From 65c9b05cff1fd52538337bdb52d04f6a60fae9fb Mon Sep 17 00:00:00 2001
From: Cameron Hyde <chyde@neoformit.com>
Date: Thu, 9 Nov 2023 14:33:21 +1000
Subject: [PATCH] planemo setup script

---
 .../workshops/incob/planemo_setup_unix.sh     | 42 ++++++++++++++-----
 1 file changed, 31 insertions(+), 11 deletions(-)

diff --git a/training/workshops/incob/planemo_setup_unix.sh b/training/workshops/incob/planemo_setup_unix.sh
index a07f8152..e73389f0 100755
--- a/training/workshops/incob/planemo_setup_unix.sh
+++ b/training/workshops/incob/planemo_setup_unix.sh
@@ -9,15 +9,29 @@ if [[ "$1" = @("-h"|"--help") ]]; then
     exit 0
 fi
 
+printf "\nThis script will download and build Galaxy release 23.1, and configure planemo to use it.\n"
+read -p "Continue? [y/n] " -n 1 -r
+echo ""
+
+if [[ ! $REPLY =~ ^[Yy]$ ]]; then
+    echo "Aborting"
+    exit 1
+fi
+
 cd ~/.planemo/
 
-echo ""
-echo "Downloading Galaxy release 23.1.1..."
-echo ""
-wget https://github.com/galaxyproject/galaxy/archive/refs/tags/v23.1.1.tar.gz
-echo "Extracting archive..."
-tar -xzf v23.1.1.tar.gz
-rm v23.1.1.tar.gz
+if [ ! -d v23.1.1.tar.gz ] && [ ! -d galaxy-23.1.1 ]; then
+    echo ""
+    echo "Downloading Galaxy release 23.1.1..."
+    echo ""
+    wget https://github.com/galaxyproject/galaxy/archive/refs/tags/v23.1.1.tar.gz
+fi
+
+if [ ! -d galaxy-23.1.1 ]; then
+    echo "Extracting archive..."
+    tar -xzf v23.1.1.tar.gz
+    rm v23.1.1.tar.gz
+fi
 
 echo ""
 echo "Building Galaxy client..."
@@ -25,10 +39,16 @@ cd galaxy-23.1.1
 make client
 echo ""
 
-echo ""
-echo "Configuring Planemo..."
-echo "" >> ~/.planemo.yml
-echo "galaxy_root: $PWD/galaxy-23.1.1" >> ~/.planemo.yml
+if [[ "$(grep -E '^\w?galaxy_root' ~/.planemo.yml)" != "" ]]; then
+    echo ""
+    echo "Configuring Planemo..."
+    echo "" >> ~/.planemo.yml
+    echo "galaxy_root: $PWD/galaxy-23.1.1"
+    echo "galaxy_root: $PWD/galaxy-23.1.1" >> ~/.planemo.yml
+else
+    echo "galaxy_root already configured in ~/.planemo.yml. Please ensure this is correct:"
+    echo "$(grep -E '^\w?galaxy_root' ~/.planemo.yml)"
+fi
 
 echo ""
 echo "Done"