--- /dev/null
+#!/bin/bash
+
+# Install script for Biopieces.
+# Copyright (C) October 2011, Martin A. Hansen
+
+bp_code="$HOME/biopieces"
+bp_data="$HOME/BP_DATA"
+ bp_log="$HOME/BP_LOG"
+ bp_tmp="/tmp"
+
+# Function that renders a given message in ASCII green.
+function echo_green
+{
+ local msg=$1
+
+ echo -e "\033[32;38m$msg\033[0m"
+}
+
+# Function that renders a given message in ASCII yellow.
+function echo_yellow
+{
+ local msg=$1
+
+ echo -e "\033[33;38m$msg\033[0m"
+}
+
+# Function that renders a given message in ASCII red.
+function echo_red
+{
+ local msg=$1
+
+ echo -e "\033[31;38m$msg\033[0m"
+}
+
+# Function to output an abort message and exit
+function exit_abort
+{
+ echo_red "abort"
+
+ exit
+}
+
+# Function to output an success message and exit
+function exit_success
+{
+ echo ""
+ echo_green "Congratulations - you have now installed Biopieces."
+ echo ""
+ echo " Now you must either run 'source ~/.bashrc' or re-login to your system."
+ echo ""
+ echo " * To test your Biopieces installation try 'bp_test'."
+ echo " * To list all available Biopieces try 'list_biopieces'."
+ echo " * To see the synopsis of a Biopiece try 'read_fastq'."
+ echo " * To see the full description and exampels try 'read_fastq -?'."
+ echo ""
+ echo " Don't forget to join the Biopieces Google Group for important"
+ echo " messages, questions, discussion, and suggestions:"
+ echo ""
+ echo " http://groups.google.com/group/biopieces"
+ echo ""
+ echo " And of cause there is the introduction:"
+ echo ""
+ echo " http://code.google.com/p/biopieces/wiki/Introduction"
+ echo ""
+ echo " Happy hacking!"
+ echo ""
+
+ exit
+}
+
+# Function to create a directory if it doesn't exist.
+function dir_create
+{
+ local dir=$1
+
+ echo -n "Creating $dir: "
+
+ if error=$( mkdir $dir 2>&1 ); then
+ echo_green "OK"
+ else
+ echo_red "FAIL"
+ echo " $error"
+ exit_abort
+ fi
+}
+
+# Function check if a directory is writable.
+function dir_writable
+{
+ local dir=$1
+ local file="$dir/bp_writable"
+
+ echo -n "Writable? $dir: "
+
+ if error=$( touch $file 2>&1 ); then
+ echo_green "OK"
+ rm $file
+ else
+ echo_red "FAIL"
+ echo " $error"
+ exit_abort
+ fi
+}
+
+# Function to prompt for continuation of installation.
+function prompt_install
+{
+ echo ""
+ echo "Welcome to the Biopieces installer."
+ echo ""
+ echo " This installer is experimental, and is being evaluated to replace"
+ echo " the previous, tedious way:"
+ echo ""
+ echo " http://code.google.com/p/biopieces/wiki/Installation"
+ echo ""
+ echo " The installer will now do the following:"
+ echo ""
+ echo " * Check for existing Biopieces installation."
+ echo " * Check prerequisites:"
+ echo " - Subversion client"
+ echo " - Perl"
+ echo " - Perl modules"
+ echo " - Ruby"
+ echo " - Ruby gems"
+ echo " - Auxillary programs"
+ echo ""
+ echo " * Create installation directories."
+ echo " * Download code from repository."
+ echo " * Set environment in .bashrc."
+ echo ""
+ echo " Problems? Check out the FAQ:"
+ echo ""
+ echo " http://code.google.com/p/biopieces/wiki/FAQ"
+ echo ""
+ echo " Help is available at the Biopieces Google Group:"
+ echo ""
+ echo " http://groups.google.com/group/biopieces"
+ echo ""
+ echo " Bugs & issues:"
+ echo ""
+ echo " http://code.google.com/p/biopieces/issues/list"
+ echo ""
+
+ while true; do
+ read -p "Continue (yes/no)? " answer
+ case $answer in
+ [Yy]* ) break;;
+ [Nn]* ) exit_abort;;
+ esac
+ done
+}
+
+# Function to prompt the checking of any existing Biopieces installation.
+function prompt_install_existing
+{
+ echo "Checking for existing Biopieces installation:"
+
+ if [ $BP_DIR ]; then
+ echo_yellow " WARNING: \$BP_DIR is already set to: $BP_DIR"
+ found=1
+ fi
+
+ if [ $BP_DATA ]; then
+ echo_yellow " WARNING: \$BP_DATA is already set to: $BP_DATA"
+ found=1
+ fi
+
+ if [ $BP_TMP ]; then
+ echo_yellow " WARNING: \$BP_TMP is already set to: $BP_TMP"
+ found=1
+ fi
+
+ if [ $BP_LOG ]; then
+ echo_yellow " WARNING: \$BP_LOG is already set to: $BP_LOG"
+ found=1
+ fi
+
+ if [ $found ]; then
+ echo ""
+ echo " An old installation of Biopeices appears to exists."
+ else
+ echo ""
+ echo " No installation of Biopeices found."
+ fi
+
+ while true; do
+ read -p "Continue (yes/no)? " answer
+ case $answer in
+ [Yy]* ) break;;
+ [Nn]* ) exit_abort;;
+ esac
+ done
+}
+
+# Function to prompt the testing of prerequisites.
+function prompt_test_prerequisites
+{
+ echo "Testing prerequisites:"
+
+ test_bash
+ test_svn
+ test_perl
+ test_perl_module "Inline"
+ test_perl_module "JSON::XS"
+ test_perl_module "SVG"
+ test_perl_module "Bit::Vector"
+ test_perl_module "Time::HiRes"
+ test_ruby
+ test_ruby_gem "gnuplot"
+ test_ruby_gem "narray"
+ test_ruby_gem "RubyInline"
+ test_ruby_gem "terminal-table"
+ test_aux_program "blastall"
+ test_aux_program "blat"
+ test_aux_program "bwa"
+ test_aux_program "bowtie"
+ test_aux_program "formatdb"
+ test_aux_program "gnuplot"
+ test_aux_program "idba_hybrid"
+ test_aux_program "muscle"
+ test_aux_program "mummer"
+ test_aux_program "mysql"
+ test_aux_program "prodigal"
+ test_aux_program "Ray"
+ test_aux_program "scan_for_matches"
+ test_aux_program "usearch"
+ test_aux_program "velveth"
+ test_aux_program "velvetg"
+ test_aux_program "vmatch"
+
+ echo ""
+ echo " Any WARNINGs indicate that the executable for that auxillary"
+ echo " program could not be found. While not critical, this will"
+ echo " cause some Biopieces to FAIL. You can install these afterwards."
+
+ while true; do
+ read -p "Continue (yes/no)? " answer
+ case $answer in
+ [Yy]* ) break;;
+ [Nn]* ) exit_abort;;
+ esac
+ done
+}
+
+# Function to prompt the selection of the code directory.
+function prompt_install_dir_code
+{
+ read -p "Enter directory for the Biopieces code (default: $bp_code): " answer;
+
+ bp_code=${answer:-"$bp_code"}
+
+ if [ ! -d "$bp_code" ]; then
+ while true; do
+ read -p "Create directory: $bp_code (yes/no)? " answer
+ case $answer in
+ [Yy]* ) dir_create $bp_code && break;;
+ [Nn]* ) exit_abort;;
+ esac
+ done
+ fi
+
+ dir_writable $bp_code
+}
+
+# Function to prompt the selection of the data directory.
+function prompt_install_dir_data
+{
+ read -p "Enter directory for the Biopieces data (default: $bp_data): " answer;
+
+ bp_data=${answer:-"$bp_data"}
+
+ if [ ! -d "$bp_data" ]; then
+ while true; do
+ read -p "Create directory: $bp_data (yes/no)? " answer
+ case $answer in
+ [Yy]* ) dir_create $bp_data && break;;
+ [Nn]* ) exit_abort;;
+ esac
+ done
+ fi
+
+ dir_writable $bp_data
+}
+
+# Function to prompt the selection of the log directory.
+function prompt_install_dir_log
+{
+ read -p "Enter directory for the Biopieces log file (default: $bp_log): " answer;
+
+ bp_log=${answer:-"$bp_log"}
+
+ if [ ! -d "$bp_log" ]; then
+ while true; do
+ read -p "Create directory: $bp_log (yes/no)? " answer
+ case $answer in
+ [Yy]* ) dir_create $bp_log && break;;
+ [Nn]* ) exit_abort;;
+ esac
+ done
+ fi
+
+ dir_writable $bp_log
+}
+
+# Function to prompt the selection of the tmp directory.
+function prompt_install_dir_tmp
+{
+ read -p "Enter directory for the Biopieces temporary files (default: $bp_tmp): " answer;
+
+ bp_tmp=${answer:-"$bp_tmp"}
+
+ if [ ! -d "$bp_tmp" ]; then
+ while true; do
+ read -p "Create directory: $bp_tmp (yes/no)? " answer
+ case $answer in
+ [Yy]* ) dir_create $bp_tmp && break;;
+ [Nn]* ) exit_abort;;
+ esac
+ done
+ fi
+
+ dir_writable $bp_tmp
+}
+
+# Function to prompt the appending of a section to bashrc.
+function prompt_append_bashrc
+{
+ local skip=0
+ local section="
+
+# >>>>>>>>>>>>>>>>>>>>>>> Enabling Biopieces <<<<<<<<<<<<<<<<<<<<<<<
+
+export BP_DIR=\"$bp_code\"
+export BP_DATA=\"$bp_data\"
+export BP_TMP=\"$bp_tmp\"
+export BP_LOG=\"$bp_log\"
+
+source \"\$BP_DIR/bp_conf/bashrc\"
+
+# >>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<
+
+"
+
+ echo ""
+ echo "We need to append the below section to your .bashrc file."
+
+ echo_yellow "$section"
+
+ while true; do
+ read -p "Append (yes/no/abort)? " answer
+ case $answer in
+ [Yy]* ) skip=0 && break;;
+ [Nn]* ) skip=1 && break;;
+ [Aa]* ) exit_abort;;
+ esac
+ done
+
+ if [ $skip == 1 ]; then
+ echo "Skipping"
+ else
+ if [ -f "$HOME/.bashrc" ]; then
+ echo "Existing .bashrc file located: $HOME/.bashrc"
+ echo -n "Creating backup: "
+
+ if ! cp "$HOME/.bashrc" "$HOME/.bashrc_biopieces"; then
+ echo_red "FAIL"
+ abort
+ else
+ echo_green "OK"
+ echo " Backup is $HOME/.bashrc_biopieces"
+ fi
+ fi
+
+ echo -n "Appending $HOME/.bashrc: "
+
+ if ! echo "$section" >> "$HOME/.bashrc"; then
+ echo_red "FAIL"
+ abort
+ else
+ echo_green "OK"
+ fi
+
+ echo -n "Testing $HOME/.bashrc: "
+
+ if ! source "$HOME/.bashrc"; then
+ echo_red "FAIL"
+ abort
+ else
+ echo_green "OK"
+ fi
+
+ export BP_DIR="$bp_code"
+ export BP_DATA="$bp_data"
+ export BP_TMP="$bp_tmp"
+ export BP_LOG="$bp_log"
+
+ echo ""
+ echo " \$BP_DIR is now set to: $BP_DIR"
+ echo " \$BP_DATA is now set to: $BP_DATA"
+ echo " \$BP_TMP is now set to: $BP_TMP"
+ echo " \$BP_LOG is now set to: $BP_LOG"
+ echo ""
+
+ while true; do
+ read -p "Continue (yes/no)? " answer
+ case $answer in
+ [Yy]* ) break;;
+ [Nn]* ) exit_abort;;
+ esac
+ done
+ fi
+}
+
+# Function to test if we are running bash.
+function test_bash
+{
+ echo -n " Testing if the running shell is bash: "
+
+ if [ `echo $SHELL | grep "bash"` ]; then
+ echo_green "OK"
+ else
+ echo_red "FAIL"
+ echo " Biopieces requires bash shell not - $SHELL."
+ exit_abort
+ fi
+}
+
+# Function to test if subversion client is in $PATH.
+function test_svn
+{
+ local program="svn"
+
+ echo -n " Testing subversion client - \"$program\": "
+
+ if command -v $program >/dev/null; then
+ echo_green "OK"
+ else
+ echo_red "FAIL"
+ echo " Subversion client $program was not found."
+ exit_abort
+ fi
+}
+
+# Function to test if the required version of Perl is installed.
+function test_perl
+{
+ echo -n " Testing Perl version: "
+
+ if error=$( perl -e 'use 5.8.0;' 2>&1 ); then
+ echo_green "OK"
+ else
+ echo_red "FAIL"
+ echo " $error" | sed "s/, stopped.*//"
+ exit_abort
+ fi
+}
+
+# Function to test if a given Perl module is installed.
+function test_perl_module
+{
+ local module=$1
+
+ echo -n " Testing required Perl module - \"$module\": "
+
+ if ! error=$( perl -M$module -e '' 2>&1 > /dev/null ); then
+ echo_red "FAIL"
+ echo " Try: perl -MCPAN -e 'install $module'"
+ exit_abort
+ else
+ echo_green "OK"
+ fi
+}
+
+# Function to test if the required version of Ruby is installed.
+function test_ruby
+{
+ echo -n " Testing Ruby version: "
+
+ if ! [ `which ruby` ]; then
+ echo_red "FAIL"
+ echo " Ruby version 1.9 required"
+ exit_abort
+ fi
+
+ if error=$( ruby -e 'raise "Ruby version 1.9 required--this is only #{RUBY_VERSION}" if RUBY_VERSION < "1.9"' 2>&1 ); then
+ echo_green "OK"
+ else
+ echo_red "FAIL"
+ echo $error
+ exit_abort
+ fi
+}
+
+# Function to test if a given Ruby gem is installed.
+function test_ruby_gem
+{
+ local gem=$1
+
+ echo -n " Testing required Ruby gem - \"$gem\": "
+
+ if error=$( gem list --local | grep $gem ); then
+ echo_green "OK"
+ elif [[ $gem == 'RubyInline' ]] && error=$( ruby -rinline -e '' ); then
+ echo_yellow "OK"
+ else
+ echo_red "FAIL"
+ echo " Try: gem install $gem"
+ exit_abort
+ fi
+}
+
+# Function to test is a given auxillary program is in $PATH.
+function test_aux_program
+{
+ local program=$1
+
+ echo -n " Testing auxiliary program - \"$program\": "
+
+ if command -v $program >/dev/null; then
+ echo_green "OK"
+ else
+ echo_yellow "WARNING"
+ fi
+}
+
+# Function to checkout the Biopieces code from subversion.
+function checkout_code
+{
+ echo -n "Downloading Biopieces code from repository (please wait): "
+
+ if error=$( svn checkout http://biopieces.googlecode.com/svn/trunk/ $bp_code ); then
+ echo_green "OK"
+ else
+ echo_red "FAIL"
+ echo " $error"
+ exit_abort
+ fi
+}
+
+# Function to checkout the Biopieces wiki from subversion.
+function checkout_wiki
+{
+ echo -n "Downloading Biopieces wiki from repository (please wait): "
+
+ if error=$( svn checkout http://biopieces.googlecode.com/svn/wiki/ "$bp_code/bp_usage" ); then
+ echo_green "OK"
+ else
+ echo_red "FAIL"
+ echo " $error"
+ exit_abort
+ fi
+}
+
+prompt_install
+prompt_install_existing
+prompt_test_prerequisites
+prompt_install_dir_code
+prompt_install_dir_data
+prompt_install_dir_log
+prompt_install_dir_tmp
+
+checkout_code
+checkout_wiki
+
+prompt_append_bashrc
+
+exit_success
+
projects / biopieces.git / blobdiff