+++ /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"
- 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