From c89ecbd52d80268dff9e31b92150e8763dbd8e50 Mon Sep 17 00:00:00 2001
From: Hauke Kirchner <hauke.gronenberg@gwdg.de>
Date: Fri, 7 Feb 2025 16:09:32 +0000
Subject: [PATCH] added new custom container for ML work with Python and R
---
code/container/dlc-python-r.def | 79 +++++++++++++++++++++++++++++++++
1 file changed, 79 insertions(+)
create mode 100644 code/container/dlc-python-r.def
diff --git a/code/container/dlc-python-r.def b/code/container/dlc-python-r.def
new file mode 100644
index 0000000..e5b4bad
--- /dev/null
+++ b/code/container/dlc-python-r.def
@@ -0,0 +1,79 @@
+Bootstrap: docker
+From: condaforge/miniforge3
+
+%post
+ export DEBIAN_FRONTEND=noninteractive
+ apt update
+ apt upgrade -y
+
+ apt install -y openssh-client
+
+ apt install -y --no-install-recommends software-properties-common dirmngr
+ wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
+ add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/"
+ add-apt-repository ppa:c2d4u.team/c2d4u4.0+
+ apt update
+
+ add-apt-repository ppa:ubuntugis/ubuntugis-unstable
+ apt-get update
+ apt-get install -y libgdal-dev libgeos++-dev libudunits2-dev libproj-dev libx11-dev libgl1-mesa-dev libglu1-mesa-dev libfreetype6-dev libxt-dev libfftw3-dev
+
+
+ apt install -y \
+ r-base \
+ r-cran-caret \
+ r-cran-crayon \
+ r-cran-devtools \
+ r-cran-forecast \
+ r-cran-hexbin \
+ r-cran-htmltools \
+ r-cran-htmlwidgets \
+ r-cran-plyr \
+ r-cran-randomforest \
+ r-cran-rcurl \
+ r-cran-reshape2 \
+ r-cran-rmarkdown \
+ r-cran-rodbc \
+ r-cran-rsqlite \
+ r-cran-shiny \
+ r-cran-tidyverse
+
+ # install lidR
+ #Rscript -e "install.packages(c('lidR'), repos='https://ftp.gwdg.de/pub/misc/cran/')"
+
+ Rscript -e "install.packages(c('assertthat', 'dbscan', 'raster', 'data.table', 'Rcpp','DBI', 'e1071', 'proxy', 'magrittr'), repos='https://ftp.gwdg.de/pub/misc/cran/')"
+
+ apt install -y libclang-dev lsb-release psmisc sudo
+ ubuntu_release=$(lsb_release --codename --short)
+ wget https://download2.rstudio.org/server/${ubuntu_release}/amd64/rstudio-server-2023.12.1-402-amd64.deb
+ dpkg --install rstudio-server-2023.12.1-402-amd64.deb
+ rm rstudio-server-2023.12.1-402-amd64.deb
+
+ echo 'ftp_proxy=http://www-cache.gwdg.de:3128' >> /usr/lib/R/etc/Renviron.site
+ echo 'https_proxy=http://www-cache.gwdg.de:3128' >> /usr/lib/R/etc/Renviron.site
+ echo 'http_proxy=http://www-cache.gwdg.de:3128' >> /usr/lib/R/etc/Renviron.site
+
+ echo '' >> /usr/lib/R/etc/Renviron.site
+
+ conda install --quiet --yes \
+ 'ipyparallel=8.8.0' \
+ 'jupyter-rsession-proxy=2.2.1' \
+ 'notebook=7.2.1' \
+ 'jupyterhub=4.1.5' \
+ 'jupyterlab=4.2.3'
+
+ conda install --quiet --yes \
+ dgl \
+ igraph \
+ keras \
+ pandas \
+ pydot \
+ scikit-learn \
+ scipy \
+ seaborn
+
+ conda install --quiet --yes --channel pytorch --channel nvidia \
+ pytorch \
+ pytorch-cuda=12.1 \
+ torchaudio \
+ torchvision
\ No newline at end of file
--
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