Merge pull request Emory-HITI#375 from rumbleFTW/install-script

Made installation script distro-independent.

install.sh

@@ -2,29 +2,64 @@
 echo "Configuring Niffler"
 sudo chmod -R 777 .
 
+name=""
+
+if [[ -e /etc/os-release ]]; then
+    . /etc/os-release
+    name=$NAME
+else
+    name="None"
+fi
+
+echo "Found distribution: $name"
+
 wget -qO- https://get.nextflow.io | bash
 sudo mv nextflow /usr/local/bin
 
 PIP=`head -n 1 init/pip.out`
 if [ "$PIP" = false ] ; then
-    sudo yum install -y python3
-    echo "Installing pip"
-    sudo yum install python3-pip
+    echo "Installing pip and python3..."
+    if [ "$name" = "Fedora" ] ; then
+        sudo yum install -y python3
+        sudo yum install -y python3-pip
+    elif [ "$name" = "Arch Linux" ] ; then
+        sudo pacman -S --noconfirm python
+        sudo pacman -S --noconfirm python-pip
+    elif [ "$name" = "Ubuntu" ] ; then
+        sudo apt-get install -y python3
+        sudo apt-get install -y python3-pip
+    fi
+
     pip install -r requirements.txt
     pip install -i https://test.pypi.org/simple/ HITI-anon-internal
-    wget https://repo.anaconda.com/archive/Anaconda3-2020.11-Linux-x86_64.sh
-    sh Anaconda3-2020.11-Linux-x86_64.sh -u
-    source ~/.bashrc
-    rm Anaconda3-2020.11-Linux-x86_64.sh
+    if command -v conda >/dev/null 2>&1 ; then
+        echo "Conda is already installed, skipping..."
+    else
+        wget https://repo.anaconda.com/archive/Anaconda3-2020.11-Linux-x86_64.sh
+        sh Anaconda3-2020.11-Linux-x86_64.sh -u
+        source ~/.bashrc
+        rm Anaconda3-2020.11-Linux-x86_64.sh
+    fi
     echo "true" > init/pip.out
 fi
 
 MISC=`head -n 1 init/misc.out`
 if [ "$MISC" = false ] ; then
     echo "Installing gdcm and mail"
     conda install -c conda-forge -y gdcm
-    sudo yum install mailx -y
-    sudo yum install sendmail sendmail-cf
+
+    if [ "$name" = "Fedora" ] ; then
+        sudo yum install mailx -y
+        sudo yum install sendmail sendmail-cf
+    elif [ "$name" = "Arch Linux" ] ; then
+        sudo pacman -S --noconfirm mailx
+        sudo pacman -S --noconfirm sendmail sendmail-cf
+
+    elif [ "$name" = "Ubuntu" ] ; then
+        sudo apt-get install -y mailutils
+        sudo apt-get install -y sendmail sendmail-cf
+    fi
+
     chmod +x modules/meta-extraction/service/mdextractor.sh
     echo "Disable THP"
     sudo cp init/disable-thp.service /etc/systemd/system/disable-thp.service
@@ -36,11 +71,19 @@ fi
 
 DCM4CHE=`head -n 1 init/dcm4che.out`
 if [ "$DCM4CHE" = false ] ; then
-    echo "Installing JDK"
-    sudo yum install java-1.8.0-openjdk-devel
-    echo "Installing Maven"
-    sudo dnf install maven
-    echo "Installing DCM4CHE"
+    echo "Installing jdk and Maven..."
+    if [ "$name" = "Fedora" ] ; then
+        sudo yum install java-1.8.0-openjdk-devel
+        sudo dnf install maven
+    elif [ "$name" = "Arch Linux" ] ; then
+        sudo pacman -S --noconfirm jdk8-openjdk
+        sudo pacman -S --noconfirm maven
+
+    elif [ "$name" = "Ubuntu" ] ; then
+        sudo apt install -y openjdk-8-jdk
+        sudo apt install -y maven
+    fi
+
     cd ..
     wget https://sourceforge.net/projects/dcm4che/files/dcm4che3/5.22.5/dcm4che-5.22.5-bin.zip/download -O dcm4che-5.22.5-bin.zip
     unzip dcm4che-5.22.5-bin.zip
@@ -51,9 +94,18 @@ fi
 
 MONGO=`head -n 1 init/mongo.out`
 if [ "$MONGO" = false ] ; then
-    echo "Installing mongo"
+    echo "Installing MongoDb..."
     sudo cp init/mongodb-org-4.2.repo /etc/yum.repos.d/
-    sudo yum install mongodb-org
+
+    if [ "$name" = "Fedora" ] ; then
+        sudo yum install mongodb-org
+    elif [ "$name" = "Arch Linux" ] ; then
+        sudo pacman -S --noconfirm mongodb
+
+    elif [ "$name" = "Ubuntu" ] ; then
+        sudo apt install -y mongodb
+    fi
+
     sudo systemctl start mongod
     sudo systemctl enable mongod
     mongo init/mongoinit.js
@@ -65,6 +117,7 @@ if [ "$MONGO" = false ] ; then
 fi
 
 SERVICE=`head -n 1 init/service.out`
+
 if [ "$SERVICE" = false ] ; then
     echo "Installing Niffler Frontend"
     pip install -r modules/frontend/requirements.txt