From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 6 Aug 2012 14:43:28 +0000 (+0000)
Subject: removed outdated installer
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=4e6e330fe5266c1ffc87a54e0a2b69614feba1cf;p=biopieces.git

removed outdated installer

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1876 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_scripts/biopieces_installer-0.45.sh b/bp_scripts/biopieces_installer-0.45.sh
deleted file mode 100755
index fd4f551..0000000
--- a/bp_scripts/biopieces_installer-0.45.sh
+++ /dev/null
@@ -1,578 +0,0 @@
-#!/bin/bash
-
-# Install script for Biopieces.
-# 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 "   To list all available Biopieces try 'list_biopieces'"
-    echo ""
-    echo "   To see the synopsis of a Biopiece try 'read_fastq'"
-    echo ""
-    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 "   *  Run tests"
-    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_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."
-
-    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 "Sourcing $HOME/.bashrc: "
-
-        if ! source "$HOME/.bashrc"; then
-            echo_red "FAIL"
-            abort
-        else
-            echo_green "OK"
-        fi
-
-        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 $module'"
-        exit_abort
-    else
-        echo_green "OK"
-    fi
-}
-
-# Function to test if the required version of Ruby is installed.
-function test_ruby
-{
-    echo -n "   Testing Ruby version: "
-
-    if error=$( 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"
-        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 "   $error"
-        exit_abort
-    fi  
-}
-
-# Function to run the Biopieces tests.
-function prompt_test_biopieces
-{
-    echo "Running the Biopieces test suite:"
-    echo ""
-
-    "$BP_DIR/bp_test/test_all"
-
-    echo ""
-    echo "   Any FAIL indicates broken Biopieces. This is probably because of"
-    echo "   missing prerequisites (see WARNINGs). You can verify this later by"
-    echo "   inspecting the documentation for those Biopieces. Otherwise - seek help!"
-
-    while true; do
-        read -p "Continue (yes/no)? " answer
-        case $answer in
-            [Yy]* ) break;;
-            [Nn]* ) exit_abort;;
-        esac
-    done
-}
-
-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
-prompt_test_biopieces
-
-exit_success
-