diff options
author | Andreas Maunz <andreas@maunz.de> | 2012-08-21 13:38:41 +0200 |
---|---|---|
committer | Andreas Maunz <andreas@maunz.de> | 2012-08-21 13:38:41 +0200 |
commit | 714111145e6ac5778dc5ce2ecb3652e4bddb34d7 (patch) | |
tree | ba7e3723cc34215fd9e48a97854e8a09b9a20e70 | |
parent | 3faf3c96fa31163e2201240e47f27a6571111ab7 (diff) | |
parent | f87da673e2437e2728b31c84b2ae1cfdf05915c5 (diff) |
Merge branch 'development' of github.com:opentox/install into development
-rwxr-xr-x | 4store-install | 2 | ||||
-rwxr-xr-x | base-install | 12 | ||||
-rwxr-xr-x | config.sh | 12 | ||||
-rw-r--r-- | debian.list | 34 | ||||
-rwxr-xr-x | install | 7 | ||||
-rw-r--r-- | ot-tools-user.sh | 65 | ||||
-rwxr-xr-x | raptor2-install | 3 | ||||
-rwxr-xr-x | rasqal-install | 2 | ||||
-rw-r--r-- | ubuntu.list | 34 | ||||
-rwxr-xr-x | utils.sh | 11 |
10 files changed, 103 insertions, 79 deletions
diff --git a/4store-install b/4store-install index c87c2d9..ee04738 100755 --- a/4store-install +++ b/4store-install @@ -25,7 +25,7 @@ cmd="make install" && run_cmd "$cmd" "Make Install" # Config echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$FST/lib\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"\$LD_LIBRARY_PATH:$FST/lib\"; fi" >> "$FST_CONF" -if ! cat "$OT_DEFAULT_CONF" | grep "four_store">/dev/null 2>&1; then echo '$four_store = { :uri => "http://localhost:8088", :user => "", :password => "" }' >> $OT_DEFAULT_CONF; fi +if ! cat "$OT_DEFAULT_CONF" | grep "four_store">/dev/null 2>&1; then echo '$four_store = { :uri => "http://localhost:9088", :user => "", :password => "" }' >> $OT_DEFAULT_CONF; fi echo "$SELF configuration has been stored in '$FST_CONF'." if ! grep "$FST_CONF" $OT_UI_CONF >/dev/null 2>&1; then diff --git a/base-install b/base-install index c7d717e..6e549d8 100755 --- a/base-install +++ b/base-install @@ -13,12 +13,20 @@ DIR=`pwd` # Not logged # Not logged [ "`id -u`" = "0" ] && echo "This script must not be run as root" 1>&2 && exit 1 -check_utils "aptitude apt-get apt-cache dpkg" +check_utils "aptitude apt-get apt-key apt-cache dpkg tee wget" echo echo "Base Packages:" echo echo "Updating index..." + +cmd="$WGET -O redland_key.asc $REDLAND_APT_KEY >/dev/null 2>&1" && run_cmd "$cmd" "Download redland apt-key" +cmd="$APT_KEY add redland_key.asc >/dev/null 2>&1; rm redland_key.asc" && run_cmd "$cmd" "Adding redland apt-key" +if ! cat "/etc/apt/sources.list" | grep "$REDLAND_DEB">/dev/null 2>&1; then + echo "deb $REDLAND_DEB ./" | sudo $TEE -a /etc/apt/sources.list >/dev/null + echo "deb-src $REDLAND_DEB ./" | sudo $TEE -a /etc/apt/sources.list >/dev/null +fi + sudo $APTITUDE update -y >/dev/null 2>&1 DISTRIB_INFO=$(cat /proc/version) @@ -30,7 +38,7 @@ case "$DISTRIB_INFO" in esac sudo $DPKG --set-selections < "$PACK_LIST" -sudo $APT_GET -y -u dselect-upgrade +sudo $APT_GET -y --force-yes -u dselect-upgrade if [ ! -f $JAVA_CONF ]; then @@ -5,7 +5,7 @@ # 1) Base setup -OT_DIST="debian" # Linux distribution (debian) +OT_DIST="debian" # Linux distribution (debian, ubuntu) OT_INSTALL="local" # Type (gem, local, server) OT_BRANCH="development" # Maturity (development -need SSH key at Github-, master) @@ -19,10 +19,11 @@ OB_NUM_VER="2.3.1" RAPTOR2_NUM_VER="2.0.8" RASQAL_NUM_VER="0.9.29" RUBY_NUM_VER="1.9.3-p194" +REDLAND_DWL="http://download.librdf.org" +REDLAND_APT_KEY="http://purl.org/net/dajobe/gnupg.asc" # Done. - ### Nothing to gain from changes below this line. JAVA_CONF="$HOME/.opentox/java.sh" FST_CONF="$HOME/.opentox/4S.sh" @@ -39,9 +40,8 @@ RAPTOR2_VER="raptor2-$RAPTOR2_NUM_VER" RASQAL_VER="rasqal-$RASQAL_NUM_VER" OB_DEST="$OT_PREFIX/$OB_VER" OB_DEST_BINDINGS="$OT_PREFIX/openbabel-ruby-install" - -RAPTOR2_DWL="http://download.librdf.org/source/$RAPTOR2_VER.tar.gz" -RASQAL_DWL="http://download.librdf.org/source/$RASQAL_VER.tar.gz" RUBY_DWL="http://ftp.ruby-lang.org/pub/ruby/1.9" RUBY_DIR="$HOME/.rbenv/versions/$RUBY_NUM_VER" - +RAPTOR2_DWL="$REDLAND_DWL/source/$RAPTOR2_VER.tar.gz" +RASQAL_DWL="$REDLAND_DWL/source/$RASQAL_VER.tar.gz" +REDLAND_DEB="$REDLAND_DWL/binaries/$OT_DIST/unstable" diff --git a/debian.list b/debian.list index d16ee3f..73be6d9 100644 --- a/debian.list +++ b/debian.list @@ -1,25 +1,25 @@ +aptitude install +automake install +avahi-daemon install build-essential install cmake install -libgsl0-dev install -libtool install -openjdk-6-jdk install -r-base install -r-base-dev install -libpcre3-dev install -librasqal3-dev install -libtool install +curl install +libavahi-glib-dev install +libavahi-client-dev install libglib2.0-dev install -ncurses-dev install -libreadline-dev install -uuid-dev install -libraptor1-dev install +libgsl0-dev install libopenbabel4 install libopenbabel-dev install -automake install -libyaml-dev install libopenssl-ruby install +libpcre3-dev install +libraptor1-dev install +libreadline-dev install libssl-dev install +libtool install libxml2-dev install -libssl-dev install -curl install -aptitude install +libyaml-dev install +ncurses-dev install +openjdk-6-jdk install +r-base-dev install +r-base install +uuid-dev install @@ -37,9 +37,8 @@ sudo echo -n "" echo [ -f $OT_PREFIX/install/utils.sh ] || (cmd="mkdir -p $OT_PREFIX/install && cp utils.sh $OT_PREFIX/install" && run_cmd "$cmd" "Install utils.sh to OT_PREFIX") -[ -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/config)") -[ -f $OT_DEFAULT_CONF ] || (cmd="echo '\$aa = { :uri => nil }' > $OT_DEFAULT_CONF" && run_cmd "$cmd" "Install default.rb to CONFIG (~/.opentox/config)") - +[ -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/config/install)") +[ -f $OT_DEFAULT_CONF ] || (cmd="echo '\$aa = { :uri => nil }' > $OT_DEFAULT_CONF" && run_cmd "$cmd" "Created default.rb service settings (stored in ~/.opentox/config)") . ./base-install # Debian specific; disable this for others. ./raptor2-install # Download, compile and build raptor2. Install to OT_PREFIX. @@ -59,7 +58,7 @@ 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") -[ -f $OT_TOOLS_CONF ] || (cmd="cp ot-tools-user.sh $OT_TOOLS_CONF" && run_cmd "$cmd" "Install ot-tools.sh to CONFIG (~/.opentox/config)") +[ -f $OT_TOOLS_CONF ] || (cmd="cp ot-tools-user.sh $OT_TOOLS_CONF" && run_cmd "$cmd" "Created ot-tools (stored in ~/.opentox)") # Install global ruby version diff --git a/ot-tools-user.sh b/ot-tools-user.sh index ca3bdbd..d60a26e 100644 --- a/ot-tools-user.sh +++ b/ot-tools-user.sh @@ -3,6 +3,7 @@ # Load server config otconfig() { source $HOME/.opentox/opentox-ui.sh + source $HOME/.opentox/config/install/config.sh } # Display log @@ -20,6 +21,18 @@ start_unicorn() { nice bash -c "nohup unicorn -p $2 >/dev/null 2>&1 &" } +# Start unicorn +# @param1 [backend_name] +# @param2 integer Port +# @example start_unicorn algorithm 8081 +start_4s() { + nice bash -c "nohup $OT_PREFIX/4S/bin/4s-backend $1 >/dev/null 2>&1 &"; + sleep 0.5; + nice bash -c "nohup $OT_PREFIX/4S/bin/4s-httpd -H localhost -p $2 -s -1 $1 >/dev/null 2>&1 &"; #-D for testing + sleep 0.5; + +} + # Start the server otstart() { if [ $# != 1 ] @@ -33,25 +46,28 @@ otstart() { otkill $1 DIR=`pwd` case "$1" in - "algorithm") start_unicorn $1 8081;; - "compound") #start_unicorn $1 8082;; + "algorithm") start_4s $1 9081; + start_unicorn $1 8081;; + "compound") start_4s $1 9082; + start_unicorn $1 8082;; + "dataset") start_4s $1 9083; + start_unicorn $1 8083;; + "feature") start_4s $1 9084; + start_unicorn $1 8084;; + "model") #start_4s $1 9085; + #start_unicorn $1 8085;; echo "$1 not available yet.";; - "dataset") start_unicorn $1 8083;; - "feature") start_unicorn $1 8084;; - "model") #start_unicorn $1 8085;; + "task") start_4s $1 9086; + start_unicorn $1 8086;; + "validation") #start_4s $1 9087; + #start_unicorn $1 8087;; echo "$1 not available yet.";; - "task") start_unicorn $1 8086;; - "validation") #start_unicorn $1 8087;; - echo "$1 not available yet.";; - "4store") nice bash -c "nohup $HOME/opentox-ruby/4S/bin/4s-backend opentox >/dev/null 2>&1 &"; - sleep 1; - nice bash -c "nohup $HOME/opentox-ruby/4S/bin/4s-httpd -D -H localhost -p 8088 opentox >/dev/null 2>&1 &"; - sleep 1; - if ! pgrep -u $USER 4s-backend>/dev/null 2>&1; then echo "Failed to start 4s-backend."; fi - if ! pgrep -u $USER 4s-httpd>/dev/null 2>&1; then echo "Failed to start 4s-httpd."; fi;; + "4store") start_4s opentox 9088;; + #if ! pgrep -u $USER 4s-backend>/dev/null 2>&1; then echo "Failed to start 4s-backend."; fi + #if ! pgrep -u $USER 4s-httpd>/dev/null 2>&1; then echo "Failed to start 4s-httpd."; fi;; "all") otstart 4store; otstart algorithm; - #otstart compound; + otstart compound; otstart dataset; otstart feature; #otstart model; @@ -61,6 +77,7 @@ otstart() { echo "usage: otstart [all|algorithm|compound|dataset|feature|model|task|validation|4store]"; return 1;; esac + sleep 1 cd $DIR } @@ -94,8 +111,7 @@ otreload() { otconfig case "$1" in "algorithm") reload_unicorn 8081;; - "compound") #reload_unicorn 8082;; - echo "$1 not available yet.";; + "compound") reload_unicorn 8082;; "dataset") reload_unicorn 8083;; "feature") reload_unicorn 8084;; "model") #reload_unicorn 8085;; @@ -107,7 +123,7 @@ otreload() { #killall 4s-backend >/dev/null 2>&1;; echo "$1 reload not available yet.";; "all") otreload algorithm; - #otreload compound; + otreload compound; otreload dataset; otreload feature; #otreload model; @@ -118,6 +134,7 @@ otreload() { echo "usage: otreload [all|algorithm|compound|dataset|feature|model|task|validation|4store]"; return 1;; esac + sleep 1 } # kill unicorn @@ -139,8 +156,7 @@ otkill() { otconfig case "$1" in "algorithm") kill_unicorn 8081;; - "compound") #kill_unicorn 8082;; - echo "$1 not available yet.";; + "compound") kill_unicorn 8082;; "dataset") kill_unicorn 8083;; "feature") kill_unicorn 8084;; "model") #kill_unicorn 8085;; @@ -151,7 +167,7 @@ otkill() { "4store") killall 4s-httpd >/dev/null 2>&1; killall 4s-backend >/dev/null 2>&1;; "all") otkill algorithm; - #otkill compound; + otkill compound; otkill dataset; otkill feature; #otkill model; @@ -162,6 +178,7 @@ otkill() { echo "usage: otkill [all|algorithm|compound|dataset|feature|model|task|validation|4store]"; return 1;; esac + sleep 1 } # get service uri @@ -232,8 +249,7 @@ otcheck() { otconfig case "$1" in "algorithm") check_service "algorithm";; - "compound") #check_service "compound";; - echo "$1 not available yet.";; + "compound") check_service "compound";; "dataset") check_service "dataset";; "feature") check_service "feature";; "model") #check_service "model";; @@ -242,9 +258,8 @@ otcheck() { "validation") #check_service "validation";; echo "$1 not available yet.";; "4store") check_service "four_store";; - #killall 4s-backend >/dev/null 2>&1;; "all") otcheck "algorithm"; - #otcheck "compound"; + otcheck "compound"; otcheck "dataset"; otcheck "feature"; #otcheck "model"; diff --git a/raptor2-install b/raptor2-install index ad44ed4..4d3be2e 100755 --- a/raptor2-install +++ b/raptor2-install @@ -5,7 +5,7 @@ DIR=`pwd` . ./utils.sh || (echo "Utils could not be loaded, check opentox-ui.sh." 1>&2 && exit 1) SELF=$(basename $0 -install) check_log $SELF -check_utils "wget tar make grep" +check_utils "apt-get wget tar make grep" # Build mkdir -p $OT_PREFIX/tmp @@ -15,6 +15,7 @@ export RAPTOR2_DIR=$OT_PREFIX/$SELF cmd="$TAR xvzf $RAPTOR2_VER.tar.gz" && run_cmd "$cmd" "Unpack" rm $RAPTOR2_VER.tar.gz cd $RAPTOR2_VER +cmd="sudo $APT_GET -y build-dep $SELF" && run_cmd "$cmd" "Build dependencies" cmd="./configure --prefix=$RAPTOR2_DIR" && run_cmd "$cmd" "Configure" cmd="$MAKE" && run_cmd "$cmd" "Make" cmd="$MAKE install" && run_cmd "$cmd" "Make Install" diff --git a/rasqal-install b/rasqal-install index bc06450..8bd9fbd 100755 --- a/rasqal-install +++ b/rasqal-install @@ -5,7 +5,7 @@ DIR=`pwd` . ./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 grep" +check_utils "apt-get wget tar make grep" # Build mkdir -p $OT_PREFIX/tmp diff --git a/ubuntu.list b/ubuntu.list index d16ee3f..73be6d9 100644 --- a/ubuntu.list +++ b/ubuntu.list @@ -1,25 +1,25 @@ +aptitude install +automake install +avahi-daemon install build-essential install cmake install -libgsl0-dev install -libtool install -openjdk-6-jdk install -r-base install -r-base-dev install -libpcre3-dev install -librasqal3-dev install -libtool install +curl install +libavahi-glib-dev install +libavahi-client-dev install libglib2.0-dev install -ncurses-dev install -libreadline-dev install -uuid-dev install -libraptor1-dev install +libgsl0-dev install libopenbabel4 install libopenbabel-dev install -automake install -libyaml-dev install libopenssl-ruby install +libpcre3-dev install +libraptor1-dev install +libreadline-dev install libssl-dev install +libtool install libxml2-dev install -libssl-dev install -curl install -aptitude install +libyaml-dev install +ncurses-dev install +openjdk-6-jdk install +r-base-dev install +r-base install +uuid-dev install @@ -77,8 +77,8 @@ install_ruby() { local DIR=`pwd` check_utils "rbenv curl make tar" if ! $RBENV versions $RUBY_NUM_VER | grep $RUBY_NUM_VER>/dev/null 2>&1; then - [ -d $DIR/tmp ] || mkdir -p $DIR/tmp && cd $DIR/tmp - ([ -d $DIR/tmp/ruby-$RUBY_NUM_VER ] || $CURL $RUBY_DWL/ruby-$RUBY_NUM_VER.tar.gz 2>/dev/null | $TAR xz) && cd ruby-$RUBY_NUM_VER + [ -d $OT_PREFIX/tmp ] || mkdir -p $OT_PREFIX/tmp && cd $OT_PREFIX/tmp + ([ -d $OT_PREFIX/tmp/ruby-$RUBY_NUM_VER ] || $CURL $RUBY_DWL/ruby-$RUBY_NUM_VER.tar.gz 2>/dev/null | $TAR xz) && cd ruby-$RUBY_NUM_VER cmd="./configure --prefix=$RUBY_DIR" && run_cmd "$cmd" "Configure" cmd="$MAKE -j2" && run_cmd "$cmd" "Make" cmd="$MAKE install" && run_cmd "$cmd" "Install" @@ -139,10 +139,11 @@ notify() { echo if ps -o stat= -p $PPID | grep "s" >/dev/null 2>&1; then echo "IMPORTANT: How to configure your system if everything went fine:" - echo "IMPORTANT: a) Include '$OT_UI_CONF' in shell startup (e.g. ~/.bashrc)." - echo "IMPORTANT: b) Manually source '$OT_UI_CONF' every time." - echo "IMPORTANT: The command in both cases: '. $OT_UI_CONF'" + echo "IMPORTANT: a) Include '$OT_TOOLS_CONF' in shell startup (e.g. ~/.bashrc)." + echo "IMPORTANT: b) Manually source '$OT_TOOLS_CONF' every time." + echo "IMPORTANT: The command in both cases: '. $OT_TOOLS_CONF'" echo "IMPORTANT: NOW would be the best time to configure!" + echo "Visit 'http://opentox.github.com/General/2012/08/09/install-opentox-development-environment/' for further information about the usage of ot-tools." echo echo "Thank you for your attention." echo |