add Dockerfile and files needed for image

Dockerfile

@@ -1,9 +1,153 @@
-FROM nfcore/base
-MAINTAINER ATACFlow Team @ RMGCH-18 <evanfloden@gmail.com>
-LABEL authors="evanfloden@gmail.com" \
-      description="Docker image containing all requirements for NCBI-Hackathons/ATACFlow pipeline"
+#FROM nfcore/base
+#MAINTAINER ATACFlow Team @ RMGCH-18 <evanfloden@gmail.com>
+#LABEL authors="evanfloden@gmail.com" \
+#      description="Docker image containing all requirements for NCBI-Hackathons/ATACFlow pipeline"
+#RUN pip install dastk --user
+#COPY environment.yml /
+#RUN conda env create -f /environment.yml && conda clean -a
+#ENV PATH /opt/conda/envs/ncbihackathons-atacflow-0.1.0/bin:$PATH
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
 
-RUN pip install dastk --user
+# Ubuntu 16.04 (xenial) from 2018-02-28
+# https://github.com/docker-library/official-images/commit/8728671fdca3dfc029be4ab838ab5315aa125181
+FROM ubuntu:xenial-20180228@sha256:e348fbbea0e0a0e73ab0370de151e7800684445c509d46195aef73e090a49bd6
+
+LABEL maintainer="Steve Tsa <mylagimail2004@yahoo.com>"
+
+USER root
+
+# Install all OS dependencies for notebook server that starts but lacks all
+# features (e.g., download as all possible file formats)
+ENV DEBIAN_FRONTEND noninteractive
+RUN apt-get update && apt-get -yq dist-upgrade \
+ && apt-get install -yq --no-install-recommends \
+    wget \
+    bzip2 \
+    ca-certificates \
+    sudo \
+    locales \
+    fonts-liberation \
+    git \
+    curl \
+ && apt-get clean \
+ && rm -rf /var/lib/apt/lists/*
+
+RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
+    locale-gen
+
+# Install Tini
+RUN wget --quiet https://github.com/krallin/tini/releases/download/v0.10.0/tini && \
+    echo "1361527f39190a7338a0b434bd8c88ff7233ce7b9a4876f3315c22fce7eca1b0 *tini" | sha256sum -c - && \
+    mv tini /usr/local/bin/tini && \
+    chmod +x /usr/local/bin/tini
+
+# Configure environment
+ENV CONDA_DIR=/opt/conda \
+    SHELL=/bin/bash \
+    NB_USER=jovyan \
+    NB_UID=1000 \
+    NB_GID=100 \
+    LC_ALL=en_US.UTF-8 \
+    LANG=en_US.UTF-8 \
+    LANGUAGE=en_US.UTF-8
+ENV PATH=$CONDA_DIR/bin:$PATH \
+    HOME=/home/$NB_USER
+
+ADD fix-permissions /usr/local/bin/fix-permissions
+# Create jovyan user with UID=1000 and in the 'users' group
+# and make sure these dirs are writable by the `users` group.
+RUN useradd -m -s /bin/bash -N -u $NB_UID $NB_USER && \
+    mkdir -p $CONDA_DIR && \
+    chown $NB_USER:$NB_GID $CONDA_DIR && \
+    chmod g+w /etc/passwd /etc/group && \
+    fix-permissions $HOME && \
+    fix-permissions $CONDA_DIR
+
+USER $NB_UID
+
+# Setup work directory for backward-compatibility
+RUN mkdir /home/$NB_USER/work && \
+    fix-permissions /home/$NB_USER
+
+# Install conda as jovyan and check the md5 sum provided on the download site
+ENV MINICONDA_VERSION 4.4.10
+RUN cd /tmp && \
+    wget --quiet https://repo.continuum.io/miniconda/Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
+    echo "bec6203dbb2f53011e974e9bf4d46e93 *Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh" | md5sum -c - && \
+    /bin/bash Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh -f -b -p $CONDA_DIR && \
+    rm Miniconda3-${MINICONDA_VERSION}-Linux-x86_64.sh && \
+    $CONDA_DIR/bin/conda config --system --prepend channels conda-forge && \
+    $CONDA_DIR/bin/conda config --system --set auto_update_conda false && \
+    $CONDA_DIR/bin/conda config --system --set show_channel_urls true && \
+    $CONDA_DIR/bin/conda update --all --quiet --yes && \
+    conda clean -tipsy && \
+    rm -rf /home/$NB_USER/.cache/yarn && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER
+
+# Install Jupyter Notebook and Hub
+RUN conda install --quiet --yes \
+    'notebook=5.4.*' \
+    'jupyterhub=0.8.*' \
+    'jupyterlab=0.32.*' && \
+    conda clean -tipsy && \
+    jupyter labextension install @jupyterlab/hub-extension@^0.8.1 && \
+    npm cache clean --force && \
+    rm -rf $CONDA_DIR/share/jupyter/lab/staging && \
+    rm -rf /home/$NB_USER/.cache/yarn && \
+    fix-permissions $CONDA_DIR && \
+    fix-permissions /home/$NB_USER
+
+USER root
+
+#####  Tools needed for the NextFlow ATACSeq Workflow
+RUN pip install dastk
+RUN pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git
+WORKDIR /home/$NB_USER/work
+RUN chmod -R 777 /home/$NB_USER/work
+#RUN conda install -n base conda
+#RUN pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
 ENV PATH /opt/conda/envs/ncbihackathons-atacflow-0.1.0/bin:$PATH
+RUN curl -s https://get.nextflow.io | bash
+RUN cp nextflow /usr/local/bin/.
+
+RUN git clone https://github.com/NCBI-Hackathons/ATACFlow.git
+RUN fix-permissions /home/$NB_USER
+RUN fix-permissions $CONDA_DIR
+
+### Graphviz installation
+#RUN conda install -c anaconda graphviz - failed
+#RUN apt-get install -y 
+
+#WORKDIR /opt/
+#RUN wget https://graphviz.gitlab.io/pub/graphviz/stable/SOURCES/graphviz.tar.gz 
+#RUN tar xvzf graphviz-2.40.1.tar.gz
+#WORKDIR /opt/graphviz-2.40.1
+#RUN ./configure
+#RUN make
+#RUN make install
+RUN pip install graphviz
+#########
+
+USER root
+RUN chmod 777 /usr/local/bin/nextflow
+EXPOSE 8888
+
+# Configure container startup
+ENTRYPOINT ["tini", "--"]
+CMD ["start-notebook.sh"]
+
+# Add local files as late as possible to avoid cache busting
+COPY start.sh /usr/local/bin/
+COPY start-notebook.sh /usr/local/bin/
+COPY start-singleuser.sh /usr/local/bin/
+COPY jupyter_notebook_config.py /etc/jupyter/
+RUN fix-permissions /etc/jupyter/
+
+# Switch back to jovyan to avoid accidental container runs as root
+USER $NB_UID
+ENV USER $NB_USER
+

fix-permissions

@@ -0,0 +1,35 @@
+#!/bin/bash
+# set permissions on a directory
+# after any installation, if a directory needs to be (human) user-writable,
+# run this script on it.
+# It will make everything in the directory owned by the group $NB_GID
+# and writable by that group.
+# Deployments that want to set a specific user id can preserve permissions
+# by adding the `--group-add users` line to `docker run`.
+
+# uses find to avoid touching files that already have the right permissions,
+# which would cause massive image explosion
+
+# right permissions are:
+# group=$NB_GID
+# AND permissions include group rwX (directory-execute)
+# AND directories have setuid,setgid bits set
+
+set -e
+
+for d in $@; do
+  find "$d" \
+    ! \( \
+      -group $NB_GID \
+      -a -perm -g+rwX  \
+    \) \
+    -exec chgrp $NB_GID {} \; \
+    -exec chmod g+rwX {} \;
+  # setuid,setgid *on directories only*
+  find "$d" \
+    \( \
+        -type d \
+        -a ! -perm -6000  \
+    \) \
+    -exec chmod +6000 {} \;
+done

jupyter_notebook_config.py

@@ -0,0 +1,39 @@
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+from jupyter_core.paths import jupyter_data_dir
+import subprocess
+import os
+import errno
+import stat
+
+c = get_config()
+c.NotebookApp.ip = '*'
+c.NotebookApp.port = 8888
+c.NotebookApp.open_browser = False
+
+# https://github.com/jupyter/notebook/issues/3130
+c.FileContentsManager.delete_to_trash = False
+
+# Generate a self-signed certificate
+if 'GEN_CERT' in os.environ:
+    dir_name = jupyter_data_dir()
+    pem_file = os.path.join(dir_name, 'notebook.pem')
+    try:
+        os.makedirs(dir_name)
+    except OSError as exc:  # Python >2.5
+        if exc.errno == errno.EEXIST and os.path.isdir(dir_name):
+            pass
+        else:
+            raise
+    # Generate a certificate if one doesn't exist on disk
+    subprocess.check_call(['openssl', 'req', '-new',
+                           '-newkey', 'rsa:2048',
+                           '-days', '365',
+                           '-nodes', '-x509',
+                           '-subj', '/C=XX/ST=XX/L=XX/O=generated/CN=generated',
+                           '-keyout', pem_file,
+                           '-out', pem_file])
+    # Restrict access to the file
+    os.chmod(pem_file, stat.S_IRUSR | stat.S_IWUSR)
+    c.NotebookApp.certfile = pem_file

ls

@@ -0,0 +1,35 @@
+#!/bin/bash
+# set permissions on a directory
+# after any installation, if a directory needs to be (human) user-writable,
+# run this script on it.
+# It will make everything in the directory owned by the group $NB_GID
+# and writable by that group.
+# Deployments that want to set a specific user id can preserve permissions
+# by adding the `--group-add users` line to `docker run`.
+
+# uses find to avoid touching files that already have the right permissions,
+# which would cause massive image explosion
+
+# right permissions are:
+# group=$NB_GID
+# AND permissions include group rwX (directory-execute)
+# AND directories have setuid,setgid bits set
+
+set -e
+
+for d in $@; do
+  find "$d" \
+    ! \( \
+      -group $NB_GID \
+      -a -perm -g+rwX  \
+    \) \
+    -exec chgrp $NB_GID {} \; \
+    -exec chmod g+rwX {} \;
+  # setuid,setgid *on directories only*
+  find "$d" \
+    \( \
+        -type d \
+        -a ! -perm -6000  \
+    \) \
+    -exec chmod +6000 {} \;
+done

start-notebook.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+set -e
+
+if [[ ! -z "${JUPYTERHUB_API_TOKEN}" ]]; then
+  # launched by JupyterHub, use single-user entrypoint
+  exec /usr/local/bin/start-singleuser.sh $*
+else
+  if [[ ! -z "${JUPYTER_ENABLE_LAB}" ]]; then
+    . /usr/local/bin/start.sh jupyter lab $*
+  else
+    . /usr/local/bin/start.sh jupyter notebook $*
+  fi
+fi

start-singleuser.sh

@@ -0,0 +1,43 @@
+#!/bin/bash
+# Copyright (c) Jupyter Development Team.
+# Distributed under the terms of the Modified BSD License.
+
+set -e
+
+# set default ip to 0.0.0.0
+if [[ "$NOTEBOOK_ARGS $@" != *"--ip="* ]]; then
+  NOTEBOOK_ARGS="--ip=0.0.0.0 $NOTEBOOK_ARGS"
+fi
+
+# handle some deprecated environment variables
+# from DockerSpawner < 0.8.
+# These won't be passed from DockerSpawner 0.9,
+# so avoid specifying --arg=empty-string
+if [ ! -z "$NOTEBOOK_DIR" ]; then
+  NOTEBOOK_ARGS="--notebook-dir='$NOTEBOOK_DIR' $NOTEBOOK_ARGS"
+fi
+if [ ! -z "$JPY_PORT" ]; then
+  NOTEBOOK_ARGS="--port=$JPY_PORT $NOTEBOOK_ARGS"
+fi
+if [ ! -z "$JPY_USER" ]; then
+  NOTEBOOK_ARGS="--user=$JPY_USER $NOTEBOOK_ARGS"
+fi
+if [ ! -z "$JPY_COOKIE_NAME" ]; then
+  NOTEBOOK_ARGS="--cookie-name=$JPY_COOKIE_NAME $NOTEBOOK_ARGS"
+fi
+if [ ! -z "$JPY_BASE_URL" ]; then
+  NOTEBOOK_ARGS="--base-url=$JPY_BASE_URL $NOTEBOOK_ARGS"
+fi
+if [ ! -z "$JPY_HUB_PREFIX" ]; then
+  NOTEBOOK_ARGS="--hub-prefix=$JPY_HUB_PREFIX $NOTEBOOK_ARGS"
+fi
+if [ ! -z "$JPY_HUB_API_URL" ]; then
+  NOTEBOOK_ARGS="--hub-api-url=$JPY_HUB_API_URL $NOTEBOOK_ARGS"
+fi
+if [ ! -z "$JUPYTER_ENABLE_LAB" ]; then
+  NOTEBOOK_BIN="jupyter labhub"
+else
+  NOTEBOOK_BIN=jupyterhub-singleuser
+fi
+
+. /usr/local/bin/start.sh $NOTEBOOK_BIN $NOTEBOOK_ARGS $@