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[REL] Update of docker-images + doc
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‎Dockerfile‎

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FROM fentechai/cdt-env-base:21.01
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FROM fentechai/cdt-env-base:22.02
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MAINTAINER Diviyan Kalainathan <[email protected]>
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LABEL description="Docker image for the Causal Discovery Toolbox"
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ARG python

‎README.md‎

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@@ -65,6 +65,50 @@ Check out how to install all R dependencies in the before-install section of the
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The [r-requirements file](https://github.com/FenTechSolutions/CausalDiscoveryToolbox/blob/master/r_requirements.txt) notes all of the R packages used by the toolbox.
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Here is an example of installation script of the R packages on Ubuntu 20.04:
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``` sh
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apt-get -qq update
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DEBIAN_FRONTEND=noninteractive apt-get install -y tzdata
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apt-get -qq install dialog apt-utils -y
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apt-get install apt-transport-https -y
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apt-get install -qq software-properties-common -y
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apt-get -qq update
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apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
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add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/' -y
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apt-get -qq update
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apt-get -qq install r-base -y
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apt-get -qq install libssl-dev -y
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apt-get -qq install libgmp3-dev -y
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apt-get -qq install git -y
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apt-get -qq install build-essential -y
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apt-get -qq install libv8-dev -y
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apt-get -qq install libcurl4-openssl-dev -y
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apt-get -qq install libgsl-dev -y
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Rscript -e 'install.packages(c("V8"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
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Rscript -e 'install.packages(c("sfsmisc"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
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Rscript -e 'install.packages(c("clue"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
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Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/randomForest/randomForest_4.6-14.tar.gz", repos=NULL, type="source")'
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Rscript -e 'install.packages(c("lattice"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
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Rscript -e 'install.packages(c("devtools"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
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Rscript -e 'install.packages(c("MASS"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
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Rscript -e 'install.packages("BiocManager")'
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Rscript -e 'BiocManager::install(c("igraph"))'
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Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/fastICA/fastICA_1.2-2.tar.gz", repos=NULL, type="source")'
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Rscript -e 'BiocManager::install(c("SID", "bnlearn", "pcalg", "kpcalg", "glmnet", "mboost"))'
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Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/CAM/CAM_1.0.tar.gz", repos=NULL, type="source")'
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Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/sparsebnUtils_0.0.8.tar.gz", repos=NULL, type="source")'
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Rscript -e 'BiocManager::install(c("ccdrAlgorithm", "discretecdAlgorithm"))'
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apt-get -qq install libxml2-dev -y
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Rscript -e 'install.packages("devtools")'
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Rscript -e 'library(devtools); install_github("cran/CAM"); install_github("cran/momentchi2"); install_github("Diviyan-Kalainathan/RCIT", quiet=TRUE, verbose=FALSE)'
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Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/sparsebn/sparsebn_0.1.2.tar.gz", repos=NULL, type="source")'
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```
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## Overview
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### General package structure
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The following figure shows how the package and its algorithms are structured

‎docs/index.rst‎

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Check out how to install all R dependencies in the before-install section of the [travis.yml](https://github.com/FenTechSolutions/CausalDiscoveryToolbox/blob/master/.travis.yml) file for debian based distributions.
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The `r-requirements file <https://github.com/FenTechSolutions/CausalDiscoveryToolbox/blob/master/r_requirements.txt>`_ notes all the R packages used by the toolbox.
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Here is an example of installation script of the R packages on Ubuntu 20.04:
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.. code-block:: sh
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apt-get -qq update
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DEBIAN_FRONTEND=noninteractive apt-get install -y tzdata
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apt-get -qq install dialog apt-utils -y
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apt-get install apt-transport-https -y
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apt-get install -qq software-properties-common -y
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apt-get -qq update
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apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
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add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/' -y
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apt-get -qq update
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apt-get -qq install r-base -y
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apt-get -qq install libssl-dev -y
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apt-get -qq install libgmp3-dev -y
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apt-get -qq install git -y
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apt-get -qq install build-essential -y
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apt-get -qq install libv8-dev -y
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apt-get -qq install libcurl4-openssl-dev -y
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apt-get -qq install libgsl-dev -y
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Rscript -e 'install.packages(c("V8"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
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Rscript -e 'install.packages(c("sfsmisc"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
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Rscript -e 'install.packages(c("clue"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
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Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/randomForest/randomForest_4.6-14.tar.gz", repos=NULL, type="source")'
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Rscript -e 'install.packages(c("lattice"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
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Rscript -e 'install.packages(c("devtools"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
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Rscript -e 'install.packages(c("MASS"),repos="http://cran.us.r-project.org", quiet=TRUE, verbose=FALSE)'
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Rscript -e 'install.packages("BiocManager")'
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Rscript -e 'BiocManager::install(c("igraph"))'
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Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/fastICA/fastICA_1.2-2.tar.gz", repos=NULL, type="source")'
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Rscript -e 'BiocManager::install(c("SID", "bnlearn", "pcalg", "kpcalg", "glmnet", "mboost"))'
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Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/CAM/CAM_1.0.tar.gz", repos=NULL, type="source")'
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Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/sparsebnUtils_0.0.8.tar.gz", repos=NULL, type="source")'
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Rscript -e 'BiocManager::install(c("ccdrAlgorithm", "discretecdAlgorithm"))'
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apt-get -qq install libxml2-dev -y
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Rscript -e 'install.packages("devtools")'
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Rscript -e 'library(devtools); install_github("cran/CAM"); install_github("cran/momentchi2"); install_github("Diviyan-Kalainathan/RCIT", quiet=TRUE, verbose=FALSE)'
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Rscript -e 'install.packages("https://cran.r-project.org/src/contrib/Archive/sparsebn/sparsebn_0.1.2.tar.gz", repos=NULL, type="source")'
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Overview
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========

‎nv-Dockerfile‎

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FROM fentechai/nv-cdt-env-base:21.01
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FROM fentechai/nv-cdt-env-base:22.02
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MAINTAINER Diviyan Kalainathan <[email protected]>
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LABEL description="Nvidia Docker image for the Causal Discovery Toolbox"
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ARG python

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