From e077d91919e0443f435bda8903c235608453a795 Mon Sep 17 00:00:00 2001 From: davor Date: Tue, 7 Aug 2012 18:10:26 +0200 Subject: Separated raptor2/rasqal and fixes. --- config.sh | 2 ++ debian.list | 3 --- install | 5 ++--- raptor2-install | 34 +++++++++++++++++++++++++++++++++ raptor_rasqal-install | 53 --------------------------------------------------- rasqal-install | 31 ++++++++++++++++++++++++++++++ services-install | 2 +- ubuntu.list | 3 --- utils.sh | 10 ++++++---- 9 files changed, 76 insertions(+), 67 deletions(-) create mode 100755 raptor2-install delete mode 100755 raptor_rasqal-install create mode 100755 rasqal-install diff --git a/config.sh b/config.sh index edc2fd2..e22c3f2 100755 --- a/config.sh +++ b/config.sh @@ -17,6 +17,8 @@ OT_JAVA_HOME="/usr/lib/jvm/java-6-openjdk" OB_NUM_VER="2.3.1" RUBY_DWL="http://ftp.ruby-lang.org/pub/ruby/1.9" +RAPTOR2_DWL="http://download.librdf.org/source/raptor2-2.0.8.tar.gz" +RASQAL_DWL="http://download.librdf.org/source/rasqal-0.9.29.tar.gz" # Done. diff --git a/debian.list b/debian.list index 603458d..862ab51 100644 --- a/debian.list +++ b/debian.list @@ -22,7 +22,4 @@ libssl-dev install libxml2-dev install libssl-dev install curl install -wget install -tar install aptitude install -find install diff --git a/install b/install index 3d1793f..dbd9fbc 100755 --- a/install +++ b/install @@ -40,7 +40,8 @@ echo [ -f $HOME/.opentox/config/install/config.sh ] || (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 # Debian specific; disable this for others. -./raptor_rasqal-install # Download, compile and build raptor2 and rasqal. Install to OT_PREFIX. +./raptor2-install # Download, compile and build raptor2. Install to OT_PREFIX. +./rasqal-install # Download, compile and build rasqal. Install to OT_PREFIX. ./4store-install # Download, compile and build 4store. Install to OT_PREFIX. if [ ! -d ~/.rbenv ]; then @@ -56,6 +57,4 @@ fi [ -f $HOME/.opentox/config/ambit_descriptors.yaml ] || (cmd="cp ambit_descriptors.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Ambit keys file") [ -f $HOME/.opentox/config/jl_keys.yaml ] || (cmd="cp jl_keys.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Joelib keys file") -. ./services-install - notify diff --git a/raptor2-install b/raptor2-install new file mode 100755 index 0000000..d4ad138 --- /dev/null +++ b/raptor2-install @@ -0,0 +1,34 @@ +#!/bin/sh +DIR=`pwd` + +# Boot +. ./utils.sh || (echo "Utils could not be loaded, check opentox-ui.sh." 1>&2 && exit 1) +SELF=$(basename $0 -install) +check_log $SELF +check_utils "wget tar make" + +# Build +mkdir -p $PREFIX/tmp +cd $OT_PREFIX/tmp/ +cmd="$WGET $RAPTOR2_DWL && run_cmd "$cmd" "Download $SELF" +export RAPTOR2_DIR=$OT_PREFIX/$SELF/ +cmd="$TAR xvzf "$SELF*.tar.gz" && run_cmd "$cmd" "Unpack $SELF" +rm "$SELF*.tar.gz" +cd "$SELF*" +cmd="./configure --prefix=$RAPTOR2_DIR" && run_cmd "$cmd" "Configure" +cmd="$MAKE" && run_cmd "$cmd" "Make" +cmd="$MAKE install" && run_cmd "$cmd" "Make Install" + +# Config +echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$RAPTOR2_DIR/lib\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"$RAPTOR2_DIR/lib:\$LD_LIBRARY_PATH\"; fi" >> "$RAPTOR2_CONF" +echo "if echo \"\$PKG_CONFIG_PATH\" | grep -v \"$RAPTOR2_DIR/lib/pkgconfig\">/dev/null 2>&1; then export PKG_CONFIG_PATH=\"$RAPTOR2_DIR/lib/pkgconfig:\$PKG_CONFIG_PATH\"; fi" >> "$RAPTOR2_CONF" +echo "$SELF configuration has been stored in '$RAPTOR2_CONF'." +if ! grep "$RAPTOR2_CONF" $OT_UI_CONF >/dev/null 2>&1; then + echo '. '$RAPTOR2_CONF >> $OT_UI_CONF +fi +cd .. +export LD_LIBRARY_PATH=$RAPTOR2_DIR"/lib:"$LD_LIBRARY_PATH +export PATH=$RAPTOR2_DIR"/bin:"$PATH +export PKG_CONFIG_PATH=$RAPTOR2_DIR"/lib/pkgconfig:"$PKG_CONFIG_PATH + +cd $DIR diff --git a/raptor_rasqal-install b/raptor_rasqal-install deleted file mode 100755 index 24d391b..0000000 --- a/raptor_rasqal-install +++ /dev/null @@ -1,53 +0,0 @@ -#!/bin/sh -DIR=`pwd` -RAPTOR2=raptor2-2.0.8 -RASQAL=rasqal-0.9.29 -# Boot -. ./utils.sh || (echo "Utils could not be loaded, check opentox-ui.sh." 1>&2 && exit 1) -SELF=$(basename $0 -install) -check_log $SELF -#[ "`id -u`" = "0" ] && echo "This script must not be run as root" 1>&2 && exit 1 -check_utils "wget tar make" - -# Build -mkdir -p $PREFIX/tmp -cd $OT_PREFIX/tmp/ -cmd="$WGET http://download.librdf.org/source/"$RAPTOR2".tar.gz" && run_cmd "$cmd" "Download $RAPTOR2" -export RAPTOR2_DIR=$OT_PREFIX/$SELF/$RAPTOR2 -cmd="$TAR xvzf "$RAPTOR2".tar.gz" && run_cmd "$cmd" "Unzip $RAPTOR2" -rm $RAPTOR2.tar.gz -cd $RAPTOR2 -cmd="./configure --prefix=$RAPTOR2_DIR" && run_cmd "$cmd" "Configure" -cmd="$MAKE" && run_cmd "$cmd" "Make" -cmd="$MAKE install" && run_cmd "$cmd" "Make Install" -# Config -echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$RAPTOR2_DIR/lib\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"$RAPTOR2_DIR/lib:\$LD_LIBRARY_PATH\"; fi" >> "$RAPTOR2_CONF" -echo "if echo \"\$PKG_CONFIG_PATH\" | grep -v \"$RAPTOR2_DIR/lib/pkgconfig\">/dev/null 2>&1; then export PKG_CONFIG_PATH=\"$RAPTOR2_DIR/lib/pkgconfig:\$PKG_CONFIG_PATH\"; fi" >> "$RAPTOR2_CONF" -echo "$RAPTOR2 configuration has been stored in '$RAPTOR2_CONF'." -if ! grep "$RAPTOR2_CONF" $OT_UI_CONF >/dev/null 2>&1; then - echo '. '$RAPTOR2_CONF >> $OT_UI_CONF -fi -cd .. -export LD_LIBRARY_PATH=$RAPTOR2_DIR"/lib:"$LD_LIBRARY_PATH -export PATH=$RAPTOR2_DIR"/bin:"$PATH -export PKG_CONFIG_PATH=$RAPTOR2_DIR"/lib/pkgconfig:"$PKG_CONFIG_PATH - -#Build -cmd="$WGET http://download.librdf.org/source/"$RASQAL".tar.gz" && run_cmd "$cmd" "Download $RASQAL" -export RASQAL_DIR=$OT_PREFIX/$SELF/$RASQAL -cmd="$TAR xvzf "$RASQAL".tar.gz" && run_cmd "$cmd" "Unzip $RASQAL" -rm $RASQAL.tar.gz -cd $RASQAL -cmd="./configure --prefix=$RASQAL_DIR" && run_cmd "$cmd" "Configure" -cmd="$MAKE" && run_cmd "$cmd" "Make" -cmd="$MAKE install" && run_cmd "$cmd" "Make Install" -# Config -echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$RASQAL_DIR/lib\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"$RASQAL_DIR/lib:\$LD_LIBRARY_PATH\"; fi" >> "$RASQAL_CONF" -echo "if echo \"\$PKG_CONFIG_PATH\" | grep -v \"$RASQAL_DIR/lib/pkgconfig\">/dev/null 2>&1; then export PKG_CONFIG_PATH=\"$RASQAL_DIR/lib/pkgconfig:\$PKG_CONFIG_PATH\"; fi" >> "$RASQAL_CONF" -echo "$RASQAL configuration has been stored in '$RASQAL_CONF'." -if ! grep "$RASQAL_CONF" $OT_UI_CONF >/dev/null 2>&1; then - echo '. '$RASQAL_CONF >> $OT_UI_CONF -fi -cd .. - -cd $DIR diff --git a/rasqal-install b/rasqal-install new file mode 100755 index 0000000..f73ddc7 --- /dev/null +++ b/rasqal-install @@ -0,0 +1,31 @@ +#!/bin/sh +DIR=`pwd` + +# Boot +. ./utils.sh || (echo "Utils could not be loaded, check opentox-ui.sh." 1>&2 && exit 1) +SELF=$(basename $0 -install) +check_log $SELF +check_utils "wget tar make" + +# Build +mkdir -p $PREFIX/tmp +cd $OT_PREFIX/tmp/ +cmd="$WGET $RASQAL_DWL" && run_cmd "$cmd" "Download $SELF" +export RASQAL_DIR=$OT_PREFIX/$SELF +cmd="$TAR xvzf $SELF*.tar.gz" && run_cmd "$cmd" "Unpack $SELF" +rm "$SELF*.tar.gz" +cd "$SELF*" +cmd="./configure --prefix=$RASQAL_DIR" && run_cmd "$cmd" "Configure" +cmd="$MAKE" && run_cmd "$cmd" "Make" +cmd="$MAKE install" && run_cmd "$cmd" "Make Install" + +# Config +echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$RASQAL_DIR/lib\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"$RASQAL_DIR/lib:\$LD_LIBRARY_PATH\"; fi" >> "$RASQAL_CONF" +echo "if echo \"\$PKG_CONFIG_PATH\" | grep -v \"$RASQAL_DIR/lib/pkgconfig\">/dev/null 2>&1; then export PKG_CONFIG_PATH=\"$RASQAL_DIR/lib/pkgconfig:\$PKG_CONFIG_PATH\"; fi" >> "$RASQAL_CONF" +echo "$SELF configuration has been stored in '$RASQAL_CONF'." +if ! grep "$RASQAL_CONF" $OT_UI_CONF >/dev/null 2>&1; then + echo '. '$RASQAL_CONF >> $OT_UI_CONF +fi +cd .. + +cd $DIR diff --git a/services-install b/services-install index bee1719..d47a62c 100755 --- a/services-install +++ b/services-install @@ -39,7 +39,7 @@ echo [ "`$RBENV local 2>/dev/null`" = "$RUBY_NUM_VER" ] || install_ruby -for SERVICE in opentox-client opentox-server dataset algorithm; do +for SERVICE in opentox-client opentox-server dataset algorithm task feature opentox-test; do install_ot_service done cd $DIR diff --git a/ubuntu.list b/ubuntu.list index 603458d..862ab51 100644 --- a/ubuntu.list +++ b/ubuntu.list @@ -22,7 +22,4 @@ libssl-dev install libxml2-dev install libssl-dev install curl install -wget install -tar install aptitude install -find install diff --git a/utils.sh b/utils.sh index 8ca267e..87013d9 100755 --- a/utils.sh +++ b/utils.sh @@ -87,10 +87,10 @@ install_ruby() { # install a ruby gem using bundler install_with_bundler() { printf "\n%50s\n" "INSTALL" - check_utils "gem rbenv" + check_utils "gem rbenv bundle" $GEM list | grep bundler >/dev/null 2>&1 || (cmd="$GEM install bundler" && run_cmd "$cmd" "Install bundler") cmd="$RBENV rehash" && run_cmd "$cmd" "Rbenv rehash" - cmd="bundle install" && run_cmd "$cmd" "Install using bundler" + cmd="$BUNDLE install" && run_cmd "$cmd" "Install using bundler" } # download opentox git repo @@ -104,6 +104,7 @@ ot_git_download(){ # install opentox service install_ot_service(){ printf "\n%50s\n" "$SERVICE" + check_utils "git rbenv" local DIR=`pwd` cd $OT_PREFIX ot_git_download @@ -111,8 +112,9 @@ install_ot_service(){ $GIT checkout $OT_BRANCH >>$LOG 2>&1 $RBENV local $RUBY_NUM_VER case "$SERVICE" in - opentox-server) install_with_bundler;; - opentox-client) install_with_bundler;; + opentox-*) install_with_bundler;; + feature) install_with_bundler;; + task) install_with_bundler;; *) cd bin; for f in `ls`; do ./$f; done;; esac cd $DIR -- cgit v1.2.3