Merge pull request #15 from hic-infra/pkgbump

Bump packages and changes for MSc 23/23

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

modules/msc_custom.sh

@@ -2,6 +2,77 @@
 
 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
+
+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"
+
+# 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
+sudo tee /usr/local/bin/nb <<EOF
+#!/bin/bash
+
+cd /home/ubuntu
+
+. \$HOME/conda/etc/profile.d/conda.sh
+conda activate msc
+
+jupyter notebook
+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 "/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 +89,6 @@ 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')"

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

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}"
@@ -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