From b84fefe1b86091a306135115bcb08e4baccc2130 Mon Sep 17 00:00:00 2001
From: Aaron Jackson <ajackson002@dundee.ac.uk>
Date: Fri, 25 Aug 2023 08:22:36 +0100
Subject: [PATCH 1/9] Bump RStudio for Ubuntu

---
 modules/rstudio.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/rstudio.sh b/modules/rstudio.sh
index c52a1d5..f019bd8 100644
--- a/modules/rstudio.sh
+++ b/modules/rstudio.sh
@@ -23,11 +23,11 @@ sudo apt install -y r-base
 # shellcheck source=/dev/null
 . /etc/lsb-release
 if [ "$DISTRIB_RELEASE" == "20.04" ] ; then
-    wget https://s3.amazonaws.com/rstudio-ide-build/desktop/bionic/amd64/rstudio-2022.07.2-576-amd64.deb
-    sudo gdebi -n rstudio-2022.07.2-576-amd64.deb
+    wget https://s3.amazonaws.com/rstudio-ide-build/electron/focal/amd64/rstudio-2023.06.1-524-amd64.deb
+    sudo gdebi -n rstudio-2023.06.1-524-amd64.deb
 elif [ "$DISTRIB_RELEASE" == "22.04" ] ; then
-    wget https://download1.rstudio.org/electron/jammy/amd64/rstudio-2022.12.0-353-amd64.deb
-    sudo gdebi -n rstudio-2022.12.0-353-amd64.deb
+    wget https://s3.amazonaws.com/rstudio-ide-build/electron/jammy/amd64/rstudio-2023.06.1-524-amd64.deb
+    sudo gdebi -n rstudio-2023.06.1-524-amd64.deb
 else
     echo "--------------------------------------------------------"
     echo "RStudio - Unsupported Ubuntu version ${DISTRIB_RELEASE}"

From 2740f271423a1439923674665f53f71d13822cb4 Mon Sep 17 00:00:00 2001
From: Aaron Jackson <ajackson002@dundee.ac.uk>
Date: Fri, 25 Aug 2023 15:46:00 +0100
Subject: [PATCH 2/9] Bump PyCharm to 2023 and add desktop shortcut symlink

---
 modules/pycharm-setup.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/modules/pycharm-setup.sh b/modules/pycharm-setup.sh
index 9d02648..82fb4be 100644
--- a/modules/pycharm-setup.sh
+++ b/modules/pycharm-setup.sh
@@ -5,8 +5,8 @@ set -eu
 SETUPDIR=$(realpath "$(dirname "${BASH_SOURCE[0]}")")
 cd "$SETUPDIR"
 
-PYCHARM_VERSION=2021.3.2
-PYCHARM_SHA256=f1ae01f471d01c6f09aab0a761c6dea9834ef584f2aaf6d6ebecdce6b55a66e8
+PYCHARM_VERSION=2023.2.1
+PYCHARM_SHA256=5956c6cb5a5bad1d9749e487b3bb69fcbf0170f52324e4ff009283b723838778
 
 echo "Installing PyCharm"
 curl -sfLO https://download-cdn.jetbrains.com/python/pycharm-community-${PYCHARM_VERSION}.tar.gz
@@ -28,3 +28,4 @@ Icon=/opt/pycharm-community-${PYCHARM_VERSION}/bin/pycharm.svg
 Type=Application
 EOF
 sudo chmod +x /opt/pycharm/PyCharm.desktop
+ln -s /opt/pycharm/PyCharm.desktop /home/ubuntu/Desktop/PyCharm.desktop

From f49bce30bbbd4e09068b087099bf90a75eaa3a85 Mon Sep 17 00:00:00 2001
From: Aaron Jackson <ajackson002@dundee.ac.uk>
Date: Fri, 25 Aug 2023 15:46:38 +0100
Subject: [PATCH 3/9] plink, gtool, snptest, jupyter notebook shortcut

---
 modules/msc_custom.sh | 89 +++++++++++++++++++++++++++++++++++++------
 1 file changed, 78 insertions(+), 11 deletions(-)

diff --git a/modules/msc_custom.sh b/modules/msc_custom.sh
index 6f97f7e..f7daa9d 100644
--- a/modules/msc_custom.sh
+++ b/modules/msc_custom.sh
@@ -2,6 +2,84 @@
 
 set -eu
 
+
+######################################################################
+# PLINK
+mkdir plink
+pushd plink
+curl -sfLO https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20230116.zip
+unzip plink_linux_x86_64_20230116.zip
+chmod +x plink
+sudo ln -s "$(pwd)/plink" /usr/local/bin/plink
+popd
+
+######################################################################
+# GTOOL
+mkdir gtool
+pushd gtool
+curl -sfLO https://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool_v0.7.5_x86_64.tgz
+tar zxvf gtool_v0.7.5_x86_64.tgz
+chmod +x gtool
+sudo ln -s "$(pwd)/gtool" /usr/local/bin/gtool
+popd
+
+######################################################################
+# SNPTEST
+mkdir snptest
+pushd snptest
+curl -sfLO http://www.well.ox.ac.uk/~gav/resources/snptest_v2.5.4-beta3_linux_x86_64_static.tgz
+tar zxvf snptest_v2.5.4-beta3_linux_x86_64_static.tgz
+sudo cp snptest_v2.5.4-beta3_linux_x86_64_static/snptest_v2.5.4-beta3 /usr/local/bin/snptest
+sudo chmod +x /usr/local/bin/snptest
+popd
+
+######################################################################
+# Some TensorFlow stuff
+eval "$(/home/ubuntu/conda/bin/conda shell.bash hook)"
+/home/ubuntu/conda/bin/conda activate msc
+export CONDA_PREFIX="$HOME/conda/envs/msc"
+mkdir -p $CONDA_PREFIX/etc/conda/activate.d
+
+echo 'CUDNN_PATH=$(dirname $(python -c "import nvidia.cudnn;print(nvidia.cudnn.__file__)"))' \
+     > $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh
+echo 'export LD_LIBRARY_PATH=$CONDA_PREFIX/lib/:$CUDNN_PATH/lib:$LD_LIBRARY_PATH' \
+     >> $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh
+
+source $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh
+
+######################################################################
+# Jupyter Notebook shortcut
+sudo tee /usr/local/bin/nb <<EOF
+#!/bin/bash
+
+cd /home/ubuntu
+eval "\$(conda shell.bash hook)"
+conda activate msc
+
+jupyter notebook &
+sleep 3
+notebook_url=\$(jupyter notebook list 2>&1 | awk "/http/ {print \$2}" | tail -n1)
+
+unset LD_LIBRARY_PATH
+xdg-open "\$notebook_url"
+
+wait
+EOF
+
+sudo chmod +x /usr/local/bin/nb
+
+cat <<EOF | tee /home/ubuntu/Desktop/Notebook.desktop
+[Desktop Entry]
+Name=Jupyter Notebook
+GenericName=Python Notebook
+Comment=Launch Jupyter Notebook
+Terminal=true
+Exec=/usr/bin/bash -c "source /home/ubuntu/conda/etc/profile.d/conda.sh && /usr/local/bin/nb"
+Icon=/home/ubuntu/conda/envs/msc/share/icons/hicolor/scalable/apps/notebook.svg
+Type=Application
+EOF
+sudo chmod +x /home/ubuntu/Desktop/Notebook.desktop
+
 ######################################################################
 # Set up R environment
 
@@ -18,17 +96,6 @@ sudo R --no-save -e "devtools::install_github('jdstorey/qvalue')"
 
 mv "${HOME}/tmp_Rprofile" "${HOME}/.Rprofile"
 
-######################################################################
-# Set up python environments
-
-# pinning numpy to supress a warning about numpy needing to be less
-# than 1.23.0 with scikit, even though the deps specify numpy 1.23.1.
-read -ra BASE_PKG <<<"numpy==1.23.0 matplotlib scikit-learn pillow pandas"
-~/conda/bin/mamba create -y -n pytorch
-~/conda/bin/mamba install -y pytorch torchvision "${BASE_PKG[@]}" -c pytorch -n pytorch
-~/conda/bin/mamba create -y -n tensorflow
-~/conda/bin/mamba install -y tensorflow "${BASE_PKG[@]}" -c anaconda -n tensorflow
-
 ######################################################################
 # Test custom installs
 R --no-save -e "library('ggrepel')"

From 4ba010f85467e8e836e2b88edfa1a984da12e227 Mon Sep 17 00:00:00 2001
From: Aaron Jackson <ajackson002@dundee.ac.uk>
Date: Fri, 25 Aug 2023 15:47:35 +0100
Subject: [PATCH 4/9] Add env var AUTOHIBERNATE_BEHAVIOUR

can be set to shutdown if hiberation isn't possible on a project's
workspace type.
---
 modules/autohibernate.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/autohibernate.sh b/modules/autohibernate.sh
index e874d97..0a3a4ab 100644
--- a/modules/autohibernate.sh
+++ b/modules/autohibernate.sh
@@ -20,6 +20,7 @@ sudo tee /usr/bin/autohibernate <<EOF
 set -eu
 
 AUTOHIBERNATE_TIME=$AUTOHIBERNATE_TIME
+AUTOHIBERNATE_BEHAVIOUR="${AUTHOHIBERNATE_BEHAVIOUR:=hibernate}"
 export DISPLAY=:1
 
 if [ \$(xprintidle) -gt \$AUTOHIBERNATE_TIME ] ; then
@@ -36,7 +37,7 @@ if [ \$(xprintidle) -gt \$AUTOHIBERNATE_TIME ] ; then
   vncconfig -disconnect
 
   # Let's hibernate.
-  sudo systemctl hibernate
+  sudo systemctl "\$AUTOHIBERNATE_BEHAVIOUR"
 
   # Without a sleep, the swap will be turned off too soon after
   # triggering the hibernate (which is async). We need to wait a

From c59c493bfd8ac46cdf303c7c1aeeacf7b24646c8 Mon Sep 17 00:00:00 2001
From: Aaron Jackson <ajackson002@dundee.ac.uk>
Date: Fri, 25 Aug 2023 15:57:15 +0100
Subject: [PATCH 5/9] Forgot to add it...

---
 modules/msc_custom.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/msc_custom.sh b/modules/msc_custom.sh
index f7daa9d..a61d274 100644
--- a/modules/msc_custom.sh
+++ b/modules/msc_custom.sh
@@ -53,8 +53,8 @@ sudo tee /usr/local/bin/nb <<EOF
 #!/bin/bash
 
 cd /home/ubuntu
-eval "\$(conda shell.bash hook)"
-conda activate msc
+eval "\$(/home/ubuntu/conda/bin/conda shell.bash hook)"
+/home/ubuntu/conda/bin/conda activate msc
 
 jupyter notebook &
 sleep 3

From 859015d65ead9bdac95a7dfd0a6099adc545d51e Mon Sep 17 00:00:00 2001
From: Aaron Jackson <ajackson002@dundee.ac.uk>
Date: Fri, 1 Sep 2023 10:48:49 +0100
Subject: [PATCH 6/9] Fix TensorFlow CuDNN and pull down EfficientNetB0

---
 modules/msc_custom.sh | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/modules/msc_custom.sh b/modules/msc_custom.sh
index a61d274..531011a 100644
--- a/modules/msc_custom.sh
+++ b/modules/msc_custom.sh
@@ -35,17 +35,15 @@ popd
 
 ######################################################################
 # Some TensorFlow stuff
-eval "$(/home/ubuntu/conda/bin/conda shell.bash hook)"
-/home/ubuntu/conda/bin/conda activate msc
-export CONDA_PREFIX="$HOME/conda/envs/msc"
-mkdir -p $CONDA_PREFIX/etc/conda/activate.d
 
-echo 'CUDNN_PATH=$(dirname $(python -c "import nvidia.cudnn;print(nvidia.cudnn.__file__)"))' \
-     > $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh
-echo 'export LD_LIBRARY_PATH=$CONDA_PREFIX/lib/:$CUDNN_PATH/lib:$LD_LIBRARY_PATH' \
-     >> $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh
+CUDNN_PATH=$(find "$HOME/conda/envs/msc" -path "*/cudnn/lib")
+echo "export LD_LIBRARY_PATH=$CUDNN_PATH:$HOME/conda/envs/msc/lib/:\$LD_LIBRARY_PATH" \
+     > "$HOME/conda/envs/msc/etc/conda/activate.d/env_vars.sh"
 
-source $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh
+# We want to trigger a download of EfficientNet weights
+~/conda/bin/conda run -n msc python -c "\
+from tensorflow.keras.applications import EfficientNetB0; \
+model = EfficientNetB0(weights='imagenet')"
 
 ######################################################################
 # Jupyter Notebook shortcut

From 41466aaaf0fbd3398d70d12753029f32700aa654 Mon Sep 17 00:00:00 2001
From: Aaron Jackson <ajackson002@dundee.ac.uk>
Date: Fri, 1 Sep 2023 10:49:29 +0100
Subject: [PATCH 7/9] Jupyter Notebook fixes MSc

---
 modules/msc_custom.sh | 14 ++++----------
 1 file changed, 4 insertions(+), 10 deletions(-)

diff --git a/modules/msc_custom.sh b/modules/msc_custom.sh
index 531011a..70ee5c4 100644
--- a/modules/msc_custom.sh
+++ b/modules/msc_custom.sh
@@ -51,17 +51,11 @@ sudo tee /usr/local/bin/nb <<EOF
 #!/bin/bash
 
 cd /home/ubuntu
-eval "\$(/home/ubuntu/conda/bin/conda shell.bash hook)"
-/home/ubuntu/conda/bin/conda activate msc
 
-jupyter notebook &
-sleep 3
-notebook_url=\$(jupyter notebook list 2>&1 | awk "/http/ {print \$2}" | tail -n1)
+. \$HOME/conda/etc/profile.d/conda.sh
+conda activate msc
 
-unset LD_LIBRARY_PATH
-xdg-open "\$notebook_url"
-
-wait
+jupyter notebook
 EOF
 
 sudo chmod +x /usr/local/bin/nb
@@ -72,7 +66,7 @@ Name=Jupyter Notebook
 GenericName=Python Notebook
 Comment=Launch Jupyter Notebook
 Terminal=true
-Exec=/usr/bin/bash -c "source /home/ubuntu/conda/etc/profile.d/conda.sh && /usr/local/bin/nb"
+Exec=/usr/bin/bash -c "/usr/local/bin/nb"
 Icon=/home/ubuntu/conda/envs/msc/share/icons/hicolor/scalable/apps/notebook.svg
 Type=Application
 EOF

From 25445bb2f422da5b7b894805efc25d6ca26db9f2 Mon Sep 17 00:00:00 2001
From: Aaron Jackson <ajackson002@dundee.ac.uk>
Date: Fri, 1 Sep 2023 15:07:22 +0100
Subject: [PATCH 8/9] Ensure env_vars path exists before generating file

---
 modules/msc_custom.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/msc_custom.sh b/modules/msc_custom.sh
index 70ee5c4..5b571a8 100644
--- a/modules/msc_custom.sh
+++ b/modules/msc_custom.sh
@@ -36,6 +36,7 @@ popd
 ######################################################################
 # Some TensorFlow stuff
 
+mkdir -p "$HOME/conda/envs/msc/etc/conda/activate.d"
 CUDNN_PATH=$(find "$HOME/conda/envs/msc" -path "*/cudnn/lib")
 echo "export LD_LIBRARY_PATH=$CUDNN_PATH:$HOME/conda/envs/msc/lib/:\$LD_LIBRARY_PATH" \
      > "$HOME/conda/envs/msc/etc/conda/activate.d/env_vars.sh"

From 1be578a77fe4c475960611b6decbe1784fb22346 Mon Sep 17 00:00:00 2001
From: Aaron Jackson <aaron@aaronsplace.co.uk>
Date: Tue, 5 Sep 2023 11:27:49 +0100
Subject: [PATCH 9/9] Add tidyverse as a base package since it has native deps

---
 modules/rstudio.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/rstudio.sh b/modules/rstudio.sh
index f019bd8..dc4535b 100644
--- a/modules/rstudio.sh
+++ b/modules/rstudio.sh
@@ -59,4 +59,5 @@ sudo apt update
 
 sudo apt install -y r-cran-odbc r-cran-dbi r-cran-qqman r-cran-metafor \
      r-cran-tidyr r-cran-ggplot2 r-cran-hmisc r-cran-data.table \
-     r-cran-dplyr r-cran-lubridate r-cran-survival r-cran-survminer
+     r-cran-dplyr r-cran-lubridate r-cran-survival r-cran-survminer \
+     r-cran-tidyverse