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Merge pull request #9 from uc-cdis/chore/fix_tb
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chore(fix bowtie and cdhit in tb)
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@diw2
diw2 authored Nov 25, 2019
2 parents 43f93f8 + 13a7088 commit a955bbd
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9 changes: 6 additions & 3 deletions jupyter-daids/Dockerfile
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@@ -1,13 +1,16 @@
FROM quay.io/cdis/jupyter-nde-base:chore_nde_base
FROM quay.io/cdis/jupyter-nde-base:1.0.2

USER root

# COPY premade notebook
RUN mkdir /home/jovyan/daids-notebook

ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/DAIDS_notebook/CHARLIE_demo.ipynb /home/jovyan/daids-notebook/
ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/DAIDS_notebook/ndh_analysis_functions.py /home/jovyan/daids-notebook/
ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/DAIDS_notebook/readme.txt /home/jovyan/daids-notebook/
RUN chmod -R 777 /home/jovyan/daids-notebook
RUN touch /home/jovyan/daids-notebook/readme.txt
RUN touch /home/jovyan/daids-notebook/CHARLIE_demo.ipynb
RUN touch /home/jovyan/daids-notebook/ndh_analysis_functions.py

USER $NB_UID
WORKDIR /home/jovyan
WORKDIR /home/jovyan
8 changes: 7 additions & 1 deletion jupyter-dait/Dockerfile
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@@ -1,4 +1,4 @@
FROM quay.io/cdis/jupyter-nde-base:chore_nde_base
FROM quay.io/cdis/jupyter-nde-base:1.0.2

USER root

Expand All @@ -9,7 +9,13 @@ ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/DAIT_notebook
ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/DAIT_notebook/Microbiome.ipynb /home/jovyan/DAIT-notebook/
ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/DAIT_notebook/microbiome.R /home/jovyan/DAIT-notebook/
ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/DAIT_notebook/ndh_analysis_functions.py /home/jovyan/DAIT-notebook/
ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/DAIT_notebook/readme.txt /home/jovyan/DAIT-notebook/
RUN chmod -R 777 /home/jovyan/DAIT-notebook
RUN touch /home/jovyan/DAIT-notebook/DAIT_lipids_demo.ipynb
RUN touch /home/jovyan/DAIT-notebook/Microbiome.ipynb
RUN touch /home/jovyan/DAIT-notebook/microbiome.R
RUN touch /home/jovyan/DAIT-notebook/ndh_analysis_functions.py
RUN touch /home/jovyan/DAIT-notebook/readme.txt

USER $NB_UID
WORKDIR /home/jovyan
9 changes: 8 additions & 1 deletion jupyter-dmid/Dockerfile
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@@ -1,4 +1,4 @@
FROM quay.io/cdis/jupyter-nde-base:chore_nde_base
FROM quay.io/cdis/jupyter-nde-base:1.0.2

USER root

Expand All @@ -10,7 +10,14 @@ ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/DMID_notebook
ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/DMID_notebook/LHV_demo.ipynb /home/jovyan/DMID-notebook/
ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/DMID_notebook/ndh_analysis_function_dmid.r /home/jovyan/DMID-notebook/
ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/DMID_notebook/ndh_analysis_functions_dmid.py /home/jovyan/DMID-notebook/
ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/DMID_notebook/readme.txt /home/jovyan/DMID-notebook/
RUN chmod -R 777 /home/jovyan/DMID-notebook
RUN touch /home/jovyan/DMID-notebook/CalU3_TypeI_ISG.txt
RUN touch /home/jovyan/DMID-notebook/DMID-LHV-R.ipynb
RUN touch /home/jovyan/DMID-notebook/LHV_demo.ipynb
RUN touch /home/jovyan/DMID-notebook/ndh_analysis_function_dmid.r
RUN touch /home/jovyan/DMID-notebook/ndh_analysis_functions_dmid.py
RUN touch /home/jovyan/DMID-notebook/readme.txt

USER $NB_UID
WORKDIR /home/jovyan
51 changes: 46 additions & 5 deletions jupyter-tb/Dockerfile
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@@ -1,10 +1,41 @@
FROM quay.io/cdis/jupyter-nde-base:chore_nde_base
FROM quay.io/cdis/jupyter-nde-base:1.0.2

USER root

RUN apt-get update && \
apt-get install -y \
mummer
curl \
python3 \
python3-pip\
python3-dev\
python3-setuptools \
python3-tk \
python3-matplotlib \
libssl-dev libcurl4-openssl-dev \
git bzip2 nodejs\
build-essential cd-hit curl\
libbz2-dev liblzma-dev \
mummer unzip wget \
zlib1g-dev && \
rm -rf /var/lib/apt/lists/*

RUN python -m pip install pandas

RUN curl -sL https://deb.nodesource.com/setup_10.x | bash -

WORKDIR /

RUN wget -q http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.9/bowtie2-2.2.9-linux-x86_64.zip \
&& unzip bowtie2-2.2.9-linux-x86_64.zip \
&& rm bowtie2-2.2.9-linux-x86_64.zip

# Need MPLBACKEND="agg" to make matplotlib work without X11, otherwise get the error
# _tkinter.TclError: no display name and no $DISPLAY environment variable
ENV ARIBA_BOWTIE2=$PWD/bowtie2-2.2.9/bowtie2 ARIBA_CDHIT=cdhit-est MPLBACKEND="agg"

RUN cd /usr/local/bin && ln -s /usr/bin/python3 python && cd

RUN mkdir /notebooks

RUN git clone https://github.com/sanger-pathogens/ariba.git \
&& cd ariba \
Expand All @@ -23,14 +54,24 @@ RUN wget -O mykrobe-data.tar.gz https://bit.ly/2H9HKTU && tar -zxvf mykrobe-data
RUN pip install .


# COPY premade notebook
# Mount 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/NIAID_plots.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/match_plot_sort_mykrobe.txt /home/jovyan/tb-notebook/
ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/TB_notebook/out.summary.csv /home/jovyan/tb-notebook/
ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/TB_notebook/readme.txt /home/jovyan/tb-notebook/
RUN chmod -R 777 /home/jovyan/tb-notebook
RUN touch /home/jovyan/tb-notebook/readme.txt
RUN touch /home/jovyan/tb-notebook/out.summary.csv
RUN touch /home/jovyan/tb-notebook/match_plot_sort_mykrobe.txt
RUN touch /home/jovyan/tb-notebook/tb_notebook.ipynb
RUN touch /home/jovyan/tb-notebook/tb_analysis_function.py
RUN touch /home/jovyan/tb-notebook/prediction_tool_visualization.ipynb
RUN touch /home/jovyan/tb-notebook/NIAID_plots.r

# CMD ariba
USER $NB_UID
WORKDIR /home/jovyan
WORKDIR /home/jovyan
7 changes: 6 additions & 1 deletion rstudio-inflammatory/Dockerfile
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Expand Up @@ -7,6 +7,11 @@ RUN mkdir /home/rstudio/inflammatory
ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/Inflammatory_RStudio/Gen3AuthHelper.R /home/rstudio/inflammatory
ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/Inflammatory_RStudio/Gen3Submission.R /home/rstudio/inflammatory
ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/Inflammatory_RStudio/immune_marker.R /home/rstudio/inflammatory
ADD https://raw.githubusercontent.com/uc-cdis/ndh-demo/master/demo/DMID_notebook/readme.txt /home/rstudio/inflammatory

RUN chmod -R 777 /home/rstudio/inflammatory

RUN chmod -R 777 /home/rstudio/inflammatory
RUN touch /home/rstudio/inflammatory/Gen3AuthHelper.R
RUN touch /home/rstudio/inflammatory/Gen3Submission.R
RUN touch /home/rstudio/inflammatory/immune_marker.R
RUN touch /home/rstudio/inflammatory/readme.txt

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