#5 add first couple of apps for ncsu use case - Grass and Netlogo

use-cases/netlogo-docker/Dockerfile

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+FROM java:openjdk-7-jdk
+
+MAINTAINER Lisa Stillwell <[email protected]>
+# See https://github.com/NetLogo/NetLogo/wiki/Controlling-API
+
+ENV NETLOGO_HOME /opt/netlogo
+
+# Download and extract NetLogo to /opt/netlogo.
+# RUN wget https://ccl.northwestern.edu/netlogo/5.2.0/netlogo-5.2.0.tar.gz && \
+	# tar xzf netlogo-5.2.0.tar.gz && \
+	# rm netlogo-5.2.0.tar.gz && \
+	# mv netlogo-5.2.0 $NETLOGO_HOME
+RUN wget https://ccl.northwestern.edu/netlogo/5.3.1/NetLogo-5.3.1-64.tgz && \
+	tar xzf NetLogo-5.3.1-64.tgz && \
+	rm NetLogo-5.3.1-64.tgz && \
+	mv netlogo-5.3.1-64 $NETLOGO_HOME
+
+ADD ./netlogo-headless.sh $NETLOGO_HOME/
+RUN chmod 755 $NETLOGO_HOME/netlogo-headless.sh
+
+# Download NetLogo extensions:
+# R extension
+#RUN wget "http://phoenixnap.dl.sourceforge.net/project/r-ext/v1.4 for NetLogo 5.3 and R3.2 and later/r_v1.4_for_NL5.3_R3.2_and_higher.zip" && \
+RUN wget "https://iweb.dl.sourceforge.net/project/r-ext/v1.4 for NetLogo 5.3 and R 3.2 and later/r_v1.4_for_NL5.3_R3.2_and_higher.zip" && \
+	unzip r_v1.4_for_NL5.3_R3.2_and_higher.zip -d $NETLOGO_HOME/extensions && \
+	rm r_v1.4_for_NL5.3_R3.2_and_higher.zip
+
+# pathdir extension
+RUN wget https://github.com/cstaelin/Pathdir-Extension/archive/v2.0.0.zip && \
+	unzip v2.0.0.zip && \
+	cd Pathdir-Extension-2.0.0 && \
+	unzip pathdir.zip -d $NETLOGO_HOME/extensions && \
+	cd / && \
+	rm -rf v2.0.0.zip Pathdir-Extension-2.0.0
+
+# Install R
+RUN useradd docker \
+	&& mkdir /home/docker \
+	&& chown docker:docker /home/docker \
+	&& addgroup docker staff
+
+RUN apt-get update \ 
+	&& apt-get install -y --no-install-recommends \
+		ed \
+		less \
+		locales \
+		vim-tiny \
+		wget \
+		ca-certificates \
+		fonts-texgyre \
+	&& rm -rf /var/lib/apt/lists/*
+
+## Configure default locale, see https://github.com/rocker-org/rocker/issues/19
+RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
+	&& locale-gen en_US.utf8 \
+		&& /usr/sbin/update-locale LANG=en_US.UTF-8
+
+ENV LC_ALL en_US.UTF-8
+ENV LANG en_US.UTF-8
+
+## Use Debian unstable via pinning -- new style via APT::Default-Release
+RUN echo "deb http://http.debian.net/debian sid main" > /etc/apt/sources.list.d/debian-unstable.list \
+	&& echo 'APT::Default-Release;' > /etc/apt/apt.conf.d/default
+
+#ENV R_BASE_VERSION 3.4.0
+ENV R_BASE_VERSION 3.4
+ENV R_HOME /usr/lib/R
+ENV JRI_HOME /usr/local/lib/R/site-library/rJava/jri
+ENV R_LIBS /usr/lib/R/library:/usr/lib/R/site-library:/usr/local/lib/R/site-library
+ENV R_LIBS_SITE /usr/lib/R/library:/usr/lib/R/site-library:/usr/local/lib/R/site-library
+ENV R_LIBS_USER /usr/lib/R/library:/usr/lib/R/site-library:/usr/local/lib/R/site-library
+
+## Now install R and littler, and create a link for littler in /usr/local/bin
+## Also set a default CRAN repo, and make sure littler knows about it too
+RUN apt-get update \
+	&& apt-get install -y --no-install-recommends \
+		littler \
+		r-cran-littler \
+		r-base=${R_BASE_VERSION}* \
+		r-base-dev=${R_BASE_VERSION}* \
+		r-recommended=${R_BASE_VERSION}* \
+	&& echo 'options(repos = c(CRAN = "https://cran.rstudio.com/"), download.file.method = "libcurl")' >> /etc/R/Rprofile.site \
+	&& echo 'source("/etc/R/Rprofile.site")' >> /etc/littler.r \
+	&& ln -s /usr/share/doc/littler/examples/install.r /usr/local/bin/install.r \
+	&& ln -s /usr/share/doc/littler/examples/install2.r /usr/local/bin/install2.r \
+	&& ln -s /usr/share/doc/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
+	&& ln -s /usr/share/doc/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \
+	&& ln -s /usr/lib/jvm/java-7-openjdk-amd64 /usr/lib/jvm/default-java \
+	&& install.r docopt \
+	&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
+	&& rm -rf /var/lib/apt/lists/*
+
+# install package rJava
+RUN /usr/local/bin/install.r rJava bnlearn readr
+
+# For debugging
+#CMD ["/bin/bash"]
+
+ENTRYPOINT ["/opt/netlogo/netlogo-headless.sh"]

use-cases/netlogo-docker/netlogo-headless.sh

@@ -0,0 +1,8 @@
+#!/bin/sh
+cd "`dirname "$0"`"             # the copious quoting is for handling paths with spaces
+# -Xmx1024m                     use up to 1GB RAM (edit to increase)
+# -Dfile.encoding=UTF-8         ensure Unicode characters in model files are compatible cross-platform
+# -classpath NetLogo.jar        specify main jar
+# org.nlogo.headless.Main       specify we want headless, not GUI
+# "$@"                          pass along any command line arguments
+java -Xmx1024m -Dfile.encoding=UTF-8 -classpath app/NetLogo.jar org.nlogo.headless.Main "$@"

use-cases/netlogo-docker/sample-data/BW_sm_grid.txt

@@ -0,0 +1,51 @@
+30.87
+32.5
+30.14
+33.88
+32.1
+26.21
+26.12
+26.58
+25.75
+28.61
+32.7
+23.05
+17.17
+16.34
+17.08
+18.11
+17.575
+19.23
+20.75
+21.41
+25.31
+27.57
+19.23
+26.91
+22.83
+23.75
+18.54
+22.37
+21.52
+21.56
+17.4
+23.29
+13.725
+16.53
+15.82
+16.83
+12.87
+12.65
+16.31
+17.88
+15.78
+15.07
+10.63
+9.22
+11.97
+8.65
+10.48
+12.81
+7.33
+10.79
+11.89

use-cases/netlogo-docker/sample-data/DH_sm_grid.txt

@@ -0,0 +1,51 @@
+7.86
+7.38
+7.5
+7.2
+7.18
+6.44
+6.47
+6.56
+6.85
+5.62
+6.56
+6.52
+5.27
+6
+5.25
+4.43
+4.89
+4.75
+4.16
+5.46
+5.72
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+7.28
+5.93
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+5.12
+5.84
+5.85
+6.1
+4.45
+5
+6.04
+5.4
+5.85
+4.35
+3.8
+4.17
+4.58
+4.26
+4.78
+3.99
+4.01
+3.2
+6.27

use-cases/netlogo-docker/sample-data/DW_sm_grid.txt

@@ -0,0 +1,51 @@
+22.63
+26
+22.03
+23.42
+26.05
+19.14
+21.05
+21.27
+19.7
+18.63
+18.79
+26.54
+35.98
+35.36
+37.12
+39.39
+46.14
+34.55
+19.8
+24.1
+27.93
+19.1
+20.82
+26.17
+26
+24.7
+20.98
+17.96
+18.08
+24.43
+30.09
+29.26
+31.27
+26.24
+32.72
+33.43
+28.29
+31.87
+30.83
+30.62
+33.22
+35.64
+37.9
+33.61
+31.74
+25.82
+26.11
+31.939
+31.75
+51.28
+41.82