Added installation files for paraview express

Dockerfile

@@ -105,35 +105,52 @@ FROM system
 
 COPY --from=builder /src/web/dist/ /usr/local/lib/web/frontend/
 
-# Install STKO
+# Install Paraview
 
 
 RUN apt update \ 
     && apt upgrade -y \
     && apt install build-essential -y
 
-RUN apt update \
-    && apt install -y \
-    python3-dev \
-    tcl8.6-dev \
-    tk8.6-dev \ 
-    libtogl-dev \
-    libglu1-mesa-dev \
-    freeglut3-dev \
-    mesa-common-dev \
-    mesa-utils \
-    libxi-dev \
-    libxmu-dev \
-    xterm 
+#old dependencies for STKO:
+#RUN apt update \
+#    && apt install -y \
+#    python3-dev \
+#    tcl8.6-dev \
+#    tk8.6-dev \ 
+#    libtogl-dev \
+#    libglu1-mesa-dev \
+#    freeglut3-dev \
+#    mesa-common-dev \
+#    mesa-utils \
+#    libxi-dev \
+#    libxmu-dev \
+#    xterm 
+
+RUN apt-get update && apt-get install -y wget bzip2 nodejs nodejs-legacy curl gnupg gnupg2 gnupg1 && \
+        wget -q http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh && \
+        bash Miniconda2-latest-Linux-x86_64.sh -p /miniconda -b && \
+        rm Miniconda2-latest-Linux-x86_64.sh && \
+        rm -rf /var/lib/apt/lists/* && \
+        apt-get purge -y wget && \
+        conda install paraview -c bioconda -c conda-forge -y
+RUN curl -sL https://deb.nodesource.com/setup_7.x | bash
+RUN apt-get install -y nodejs protobuf-compiler
+RUN npm install -g pvw-visualizer
+RUN echo $CONDA/lib/paraview-5.2/ > /etc/ld.so.conf.d/paraview.conf && \
+    ldconfig && \
+    mkdir /usr/local/opt/ && \
+    mkdir /Applications
+RUN ldconfig /usr/local/lib /miniconda/lib/paraview-5.2
 
 RUN apt update \
     && apt install -y \
     libxkbcommon-x11-0
 
-# Add stko executable
-ADD STKO-Install /STKO-Install
+# Add paraview executable
+ADD Paraview-Install /Paraview-Install
 # Use/overwrite script so that it uses qt libs that will be installed by online installer
-COPY STKO.sh /STKO-Install/STKO.sh
+COPY Paraview.sh /Paraview-Install/Paraview.sh
 
 # Install qt 5.12.4 using online installer
 COPY qt_install_utils/ /qt_temp

README_Paraview.md

@@ -1,17 +1,17 @@
-STKO app
+ app
 --------
 Here are some notes on this app's image.
 
 
 Building Docker image
 ================
-Get  STKO-Install.zip from developers and unzip into this diretory
+Get paraview-Install.zip from developers and unzip into this diretory
 ```
 docker build -t tagname  .
 ```
 
 Other files of interest used in image
 =========================
-STKO.sh  is an edited version of STKO-Install/STKO.sh (provided by STKO devs) which uses a system-installed qt version instead of the libs they provided
+Paraview is an edited version of Paraview-Install/paraview.sh which uses a system-installed qt version instead of the libs they provided
 `qt_install_utils/qt-installer.qs` is an input script to online qt installer (see Dockerfile for more details on how its used) 
 `qt_install_utils/extract-qt-installer` can be used to see a list of modules which might be helpful when editing qt-installer.qs (`./extract-qt-installer --list qt-opensource-linux-x64-5.12.4.run`)

docker-paraviewweb/.travis.yml

@@ -0,0 +1,14 @@
+sudo: required
+
+language: python
+python: 2.7
+
+services:
+  - docker
+
+before_install:
+  - docker build -t bmcv/galaxy-paraviewweb .
+  - docker run -d -p 8777:8777 bmcv/galaxy-paraviewweb
+
+script:
+  - docker ps

docker-paraviewweb/Dockerfile

@@ -0,0 +1,40 @@
+FROM nginx
+
+MAINTAINER Thomas Wollmann <thomas.wollmann@bioquant.uni-heidelberg.de>
+
+ENV CONDA /miniconda/
+ENV PATH $CONDA/bin:$PATH
+
+RUN apt-get update && apt-get install -y wget bzip2 npm nodejs-legacy && \
+	wget -q http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh && \
+	bash Miniconda2-latest-Linux-x86_64.sh -p /miniconda -b && \
+	rm Miniconda2-latest-Linux-x86_64.sh && \
+	rm -rf /var/lib/apt/lists/* && \
+	apt-get purge -y wget && \
+	conda install paraview -c bioconda -c conda-forge -y && \
+        npm install -g pvw-visualizer
+
+RUN echo $CONDA/lib/paraview-5.2/ > /etc/ld.so.conf.d/paraview.conf && \
+    ldconfig && \
+    mkdir /usr/local/opt/ && \
+    mkdir /Applications
+
+ADD nginx.conf /etc/nginx/nginx.conf
+
+WORKDIR /input
+
+ENV DEBUG=false \
+    GALAXY_WEB_PORT=10000 \
+    NOTEBOOK_PASSWORD=none \
+    CORS_ORIGIN=none \
+    DOCKER_PORT=none \
+    API_KEY=none \
+    HISTORY_ID=none \
+    REMOTE_HOST=none \
+    GALAXY_URL=none
+
+EXPOSE 8777
+
+ADD startup.sh /
+RUN chmod +x /startup.sh
+CMD /startup.sh

docker-paraviewweb/LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2016 
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

docker-paraviewweb/README.md

@@ -0,0 +1,46 @@
+
+[![Build Status](https://travis-ci.org/BMCV/docker-paraviewweb.svg?branch=master)](https://travis-ci.org/BMCV/docker-paraviewweb)
+[![Docker Pulls](https://img.shields.io/docker/pulls/bmcv/galaxy-paraviewweb.svg)](https://hub.docker.com/r/bmcv/galaxy-paraviewweb/) 
+[![Docker Stars](https://img.shields.io/docker/stars/bmcv/galaxy-paraviewweb.svg)](https://hub.docker.com/r/bmcv/galaxy-paraviewweb/) 
+
+Docker ParaViewWeb Container
+========================
+
+
+This [ParaViewWeb](http://paraviewweb.kitware.com/) Docker container is used by the [Galaxy Project](https://galaxyproject.org/).
+
+![screenshot](screenshot.png)
+
+Usage
+=====
+
+* Build your own image and run it
+
+ [Docker](https://www.docker.com) is a pre-requirement for this project. You can build the container with:
+ ```bash
+  docker build -t paraviewweb .
+ ```
+ The build process can take some time, but if finished you can run your container with:
+ ```bash
+  docker run -p 8777:8777 -v /home/user/paraviewweb/input/:/input/ -v /home/user/paraviewweb/output/:/output/ paraviewweb
+ ```
+ and you will have a running [ParaViewWeb](http://paraviewweb.kitware.com/) instance on ``http://localhost:8777/apps/Visualizer``.
+
+ Environment Variables
+ =====================
+
+ Some environment variables are made available to the user which will allow for configuring the behaviour of individual instances.
+
+ Variable            | Use
+ ------------------- | ---
+ `DATASET_HID`           | Path of file relative to /input which is loaded on startup
+
+Acknowledgment
+========================
+This work was supported by the BMBF-funded Heidelberg Center for Human Bioinformatics (HD-HuB) within the German Network for Bioinformatics Infrastructure (de.NBI) #031A537C.
+
+Works best with
+=====================
+
+ * [Galaxy Image Analysis Tools](https://github.com/ThomasWollmann/galaxy-image-analysis)
+ * [Galaxy Imaging](https://github.com/bgruening/docker-galaxy-imaging)

docker-paraviewweb/nginx.conf

@@ -0,0 +1,28 @@
+events {
+    worker_connections  128;
+}
+
+http {
+	map $http_upgrade $connection_upgrade {
+	       	default upgrade;
+	       	''      close;
+	}
+
+	server {
+		listen   8777;
+		server_name 0.0.0.0; 
+
+		location / {
+			proxy_pass http://127.0.0.1:9777;
+
+			add_header Access-Control-Allow-Origin *;
+			add_header 'Access-Control-Allow-Credentials' 'true';
+			add_header 'Access-Control-Allow-Methods' 'GET, POST, PUT, DELETE, OPTIONS';
+			add_header 'Access-Control-Allow-Headers' 'Accept,Authorization,Cache-Control,Content-Type,DNT,If-Modified-Since,Keep-Alive,Origin,User-Agent,X-Mx-ReqToken,X-Requested-With';
+
+			proxy_http_version 1.1;
+			proxy_set_header Upgrade $http_upgrade;
+		        proxy_set_header Connection $connection_upgrade;
+		}
+	}
+}

docker-paraviewweb/startup.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+service nginx start
+
+if [ -z "$DATASET_HID" ]
+then
+    Visualizer --paraview $CONDA/lib/paraview-5.2/ \
+        --data /input \
+        --port 8777 \
+	--server-only
+else
+    Visualizer --paraview $CONDA/lib/paraview-5.2/ \
+        --data /input \
+        --port 8777 \
+	--server-only \
+        --load-file $DATASET_HID
+fi