apply JARVICE build to original source tree itself

Dockerfile.JARVICE

@@ -0,0 +1,48 @@
+FROM ubuntu:xenial
+
+RUN apt-get update && apt-get -y install redir curl bzip2 git iputils-ping libgl1 && apt-get clean
+RUN curl -H 'Cache-Control: no-cache' https://raw.githubusercontent.com/nimbix/image-common/master/install-nimbix.sh | bash
+
+# JARVICE doesn't support straight Debian containers, so install Anaconda 2
+# into this Ubuntu one rather than use FROM continuumio/anaconda above
+WORKDIR /tmp
+ENV PATH=/opt/anaconda2/bin:${PATH}
+RUN curl -O https://repo.anaconda.com/archive/Anaconda2-5.1.0-Linux-x86_64.sh && bash ./Anaconda2-5.1.0-Linux-x86_64.sh -b -p /opt/anaconda2 && rm -f Anaconda2-5.1.0-Linux-x86_64.sh && conda update -n base conda && conda clean -y --all
+
+# helper in case someone runs sudo conda
+COPY JARVICE/conda /usr/bin/conda
+RUN ln -s /opt/anaconda2/etc/profile.d/conda.sh /etc/profile.d/conda.sh
+
+# deploy the Anaconda EULA so that JARVICE prompts the end user to accept it,
+# since we accepted it in batch above
+RUN mkdir -p /etc/NAE && cp -f /opt/anaconda2/LICENSE.txt /etc/NAE/license.txt
+
+# Create the ml-suite Anaconda Virtual Environment...
+# see: https://github.com/Xilinx/ml-suite/blob/v1.0-ea/docs/tutorials/start-anaconda.md
+RUN conda create -y --name ml-suite python=2.7 jupyter caffe pydot pydot-ng graphviz -c conda-forge && conda clean -y --all
+
+# Deploy this repository into the container
+COPY --chown=nimbix:nimbix . /usr/src/ml-suite/
+
+# install Git LFS
+#RUN apt-get update && apt-get -y install software-properties-common && apt-add-repository -y ppa:git-core/ppa && curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash && apt-get install git-lfs && apt-get clean && git lfs install
+
+
+# clone ml-suite from Xilinx to /usr/src, then link it into $HOME in skep
+#WORKDIR /usr/src
+#ENV XILINX_ML_SUITE_BRANCH master
+#ENV XILINX_ML_SUITE_CLONE_TIMESTAMP "Tue Jul 24 14:37:45 UTC 2018"
+#RUN git clone -b ${XILINX_ML_SUITE_BRANCH} https://github.com/Xilinx/ml-suite.git && cd ml-suite && git lfs install --local && make -C apps/yolo/nms && cd .. && chown -R nimbix:nimbix ml-suite
+RUN ln -s /usr/src/ml-suite /etc/skel/ml-suite
+#WORKDIR /data
+
+# Fix up - temporarily link in anaconda2 so we don't have to modify the script
+RUN ln -s /opt/anaconda2 ~/anaconda2 && bash /etc/skel/ml-suite/fix_caffe_opencv_symlink.sh && rm -f ~/anaconda2
+
+# motd and AppDef, URL override, and launcher for notebooks
+COPY JARVICE/motd /etc/motd
+COPY JARVICE/AppDef.json /etc/NAE/AppDef.json
+COPY JARVICE/url.txt /etc/NAE/url.txt
+COPY JARVICE/ml-notebooks /usr/local/bin/ml-notebooks
+RUN curl --fail -X POST -d @/etc/NAE/AppDef.json https://api.jarvice.com/jarvice/validate
+

JARVICE/AppDef.json

@@ -0,0 +1,33 @@
+{
+    "name": "Xilinx ML Suite",
+    "description": "Interactive environment for FPGA machine learning development and testing using the Xilinx ML Suite - https://github.com/Xilinx/ml-suite",
+    "author": "Xilinx",
+    "licensed": true,
+    "classifications": [
+        "Software Development/Software Testing",
+        "Machine Learning"
+    ],
+    "machines": [
+        "nx5"
+    ],
+    "vault-types": [
+        "FILE",
+        "BLOCK",
+        "BLOCK_ARRAY",
+        "OBJECT"
+    ],
+    "commands": {
+        "Notebook": {
+            "path": "/usr/local/bin/ml-notebooks",
+            "interactive": true,
+            "name": "Notebook",
+            "description": "Launch an interactive Jupyter Notebook session and connect directly in your browser.  Connection address and credentials for SSH will also appear in your web browser once available.",
+            "parameters": {}
+        }
+    },
+    "image": {
+        "type": "image/png",
+        "data": 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"
+    },
+    "id": "jarvice-xilinx_ml_suite"
+}

JARVICE/LICENSE

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+BSD 3-Clause License
+
+Copyright (c) 2018, Nimbix, Inc.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the copyright holder nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

JARVICE/README.md

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+# Xilinx ML Suite development environment for JARVICE
+This directory contains the scripts and metadata files used while building the application environment container for deploying on Nimbix's JARVICE supercomputing cloud platform.  See ```../Dockerfile.JARVICE``` for the actual Dockerfile used for this container build.
+

JARVICE/conda

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+#!/bin/sh
+
+exec /opt/anaconda2/bin/conda "$@"
+

JARVICE/ml-notebooks

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+#!/bin/bash -l
+
+sudo service ssh start
+sudo redir --lport=443 --cport=8443 --caddr=localhost &
+cd ~/ml-suite
+conda activate ml-suite
+source ./overlaybins/setup.sh nimbix
+exec jupyter notebook --notebook-dir=notebooks --no-browser --port=8443 --certfile=/etc/JARVICE/cert.pem --NotebookApp.token=
+

JARVICE/motd

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+
+The Xilinx ML Suite git repository is cloned in ~/ml-suite
+
+For more information, please see:
+    https://github.com/Xilinx/ml-suite/
+
+- The ml-suite conda environment has already been set up and can be activated
+- By using this environment you agree to the terms of the Anaconda EULA:
+    /opt/anaconda2/LICENSE.txt
+

JARVICE/url.txt

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+https://%PUBLICADDR%/