Merge pull request #5 from uc-cdis/fix/tb

Fix/tb
uc-cdis · Nov 1, 2019 · 521c92a · 521c92a
2 parents 8e207a4 + 8f0e5bf
commit 521c92a
Showing 1 changed file with 15 additions and 122 deletions.
diff --git a/jupyter-tb/Dockerfile b/jupyter-tb/Dockerfile
@@ -1,148 +1,41 @@
-# Copyright (c) Jupyter Development Team.
-# Distributed under the terms of the Modified BSD License.
-FROM jupyter/scipy-notebook:d4cbf2f80a2a 
+FROM quay.io/cdis/jupyter-notebook:latest
 
 USER root
 
-RUN pip install --upgrade nbconvert==5.4.1
-
-#
-# R pre-requisites
-#  https://github.com/rocker-org/rocker/blob/master/r-base/Dockerfile
-#
-## Configure default locale, see https://github.com/rocker-org/rocker/issues/19
-RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
-    && locale-gen en_US.utf8 \
-    && /usr/sbin/update-locale LANG=en_US.UTF-8
-
-ENV LC_ALL en_US.UTF-8
-ENV LANG en_US.UTF-8
-
-ENV R_BASE_VERSION 3.6.0
-
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends \
-    autoconf \
-    ca-certificates \
-    fonts-dejavu \
-    fonts-texgyre \
-    gfortran \
-    gcc \
-    make \
-    automake \
-    perl \
-    less \
-    locales \
-    libssl1.0.0 \
-    libssl-dev \
-    tzdata \
-    vim \
-    zlib1g \
-    zlib1g-dev \
-    libbz2-dev \
-    libcurl4-gnutls-dev \
-    liblzma-dev 
-
-## Now install R and littler, and create a link for littler in /usr/local/bin
-#RUN apt-get update \
-#   && apt-get install -t unstable -y --no-install-recommends \
-#       littler \
-#    r-cran-littler \
-#       r-base=${R_BASE_VERSION}-* \
-#       r-base-dev=${R_BASE_VERSION}-* \
-#       r-recommended=${R_BASE_VERSION}-* \
-#   && ln -s /usr/lib/R/site-library/littler/examples/install.r /usr/local/bin/install.r \
-#   && ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
-#   && ln -s /usr/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
-#   && ln -s /usr/lib/R/site-library/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \
-#   && install.r docopt \
-#   && rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
-
-RUN apt-get clean \
-    && rm -rf /var/lib/apt/lists/*
-
-#
-# R packages including IRKernel which gets installed globally.
-# See https://github.com/rocker-org/rocker/blob/master/r-base/Dockerfile
-#
-RUN conda config --system --append channels r && \
-    conda install --quiet --yes \
-    'rpy2' \
-    "r-base=$R_BASE_VERSION" \
-    'r-irkernel' \
-    'r-plyr' \
-    'r-devtools' \
-    'r-tidyverse' \
-    'r-shiny' \
-    'r-rmarkdown' \
-    'r-forecast' \
-    'r-rsqlite' \
-    'r-reshape2' \
-    'r-nycflights13' \
-    'r-caret' \
-    'r-rcurl' \
-    'r-crayon' \
-    'r-randomforest' \
-    'r-rmysql' \
-    'r-gplots' \
-    'r-gtools' \
-    'r-catools' \
-    && conda clean -tipsy && \
-    fix-permissions $CONDA_DIR && \
-    fix-permissions /home/$NB_USER
-
-RUN wget https://github.com/arq5x/lumpy-sv/releases/download/0.3.0/lumpy-sv.tar.gz; \
-    tar -zxvf lumpy-sv.tar.gz lumpy-sv; rm lumpy-sv.tar.gz; \
-    cd lumpy-sv; make; cp bin/* /usr/local/bin/.; \
-    rm -rf data/ src/ .git;
-
-COPY resources/templates/ /opt/conda/lib/python3.7/site-packages/notebook/templates
-
-USER $NB_UID
-
-COPY resources/custom.js /home/$NB_USER/.jupyter/custom/
-COPY resources/jupyter_notebook_config.py /home/$NB_USER/.jupyter/tmp.py
-RUN cat /home/$NB_USER/.jupyter/tmp.py >> /home/$NB_USER/.jupyter/jupyter_notebook_config.py && rm /home/$NB_USER/.jupyter/tmp.py
-
-RUN echo "load.lib<-c('httr','jsonlite','dplyr','gplots','ggplot2','ggpubr','RColorBrewer','xml2','repr','VennDiagram'); install.lib<-load.lib[!load.lib %in% installed.packages()]; install.packages(install.lib,dependencies=TRUE, repos='http://cran.us.r-project.org', type='source')" | R --no-save
-RUN echo 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager",dependencies=TRUE, repos="http://cran.us.r-project.org"); BiocManager::install(ask=FALSE)' | R --no-save
-RUN echo "load.s3<-c('maftools', 'phyloseq', 'DESeq2', 'dada2', 'vcfR'); install.s3<-load.s3[!load.s3 %in% installed.packages()]; for(s3 in install.s3) BiocManager::install(s3, ask=FALSE);" | R --no-save
-
-
-USER root
-
 RUN apt-get update && \
     apt-get install -y \
     mummer
-
+
 RUN git clone https://github.com/sanger-pathogens/ariba.git \
   && cd ariba \
   && git checkout v2.13.4 \
   # && python3 setup.py test \
   && python3 setup.py install
-
+
 RUN git clone https://github.com/Mykrobe-tools/mykrobe.git mykrobe \
     && cd mykrobe
-
+
 WORKDIR mykrobe
-
+
 ## Download pre-built probesets
 RUN wget -O mykrobe-data.tar.gz https://bit.ly/2H9HKTU && tar -zxvf mykrobe-data.tar.gz && rm -fr src/mykrobe/data && mv mykrobe-data src/mykrobe/data
-
+
 RUN pip install .
-
+
 ## Append custom settings to jupyter config file
 COPY jupyter_notebook_config.py /home/$NB_USER/.jupyter/tmp.py
 RUN cat /home/$NB_USER/.jupyter/tmp.py >> /home/$NB_USER/.jupyter/jupyter_notebook_config.py && rm /home/$NB_USER/.jupyter/tmp.py
-
-# CMD ariba
-
-USER $NB_UID
-WORKDIR /home/jovyan
+
 
 # COPY premade notebook 
 RUN mkdir /home/jovyan/tb-notebook
 ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/TB_notebook/NIAID_plots_2.r /home/jovyan/tb-notebook/
 ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/TB_notebook/prediction_tool_visualization.ipynb /home/jovyan/tb-notebook/
 ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/TB_notebook/tb_analysis_function.py /home/jovyan/tb-notebook/
-ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/TB_notebook/tb_notebook.ipynb /home/jovyan/tb-notebook/
+ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/TB_notebook/tb_notebook.ipynb /home/jovyan/tb-notebook/
+RUN chmod -R 777 /home/jovyan/tb-notebook
+
+# CMD ariba
+
+USER $NB_UID
+WORKDIR /home/jovyan