From 269d0a46680ba6a5dabad0216235617fe1c5e3b8 Mon Sep 17 00:00:00 2001
From: Steffen Bollmann <s.bollmann@uq.edu.au>
Date: Tue, 19 Sep 2023 05:42:16 +0000
Subject: [PATCH] update matlab to 2023 and add lmod support

---
 recipes/matlab/README.md |  4 ++--
 recipes/matlab/build.sh  | 25 ++++++++++++++++++++++---
 2 files changed, 24 insertions(+), 5 deletions(-)

diff --git a/recipes/matlab/README.md b/recipes/matlab/README.md
index 71810c66..74733ae5 100644
--- a/recipes/matlab/README.md
+++ b/recipes/matlab/README.md
@@ -1,6 +1,6 @@
 
 ----------------------------------
-## matlab/2022a ##
+## matlab/2023a ##
 Matlab IDE
 
 Important note about licensing
@@ -44,7 +44,7 @@ More documentation can be found here
 To run applications outside of this container
 ---------------------------------------------
 
-  ml matlab/2022a
+  ml matlab/2023a
 
 Citation
 --------
diff --git a/recipes/matlab/build.sh b/recipes/matlab/build.sh
index 4f76da94..e1b9d9d4 100755
--- a/recipes/matlab/build.sh
+++ b/recipes/matlab/build.sh
@@ -3,7 +3,7 @@ set -e
 
 # this template file builds datalad and is then used as a docker base image for layer caching + it contains examples for various things like github install, curl, ...
 export toolName='matlab'
-export toolVersion='2022a' #the version number cannot contain a "-" - try to use x.x.x notation always
+export toolVersion='2023a' #the version number cannot contain a "-" - try to use x.x.x notation always
 # Don't forget to update version change in README.md!!!!!
 # toolName or toolVersion CANNOT contain capital letters or dashes or underscores (Docker registry does not accept this!)
 
@@ -25,18 +25,37 @@ source ../main_setup.sh
 # NOTE 2: THE BACKSLASH (\) AT THE END OF EACH LINE MUST FOLLOW THE COMMENT. A BACKSLASH BEFORE THE COMMENT WON'T WORK!
 ##########################################################################################################################################
 neurodocker generate ${neurodocker_buildMode} \
-   --base-image mathworks/matlab-deep-learning:r2022a                 `# use Matlab deep learning 2022a docker container provided by Mathworks` \
+   --base-image mathworks/matlab-deep-learning:r${toolVersion}                 `# use Matlab deep learning 2022a docker container provided by Mathworks` \
    --user root                                          `# change user to root, as the Matlab container runs with Matlab user` \
    --env DEBIAN_FRONTEND=noninteractive                 `# The matlab image uses Ubuntu, so it's Debian` \
    --pkg-manager apt                                    `# desired package manager, has to match the base image (e.g. debian needs apt; centos needs yum)` \
    --run="printf '#!/bin/bash\nls -la' > /usr/bin/ll"   `# define the ll command to show detailed list including hidden files`  \
    --run="chmod +x /usr/bin/ll"                         `# make ll command executable`  \
    --run="mkdir -p ${mountPointList}"                      `# create folders for singularity bind points` \
-   --install wget git curl ca-certificates datalad unzip libfftw3-3 `# install apt-get packages` \
+   --install wget git curl ca-certificates datalad unzip libfftw3-3 apt-transport-https coreutils\
+   cryptsetup squashfs-tools lua-bit32 lua-filesystem lua-json lua-lpeg lua-posix lua-term lua5.2 lmod imagemagick less nano tree \
+   gcc libzstd1 zlib1g-dev zip build-essential uuid-dev libgpgme-dev libseccomp-dev pkg-config \
    --miniconda version=latest \
    --env PATH='${PATH}'":/opt/matlab/R${toolVersion}/bin/"   	 `# set PATH; not required to run matlab, but required for other Matlab tools like mex` \
    --env DEPLOY_BINS=datalad:matlab:mex                 `# specify individual binaries (separated by :) on the PATH that should be exposed outside the container for the module system` \
    --env MLM_LICENSE_FILE='~/Downloads'		 `# tell Matlab to look for the license file in Downloads under the home directory. There is the default download folder in Neurodesktop` \
+   --env GOPATH='$HOME'/go \
+   --env PATH='$PATH':/usr/local/go/bin:'$PATH':${GOPATH}/bin \
+   --run="wget https://dl.google.com/go/go$GO_VERSION.$OS-$ARCH.tar.gz \
+    && tar -C /usr/local -xzvf go$GO_VERSION.$OS-$ARCH.tar.gz \
+    && rm go$GO_VERSION.$OS-$ARCH.tar.gz \
+    && mkdir -p $GOPATH/src/github.com/sylabs \
+    && cd $GOPATH/src/github.com/sylabs \
+    && wget https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz \
+    && tar -xzvf singularity-ce-${SINGULARITY_VERSION}.tar.gz \
+    && cd singularity-ce-${SINGULARITY_VERSION} \
+    && ./mconfig --without-suid --prefix=/usr/local/singularity \
+    && make -C builddir \
+    && make -C builddir install \
+    && cd .. \
+    && rm -rf singularity-ce-${SINGULARITY_VERSION} \
+    && rm -rf /usr/local/go $GOPATH \
+    && ln -s /usr/local/singularity/bin/singularity /bin/" \
    --copy README.md /README.md                          `# include readme file in container` \
    --run="rm /usr/local/bin/matlab"			`# rm original matlab symbolic link` \
    --copy matlab /usr/local/bin/matlab `# replace original matlab with a script that sets MLM_LICENSE_FILE and then call matlab; license dir is set to ~/Downloads because there is where Firefox download the license to` \