From f1ec9c43ad3e06c1d06e6121a84636b2de9f42e5 Mon Sep 17 00:00:00 2001 From: Andreas Maunz Date: Wed, 28 Mar 2012 16:45:17 +0200 Subject: Removed manual OB --- base-install.sh | 2 +- install | 26 +++++++++----------------- openbabel.sh | 55 ------------------------------------------------------- utils.sh | 19 +------------------ 4 files changed, 11 insertions(+), 91 deletions(-) delete mode 100755 openbabel.sh diff --git a/base-install.sh b/base-install.sh index 336126d..f6d8b4d 100755 --- a/base-install.sh +++ b/base-install.sh @@ -24,7 +24,7 @@ done touch "$OT_UI_CONF" # Pkgs -packs="binutils build-essential cmake gnuplot hostname libcurl4-openssl-dev libgsl0-dev libreadline6-dev libreadline-dev libsqlite3-dev libssl-dev libyaml-dev libxml2-dev libxslt1-dev lsb-release openjdk-6-jdk psmisc pwgen raptor-utils r-base r-base-core r-base-dev sqlite3 udev wget xsltproc zlib1g-dev" +packs="binutils build-essential cmake curl gnuplot hostname libcurl4-openssl-dev libgsl0-dev libopenbabel4 libopenbabel-dev libreadline6-dev libreadline-dev libsqlite3-dev libssl-dev libyaml-dev libxml2-dev libxslt1-dev lsb-release openjdk-6-jdk psmisc pwgen raptor-utils r-base r-base-core r-base-dev sqlite3 udev wget xsltproc zlib1g-dev" echo echo "Base Packages:" diff --git a/install b/install index fa35845..1a3b7c3 100755 --- a/install +++ b/install @@ -8,15 +8,14 @@ if [ "$(id -u)" = "0" ]; then fi echo -echo "Warning! Hit If all services are stoppped, else ." -echo "Note: CONFIG (~/.opentox) will be backupped." -read help_var +echo "OpenTox Ruby" +echo "Hit If all services are stoppped, else hit ." +read delete_me +echo "Note: CONFIG (~/.opentox) will be backupped." mkdir -p $OT_PREFIX/tmp/ >/dev/null 2>&1 DATE=`date +_%Y%m%d_%H_%M` - -echo "Backups (if any)." -echo +echo "Backups (if any):" backup_targets="$HOME/.opentox $HOME/opentox-ruby" for bt in $backup_targets; do if [ -f $bt ]; then @@ -25,29 +24,22 @@ for bt in $backup_targets; do mv -v --backup=numbered -T $bt $bt$DATE fi done +echo "Backup finished." . ./utils.sh - - LOG="$OT_PREFIX/tmp/`basename $0`.log" echo echo "Welcome to base installation for OpenTox compatible services on Ruby and Debian." -echo "This will install:" -echo "- Debian packages" -echo "- OpenBabel (from source)." -echo -echo "IMPORTANT: press Ctrl+C to adjust config.sh first ( to continue)." +echo "IMPORTANT: Hit to adjust config.sh first ( to continue)." read delete_me echo -echo "You may need to give root password for some privileged actions right now and later:" -echo -cmd="sudo echo -n \"\"" && run_cmd "$cmd" "Acquire privileges" +echo -n "We need to install some packages. " +sudo echo -n "" rm -rf $OT_PREFIX/tmp/openbabel* $OT_PREFIX/tmp/ruby* cmd="mkdir -p $OT_PREFIX/install && cp utils.sh $OT_PREFIX/install" && run_cmd "$cmd" "Install utils.sh to OT_PREFIX" cmd="mkdir -p $HOME/.opentox/config/install && cp config.sh $HOME/.opentox/config/install" && run_cmd "$cmd" "Install config.sh to CONFIG (~/.opentox)" . ./base-install.sh -. ./openbabel.sh echo echo "Installation finished." diff --git a/openbabel.sh b/openbabel.sh deleted file mode 100755 index 93d606c..0000000 --- a/openbabel.sh +++ /dev/null @@ -1,55 +0,0 @@ -#!/bin/sh - -# Installs Openbabel. -# Author: Christoph Helma, Andreas Maunz. -# A configuration file is created and included in your 'OT_UI_CONF' (see config.sh). - -. ./utils.sh -DIR=`pwd` -OB_DWL="http://downloads.sourceforge.net/sourceforge/openbabel/$OB_NUM_VER/$OB_VER.tar.gz" - -[ "`id -u`" = "0" ] && echo "This script must be run as non-root." 1>&2 && exit 1 - -# check utils -utils="curl cmake" -for u in $utils; do - eval `echo $u | tr "[:lower:]" "[:upper:]"`=`which $u` || (echo "'$u' missing. Install '$u' first." 1>&2 && exit 1) -done - -# check openbabel -LOG="$OT_PREFIX/tmp/`basename $0`.log" -echo -echo "Openbabel ('$OB_DEST', '$LOG'):" -mkdir "$OB_DEST" >/dev/null 2>&1 -if [ ! -d "$OB_DEST" ]; then - echo "Install directory '$OB_DEST' is not available! Aborting..." - exit 1 -else - if ! rmdir "$OB_DEST" >/dev/null 2>&1; then # if not empty this will fail - OB_DONE=true - fi -fi - -if [ ! $OB_DONE ]; then - cd "$OT_PREFIX/tmp">>$LOG 2>/dev/null - ([ -d "$OT_PREFIX/tmp/$OB_VER" ] || $CURL -L -d use_mirror=netcologne $OB_DWL 2>/dev/null | tar zx) && cd $OB_VER - cmd="$CMAKE -DCMAKE_INSTALL_PREFIX=$OB_DEST" && run_cmd "$cmd" "Configure" - cmd="make -j2" && run_cmd "$cmd" "Make" - cmd="make install" && run_cmd "$cmd" "Install" -fi - -if [ ! -f "$OB_CONF" ]; then - echo "if echo \"\$PATH\" | grep -v \"$OB_DEST\">/dev/null 2>&1; then export PATH=\"$OB_DEST/bin:\$PATH\"; fi" >> "$OB_CONF" - echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$OB_DEST\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"$OB_DEST/lib:\$LD_LIBRARY_PATH\"; fi" >> "$OB_CONF" - echo "if ! [ -d \"$OB_DEST\" ]; then echo \"\$0: '$OB_DEST' is not a directory!\"; fi" >> "$OB_CONF" - echo "if [ -z \"\$BABEL_LIBDIR\" ]; then export BABEL_LIBDIR=\"$OB_DEST/lib/openbabel/$OB_NUM_VER\"; fi" >> "$OB_CONF" - echo "if ! [ -d \"\$BABEL_LIBDIR\" ]; then echo \"\$0: '\$BABEL_LIBDIR' is not a directory!\"; fi" >> "$OB_CONF" - echo "if [ -z \"\$BABEL_DATADIR\" ]; then export BABEL_DATADIR=\"$OB_DEST/share/openbabel/$OB_NUM_VER\"; fi" >> "$OB_CONF" - echo "if ! [ -d \"\$BABEL_DATADIR\" ]; then echo \"\$0: '\$BABEL_DATADIR' is not a directory!\"; fi" >> "$OB_CONF" - echo "Openbabel configuration has been stored in '$OB_CONF'." - if ! grep "$OB_CONF" $OT_UI_CONF >/dev/null 2>&1 ; then - echo ". \"$OB_CONF\"" >> $OT_UI_CONF - fi -fi - -cd "$DIR" diff --git a/utils.sh b/utils.sh index 5cfec28..8b5bbd0 100755 --- a/utils.sh +++ b/utils.sh @@ -24,7 +24,7 @@ run_cmd () tail -10 "$LOG" exit 1 fi - printf " [ \033[32m%s\033[m ]\n" "OK" + printf " [ \033[32m%s\033[m ]\n" "OK" } @@ -52,23 +52,6 @@ install_ruby() { } -install_ob_ruby() { - printf "\n%50s\n" "OB RUBY BINDINGS" - local DIR=`pwd` - check_utils "rbenv make" - SRC_DIR=$(dirname $(find $OT_PREFIX -name openbabel-ruby.cpp)) - [ -d "$SRC_DIR" ] || (echo "Sources not found." 1>&2 && exit 1) - cd $SRC_DIR - cmd="$RBENV local $RUBY_NUM_VER" && run_cmd "$cmd" "Configure Ruby" - sed -i 's/Init_OpenBabel/Init_openbabel/g' openbabel-ruby.cpp # apply fix - cmd="ruby extconf.rb --with-openbabel-include=../../include --with-openbabel-lib=../../src/.libs" && run_cmd "$cmd" "Extconf ruby bindings" - cmd="$MAKE" && run_cmd "$cmd" "Make OB ruby bindings" - cmd="$MAKE install" && run_cmd "$cmd" "Install OB ruby bindings" - cd $DIR - cmd="$RBENV rehash" && run_cmd "$cmd" "Rbenv rehash" -} - - install_with_bundler() { printf "\n%50s\n" "INSTALL" check_utils "gem rbenv" -- cgit v1.2.3