, not $SHELL
+c.NotebookApp.terminado_settings = { "shell_command": ["bash"] }
+
+c.ServerProxy.servers = {
+  'http-server': {
+    'command': ['python3', '-m', 'http.server', '{port}'],
+    'absolute_url': False,
+    'launcher_entry': {
+      'title': "HTTP Server"
+    }
+  }
+}

deployments/biology/image/postBuild

@@ -15,27 +15,27 @@ chmod +x ${CONDA_DIR}/bin/paup
 ############################
 # Install packages for IB134L
 ############################
-LOCAL_BIN=${REPO_DIR}/.local/bin
-mkdir -p ${LOCAL_BIN}
-
-# mitoZ installation
-
-wget https://raw.githubusercontent.com/linzhi2013/MitoZ/master/version_2.4-alpha/release_MitoZ_v2.4-alpha.tar.bz2 -O ${REPO_DIR}/release_MitoZ_v2.4-alpha.tar.bz2
-pushd ${REPO_DIR}
-tar -jxvf release_MitoZ_v2.4-alpha.tar.bz2
-rm release_MitoZ_v2.4-alpha.tar.bz2
-cd release_MitoZ_v2.4-alpha
-wget https://raw.githubusercontent.com/linzhi2013/MitoZ/master/version_2.4-alpha/mitozEnv.yaml
-cd ..
-
-## create mitoZ env
-conda env create -n mitozEnv -f release_MitoZ_v2.4-alpha/mitozEnv.yaml # worked after reinstallation of conda
-
-## patch ncbiquery.py
-cp patches/ncbiquery.py /srv/conda/envs/mitozEnv/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py
-
-## download annotations
-#source activate mitozEnv
-#python3 mitozEnv_config.py
-#source deactivate
+#LOCAL_BIN=${REPO_DIR}/.local/bin
+#mkdir -p ${LOCAL_BIN}
+#
+## mitoZ installation
+#
+#wget https://raw.githubusercontent.com/linzhi2013/MitoZ/master/version_2.4-alpha/release_MitoZ_v2.4-alpha.tar.bz2 -O ${REPO_DIR}/release_MitoZ_v2.4-alpha.tar.bz2
+#pushd ${REPO_DIR}
+#tar -jxvf release_MitoZ_v2.4-alpha.tar.bz2
+#rm release_MitoZ_v2.4-alpha.tar.bz2
+#cd release_MitoZ_v2.4-alpha
+#wget https://raw.githubusercontent.com/linzhi2013/MitoZ/master/version_2.4-alpha/mitozEnv.yaml
+#cd ..
+#
+### create mitoZ env
+#conda env create -n mitozEnv -f release_MitoZ_v2.4-alpha/mitozEnv.yaml # worked after reinstallation of conda
+#
+### patch ncbiquery.py
+#cp patches/ncbiquery.py /srv/conda/envs/mitozEnv/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py
+#
+### download annotations
+##source activate mitozEnv
+##python3 mitozEnv_config.py
+##source deactivate
 

deployments/biology/image/rsession.conf

@@ -0,0 +1,2 @@
+# Use binary packages!
+r-cran-repos=https://packagemanager.rstudio.com/all/__linux__/focal/latest

jupyter_notebook_config.py

@@ -0,0 +1,12 @@
+# This is sh (dash) by default, not $SHELL
+c.NotebookApp.terminado_settings = { "shell_command": ["bash"] }
+
+c.ServerProxy.servers = {
+  'http-server': {
+    'command': ['python3', '-m', 'http.server', '{port}'],
+    'absolute_url': False,
+    'launcher_entry': {
+      'title': "HTTP Server"
+    }
+  }
+}