cytoscape_requirments_linux.sh

#!/bin/bash

####################################
# System checker script for Linux
####################################

# Target Cytoscape version for this script
CYTOSCAPE_VERSION="3.3.0"

# Supported Distributions
SUPPORTED_DISTRIBUTIONS=("ubuntu" "centos" "fedora")

UBUNTU_VERSIONS=()
CENTOS_VERSIONS=()
FEDORA_VERSIONS=()

# Supported Java verisons
SUPPORTED_JAVA_VERSIONS=("1.8.0")

# This user's shell
shell=$(echo $SHELL | awk -F'/' '{print $(NF)}')

echo "############# Cytoscape System Requirements Checker for Linux ##############"
echo "Target Cytoscape version: $CYTOSCAPE_VERSION"
echo "Your shell is $shell"

# Extract major version
distribution=$(lsb_release -si)
os_version=$(lsb_release -sr)

# Check distribution
dist_lower=$(echo $distribution | awk '{print tolower($0)}')

echo "Linux Distribution: $dist_lower"
echo "OS Version: $os_version"

os_pass=0
for dist in "${SUPPORTED_DISTRIBUTIONS[@]}"
do
    echo "Checking: $dist"
    if [[ $dist == $dist_lower ]]; then
        echo "Compatible distribution found: $dist_lower"
        os_pass=1
        break
    fi
done

if [ "$os_pass" -eq 1 ]
then
    echo " - Pass: Distribution = $distribution"
else
    echo "Fail: This Linux distribution is not supported: $distribution"
    echo "Please upgrade your system to any of the following:"
    echo ${SUPPORTED_DISTRIBUTIONS[0]}
    for dist in "${SUPPORTED_DISTRIBUTIONS[@]}"
    do
        echo " - $dist"
    done
    exit 1
fi

# Check version of the distribution
#
# TODO

# Test 2: Try java -version command
java_version_original=$(java -version 2>&1)
java_version=$(echo $java_version_original | awk 'NR==1{gsub(/"/,""); print $3}')

java_major_version=$(echo $java_version | awk -F'_' '{print $1}')

if [[ $java_major_version == ${SUPPORTED_JAVA_VERSIONS[0]} ]]
then
    echo " - Pass: Current Java Version = $java_version"
else
    echo "Fail: Java is not reachable.  Need to set PATH to JAVA_HOME/bin "
    echo "Your current path:"
    echo $PATH
fi

# Tets 3: Check Java Home
if [[ $JAVA_HOME != "" ]]; then
    echo " - Pass: JAVA_HOME found: $JAVA_HOME"
else
    echo "JAVA_HOME is not set."
    echo "Please add the following to your .${shell}rc file:"
    echo "export JAVA_HOME=/YOUR_JDK_DIRECTORY/jdk1.8.0_*"
    echo "where * is the latest Java 8 update number."
    echo "And then type 'source ~/.${shell}rc'"
    exit 1
fi

# Test 4: Connect to App Store
NUM_TRY=5
echo "Checking connection to Cytoscape App Store..."
ping_result=$(ping -c $NUM_TRY -t 15 apps.cytoscape.org | grep loss)

num_success=$(echo $ping_result | awk '{print $4}')

echo $ping_result

if [[ $num_success -eq $NUM_TRY ]]; then
    echo "Done!  You are ready to run Cytoscape $CYTOSCAPE_VERSION"
else
    echo "Looks connection to App Store is unstable."
    echo "traceroute result:"
    traceroute apps.cytoscape.org
    exit 1
fi

exit 0