rbbt-image 0.1.22 → 0.1.23

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: f50f19d65d7e0b5aeac62e088eb649a89b8f3d69
-  data.tar.gz: 04c5e4b3bceb73f38c5c5fb62003eb17f6812117
+  metadata.gz: 985e74d5183e70ec0ba00624edf6bf6a5fc32479
+  data.tar.gz: 9f983398ac5b35b6ea43d36dc7d1d8c734190235
 SHA512:
-  metadata.gz: 5901297085f63d32fdfafc603034f55a9a8fe5775b81e766b586b30be00b974bcf9de21c3cb8336cb98ca3861ede62bda41637e90061fe1aad8c00ce04a7945b
-  data.tar.gz: dac403f6cbfcb5817c0c228dded58533481653130d077ae1ecdc03330e86c960d17169db89ff9f2aeb046364382e79ed62961db187ad8aaba758ee215fe021fe
+  metadata.gz: 853f5b6d1221b2da5e48c4e553bfe69b96758df9d44c35ede7c642de519fe57e6b07995720ca2766fce4a34ebc21614168b4ba2dbb4b630f572637080efd55f2
+  data.tar.gz: 43f68462a65f1b1affea381f1cd569b69c4407ce2b8675b530c3429d55c0f05cf2ecf771020ad476c04f5d74e494348e23eb25e484ab4b8118531d0eb49b20c5

data/Dockerfile

@@ -1,6 +1,8 @@
-FROM ubuntu
+FROM ubuntu:xenial
 USER root
+# START PROVISION
 ADD provision.sh /tmp/provision.sh
 RUN /bin/bash /tmp/provision.sh
+# END PROVISION
 USER rbbt
 ENV HOME /home/rbbt

data/bin/build_rbbt_provision_sh.rb

@@ -26,19 +26,25 @@ $ #{$0} [options]
 -rr--remote_resources* Remote resources to gather from file-server
 -rw--remote_workflows* Remote workflows server from workflow-server
 -ss--skip_base_system Skip base system installation
+-st--skip_tokyocabinet Skip tokyocabinet setup installation
 -sr--skip_ruby Skip ruby setup installation
 -sg--skip_gem Skip ruby gem installation
 -su--skip_user_setup Skip user setup
 -sb--skip_bootstrap Skip user bootstrap
+-Rc--R_custom Install a custom installation of R
+-Rp--R_packages Install basic R packages
 -c--concurrent Prepare system for high-concurrency
+-Rbv--ruby_version* Ruby version to use, using three numbers (defaults to 2.4.1)
 -op--optimize Optimize files under ~/.rbbt
 -dt--docker* Build docker image using the provided name
 -df--docker_file* Use a Dockerfile different than the default
 -dd--docker_dependency* Use a different image in the Dockerfile FROM
+-si--singularity* Build singularity image using the provided name
 -v--volumnes* List of volumes to set-up
 --nocolor Prevent rbbt from using colors and control sequences in the logs while provisioning
 --nobar Prevent rbbt from using progress bars while provisioning
 EOF
+
 if options[:help]
   if defined? rbbt_usage
     rbbt_usage and exit 0 
@@ -51,9 +57,16 @@ end
 root_dir = File.dirname(File.dirname(File.expand_path(__FILE__)))
 script_dir = File.join(root_dir, "share/provision_scripts/")
 
+if options[:singularity]
+  options[:skip_user_setup] = true
+  options[:skip_bootstrap] = true
+end
+
 USER = options[:user] || 'rbbt'
 SKIP_BASE_SYSTEM = options[:skip_base_system]
+SKIP_TOKYOCABINET= options[:skip_tokyocabinet]
 SKIP_RUBY = options[:skip_ruby]
+R_CUSTOM = options[:R_custom]
 SKIP_BOOT = options[:skip_bootstrap]
 SKIP_USER = options[:skip_user_setup]
 SKIP_GEM = options[:skip_gem]
@@ -75,6 +88,8 @@ VARIABLES[:REMOTE_WORKFLOWS] = options[:remote_workflows].split(/[\s,]+/)*" " if
 VARIABLES[:RBBT_NOCOLOR] = "true" if options[:nocolor]
 VARIABLES[:RBBT_NO_PROGRESS] = "true" if options[:nobar]
 
+options[:ruby_version] ||= "2.4.1"
+
 
 provision_script =<<-EOF
 #!/bin/bash -x
@@ -82,6 +97,9 @@ provision_script =<<-EOF
 echo "RUNNING PROVISION"
 echo
 echo "CMD: #{File.basename($0) + " " + orig_argv.collect{|a| a =~ /\s/ ? "\'#{a}\'" : a }.join(" ")}"
+echo
+echo -n "Starting: "
+date
 
 EOF
 
@@ -95,16 +113,32 @@ else
 end 
 }
 
-echo "2. Setting up ruby"
+#{
+if not SKIP_BASE_SYSTEM and R_CUSTOM
+  "echo 1.1 Setting custom R"
+  File.read(script_dir + 'R_setup.sh') 
+end 
+}
+
+echo "2. Setting up tokyocabinet"
+#{
+if not SKIP_TOKYOCABINET
+  File.read(script_dir + 'tokyocabinet_setup.sh')
+else
+  "echo SKIPPED\necho"
+end
+}
+
+echo "3. Setting up ruby"
 #{
 if not SKIP_RUBY
-  File.read(script_dir + 'ruby_setup.sh') 
+  "export RUBY_VERSION='#{options[:ruby_version]}'\n" << File.read(script_dir + 'ruby_setup.sh') 
 else
   "echo SKIPPED\necho"
 end 
 }
 
-echo "3. Setting up gems"
+echo "3.1. Setting up gems"
 #{
 if not SKIP_GEM
   File.read(script_dir + 'gem_setup.sh') 
@@ -220,6 +254,8 @@ rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /usr/share/doc /usr/share/man /usr
 
 echo
 echo "Installation done."
+date
+
 EOF
 
 docker_dependency = options[:docker_dependency]
@@ -234,6 +270,9 @@ if options[:docker]
     volumnes = options[:volumnes].split(/\s*[,|]\s*/).collect{|d| "VOLUME " << d} * "\n"
     dockerfile_text.sub!(/^RUN/, volumnes + "\nRUN")
   end
+  if options[:R_packages]
+    dockerfile_text.sub!(/^(# END PROVISION)/, '\1' + "\n" + Open.read(File.join(script_dir, 'Dockerfile.R-packages')) + "\n" )
+  end
   TmpFile.with_file(nil, false) do |dir|
     FileUtils.mkdir_p dir
     Path.setup(dir)
@@ -252,3 +291,44 @@ else
   puts provision_script
 end
 
+if singularity_image = options[:singularity]
+  docker_dep = options[:docker_dependency] || 'ubuntu'
+
+  TmpFile.with_file(nil, false) do |dir|
+    Path.setup(dir)
+
+    provision_file = dir['provision.sh']
+
+    bootstrap_text=<<-EOF
+Bootstrap: docker
+From: #{docker_dep}
+
+%post
+  cat > /tmp/rbbt_provision.sh <<"EOS"
+  #{provision_script}
+EOS
+  bash /tmp/rbbt_provision.sh
+EOF
+    FileUtils.mkdir_p dir
+    Open.write(dir["singularity_bootstrap"].find, bootstrap_text)
+    Open.write(provision_file, provision_script)
+
+    puts "RUN"
+    puts "==="
+    cmd_create =  "singularity create -s 2048 #{singularity_image}"
+    cmd_boot =  "singularity bootstrap #{singularity_image} '#{dir["singularity_bootstrap"]}'"
+    puts cmd_create
+    io = CMD.cmd(cmd_create, :pipe => true, :log => true)
+    while line = io.gets
+      puts line
+    end
+
+    puts cmd_boot
+    io = CMD.cmd(cmd_boot, :pipe => true, :log => true)
+    while line = io.gets
+      puts line
+    end
+  end
+
+end
+

data/share/provision_scripts/Dockerfile.R-packages

@@ -0,0 +1,16 @@
+RUN echo "install.packages(c('Rcpp','RJSONIO','XML'), repos='http://cran.us.r-project.org')" | R --vanilla
+RUN wget 'https://cran.r-project.org/src/contrib/Archive/plyr/plyr_1.8.1.tar.gz' -O /tmp/plyr_1.8.1.tar.gz
+RUN R CMD INSTALL /tmp/plyr_1.8.1.tar.gz
+RUN wget 'https://cran.r-project.org/src/contrib/Archive/car/car_2.0-22.tar.gz' -O /tmp/car_2.0-22.tar.gz
+RUN R CMD INSTALL /tmp/car_2.0-22.tar.gz
+RUN echo "install.packages(c('digest', 'gtable', 'reshape2', 'scales', 'proto'), repos='http://cran.us.r-project.org')" | R --vanilla
+RUN wget 'https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_1.0.0.tar.gz' -O /tmp/ggplot2_1.0.0.tar.gz
+RUN R CMD INSTALL /tmp/ggplot2_1.0.0.tar.gz
+RUN wget 'https://cran.r-project.org/src/contrib/Archive/ggthemes/ggthemes_1.7.0.tar.gz' -O /tmp/ggthemes_1.7.0.tar.gz
+RUN R CMD INSTALL /tmp/ggthemes_1.7.0.tar.gz
+RUN wget 'https://cran.r-project.org/src/contrib/gridSVG_1.5-0.tar.gz' -O /tmp/gridSVG_1.5-0.tar.gz
+RUN R CMD INSTALL /tmp/gridSVG_1.5-0.tar.gz
+RUN echo "install.packages(c('NMF'), repos='http://cran.us.r-project.org')" | R --vanilla
+RUN echo "install.packages(c('Cairo','drc', 'Rserve'), repos='http://cran.us.r-project.org')" | R --vanilla
+RUN echo "source('http://bioconductor.org/biocLite.R'); biocLite('limma')" | R --vanilla
+RUN rm /tmp/*.gz

data/share/provision_scripts/R_setup.sh

@@ -0,0 +1,25 @@
+#!/bin/bash -x
+
+# R INSTALL
+# ============
+
+cd /tmp
+
+apt-get remove r-base-core
+
+wget https://cran.r-project.org/src/base/R-3/R-3.3.2.tar.gz
+tar -xvzf R-3.3.2.tar.gz
+
+cd R-3.3.2/
+./configure --prefix=/usr/local --enable-R-shlib
+make && make install
+
+grep -v R_HOME /etc/profile > profile.tmp
+echo >> profile.tmp
+echo "# For RSRuby gem " >> profile.tmp
+echo "export R_HOME='/usr/local/lib/R'" >> profile.tmp
+echo "export LD_LIBRARY_PATH=\"\$LD_LIBRARY_PATH:\$R_HOME/lib\"" >> profile.tmp
+echo "export LD_RUN_PATH=\"\$LD_RUN_PATH:\$R_HOME/lib\"" >> profile.tmp
+mv profile.tmp /etc/profile
+
+. /etc/profile

data/share/provision_scripts/gem_setup.sh

@@ -3,16 +3,21 @@
 # RUBY GEMS and RBBT
 # =================
 
+. /etc/profile
+
 export REALLY_GEM_UPDATE_SYSTEM=true
 env REALLY_GEM_UPDATE_SYSTEM=true gem update --no-ri --no-rdoc --system
 gem install --force --no-ri --no-rdoc ZenTest
 gem install --force --no-ri --no-rdoc RubyInline
 
 # R (extra config in gem)
-gem install --conservative --no-ri --no-rdoc rsruby -- --with-R-dir=/usr/lib/R --with-R-include=/usr/share/R/include --with_cflags="-fPIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wall -fno-strict-aliasing"
+. /etc/profile
+export R_INCLUDE="$(echo "$R_HOME" | sed 's@/usr/lib\(32\|64\)*@/usr/share@')/include"
+gem install --conservative --no-ri --no-rdoc rsruby -- --with-R-dir="$R_HOME" --with-R-include="$R_INCLUDE" \
+  --with_cflags="-fPIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wall -fno-strict-aliasing"
 
 # Java (extra config in gem)
-export JAVA_HOME=$(echo /usr/lib/jvm/java-7-openjdk-*)
+export JAVA_HOME=$(echo /usr/lib/jvm/java-?-openjdk-*)
 gem install --conservative --force --no-ri --no-rdoc rjb
 
 # Rbbt and some optional gems
@@ -28,3 +33,5 @@ gem install --no-ri --no-rdoc --force \
 wget http://ubio.bioinfo.cnio.es/people/mvazquezg/lockfile-2.1.4.gem -O /tmp/lockfile-2.1.4.gem
 gem install --no-ri --no-rdoc /tmp/lockfile-2.1.4.gem
 
+# Extra things for web interface
+gem install --no-ri --no-rdoc bio-svgenes mimemagic

data/share/provision_scripts/ruby_setup.sh

@@ -3,13 +3,19 @@
 # RUBY INSTALL
 # ============
 
+_small_version=`echo $RUBY_VERSION | cut -f 1,2 -d.`
 cd /tmp
-wget https://cache.ruby-lang.org/pub/ruby/2.3/ruby-2.3.0.tar.gz
-tar -xvzf ruby-2.3.0.tar.gz
-cd ruby-2.3.0/
+wget https://cache.ruby-lang.org/pub/ruby/$_small_version/ruby-${RUBY_VERSION}.tar.gz -O "ruby.tar.gz"
+tar -xvzf ruby.tar.gz
+cd ruby-*/
 ./configure --prefix=/usr/local
 make && make install
 
-grep "#Ruby2" /etc/profile || echo 'export PATH="/usr/local/bin:$PATH" #Ruby2' >> /etc/profile
+unset _small_version
+
+grep '#Ruby2' /etc/profile || echo 'export PATH="/usr/local/bin:$PATH" #Ruby2' >> /etc/profile
 . /etc/profile
 
+#\curl -sSL https://get.rvm.io | bash -s stable
+#source /etc/profile.d/rvm.sh
+#rvm install $RUBY_VERSION

data/share/provision_scripts/tokyocabinet_setup.sh

@@ -0,0 +1,11 @@
+#!/bin/bash -x
+
+# TOKYOCABINET INSTALL
+# ===================
+
+cd /tmp
+wget http://fallabs.com/tokyocabinet/tokyocabinet-1.4.48.tar.gz -O "tokyocabinet.tar.gz"
+tar -xvzf tokyocabinet.tar.gz
+cd tokyocabinet-1.4.48
+./configure --prefix=/usr/local
+make && make install

data/share/provision_scripts/ubuntu_setup.sh

@@ -11,16 +11,19 @@ apt-get -y install \
   bison autoconf g++ libxslt1-dev make \
   zlib1g-dev libbz2-dev libreadline6 libreadline6-dev \
   wget curl git openssl libyaml-0-2 libyaml-dev \
-  ruby2.0 ruby-dev \
-  r-base-core r-base-dev r-cran-rserve \
-  openjdk-7-jdk \
-  libtokyocabinet-dev tokyocabinet-bin \
+  openjdk-8-jdk \
+  libcairo2 libcairo2-dev r-base-core r-base-dev r-cran-rserve liblzma5 liblzma-dev libcurl4-openssl-dev \
   build-essential zlib1g-dev libssl-dev libreadline6-dev libyaml-dev libffi-dev
 
+# This link was broken for some reason
+rm /usr/lib/R/bin/Rserve
+ln -s /usr/lib/R/site-library/Rserve/libs/Rserve /usr/lib/R/bin/Rserve
 
 grep R_HOME /etc/profile || echo "export R_HOME='/usr/lib/R' # For Ruby's RSRuby gem" >> /etc/profile
 . /etc/profile
 
-# This link was broken for some reason
-rm /usr/lib/R/bin/Rserve
-ln -s /usr/lib/R/site-library/Rserve/libs/Rserve /usr/lib/R/bin/Rserve
+apt-get clean
+rm -rf /var/lib/apt/lists/* 
+
+
+

data/share/provision_scripts/variables.sh

@@ -16,3 +16,4 @@ test -z ${BOOTSTRAP_CPUS+x}       && BOOTSTRAP_CPUS="2"
 
 test -z ${RBBT_LOG+x}  && RBBT_LOG="LOW"
 
+test -z ${RUBY_VERSION+x}  && RUBY_VERSION="2.4.1"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-image
 version: !ruby/object:Gem::Version
-  version: 0.1.22
+  version: 0.1.23
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-09-11 00:00:00.000000000 Z
+date: 2017-10-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -39,9 +39,12 @@ files:
 - bin/build_rbbt_provision_sh.rb
 - bin/run_rbbt_docker.rb
 - lib/rbbt/docker.rb
+- share/provision_scripts/Dockerfile.R-packages
+- share/provision_scripts/R_setup.sh
 - share/provision_scripts/bootstrap.sh
 - share/provision_scripts/gem_setup.sh
 - share/provision_scripts/ruby_setup.sh
+- share/provision_scripts/tokyocabinet_setup.sh
 - share/provision_scripts/ubuntu_setup.sh
 - share/provision_scripts/user_setup.sh
 - share/provision_scripts/variables.sh
@@ -65,7 +68,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.6
+rubygems_version: 2.6.13
 signing_key: 
 specification_version: 4
 summary: Build docker and Vagrant (VM) images