rbbt-image 0.1.24 → 0.1.25

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 7ed58604b057907a38851a6a92d7194f18053a7b
-  data.tar.gz: 2d388128b25ad6bab542ea78d4c5f2c2ddeed92e
+  metadata.gz: 0537ca8e50ce927886c8a21afbe078059aa75c09
+  data.tar.gz: 97cd46d82ff5951459fa3e5a144b409ad7f8b5e8
 SHA512:
-  metadata.gz: 38d6594b2ecd3bca2b2072bcef5e5d6860445897a2893736410f6a57e1d499719052f836ab16b963ea6f793188ac60f8dcc906cccaaa48c5996aa703a2659e07
-  data.tar.gz: 57bb41af613cbb225121ec437802ac2408eeb3d6fe6087398db207c38a054ab95cb0547c5c64a4d8b7286824840a43c87e60784737fd03cd1f5389502c6d7482
+  metadata.gz: 1418697fc48d5fc3a863801a56f3e40c8b711db2f914569d952e2c16efe276ecac4419e0cad85b91757ab2e08ec05a36acb5d397a1437e28e6338674e4141a2d
+  data.tar.gz: 8dadc56b89c8cb4de7f6720f35a4ee3fdfed10eef8fad619d4253e43ac6bc7b43ad39b108e253a88df070c9ea372124e9682dff9c10501b1d3c70ab9b2bc9ab9

data/bin/build_rbbt_provision_sh.rb

@@ -29,6 +29,7 @@ $ #{$0} [options]
 -st--skip_tokyocabinet Skip tokyocabinet setup installation
 -sr--skip_ruby Skip ruby setup installation
 -sg--skip_gem Skip ruby gem installation
+-sR--skip_R Skip R setup
 -su--skip_user_setup Skip user setup
 -sb--skip_bootstrap Skip user bootstrap
 -Rc--R_custom Install a custom installation of R
@@ -68,6 +69,7 @@ SKIP_BASE_SYSTEM = options[:skip_base_system]
 SKIP_TOKYOCABINET= options[:skip_tokyocabinet]
 SKIP_RUBY = options[:skip_ruby]
 R_CUSTOM = options[:R_custom]
+SKIP_R = options[:skip_R]
 SKIP_BOOT = options[:skip_bootstrap]
 SKIP_USER = options[:skip_user_setup]
 SKIP_GEM = options[:skip_gem]
@@ -114,6 +116,8 @@ else
 end 
 }
 
+echo "source /etc/rbbt_environment" >> /etc/profile
+
 #{
 if not SKIP_BASE_SYSTEM and R_CUSTOM
   "echo 1.1 Setting custom R"
@@ -121,6 +125,13 @@ if not SKIP_BASE_SYSTEM and R_CUSTOM
 end 
 }
 
+#{
+if not SKIP_R 
+  "echo 1.2 Install R packages"
+  File.read(script_dir + 'R_packages.sh') 
+end 
+}
+
 echo "2. Setting up tokyocabinet"
 #{
 if not SKIP_TOKYOCABINET
@@ -271,9 +282,13 @@ if docker_image = options[:docker]
     volumnes = options[:docker_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
+
+  # NOTE: Not used like this now. Used in provision script
+  #
+  #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)
@@ -305,6 +320,7 @@ From: #{container_dependency}
 
 %post
   cat > /tmp/rbbt_provision.sh <<"EOS"
+  echo "source /etc/rbbt_environment" > /.singularity/env/99-rbbt_environment
   #{provision_script}
 EOS
   bash /tmp/rbbt_provision.sh
@@ -359,7 +375,6 @@ Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
 end
     EOF
 
-    iii dir
     Misc.in_dir(dir) do
       io = CMD.cmd('vagrant up', :pipe => true, :log => true)
       while line = io.gets

data/share/provision_scripts/R_packages.sh

@@ -0,0 +1,39 @@
+#!/bin/bash -x
+
+# INSTALL
+# =======
+
+# R packages
+# ----------
+
+function R_install_packages(){
+  pkgs="'$1'"
+  shift
+  for p in $@; do
+    pkgs="$pkgs, '$p'"
+  done
+  echo "install.packages(c($pkgs), repos='http://cran.us.r-project.org')" | R --vanilla
+}
+
+function R_CMD_install(){
+  url=$1
+  name=$2
+  wget "$url" -O /tmp/R-pkg-"$name".tar.gz
+  R CMD INSTALL /tmp/R-pkg-"$name".tar.gz
+}
+
+R_install_packages Rcpp RJSONIO XML
+R_CMD_install 'https://cran.r-project.org/src/contrib/Archive/plyr/plyr_1.8.1.tar.gz' plyr
+R_CMD_install 'https://cran.r-project.org/src/contrib/Archive/car/car_2.0-22.tar.gz' car
+R_install_packages 'digest', 'gtable', 'reshape2', 'scales', 'proto'
+
+R_CMD_install 'https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_1.0.0.tar.gz' ggplot2
+R_CMD_install 'https://cran.r-project.org/src/contrib/Archive/ggthemes/ggthemes_1.7.0.tar.gz' ggthemes
+R_CMD_install 'https://cran.r-project.org/src/contrib/gridSVG_1.5-0.tar.gz' gridSVG
+
+R_install_packages NMF Cairo drc Rserve
+echo "source('http://bioconductor.org/biocLite.R'); biocLite('limma')" | R --vanilla
+
+R_install_packages pheatmap VennDiagram Hmisc pls
+
+rm /tmp/R-pkg-*.tar.gz

data/share/provision_scripts/R_setup.sh

@@ -14,12 +14,10 @@ cd R-*/
 ./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
+echo "# For RSRuby gem " >> /etc/rbbt_environment
+echo "export R_HOME='/usr/local/lib/R'" >> /etc/rbbt_environment
+echo "export PATH=\"$R_HOME/bin:$PATH\"" >> /etc/rbbt_environment
+echo "export LD_LIBRARY_PATH=\"\$LD_LIBRARY_PATH:\$R_HOME/lib\"" >> /etc/rbbt_environment
+echo "export LD_RUN_PATH=\"\$LD_RUN_PATH:\$R_HOME/lib\"" >> /etc/rbbt_environment
 
-. /etc/profile
+. /etc/rbbt_environment

data/share/provision_scripts/gem_setup.sh

@@ -3,7 +3,7 @@
 # RUBY GEMS and RBBT
 # =================
 
-. /etc/profile
+. /etc/rbbt_environment
 
 export REALLY_GEM_UPDATE_SYSTEM=true
 env REALLY_GEM_UPDATE_SYSTEM=true gem update --no-ri --no-rdoc --system
@@ -11,7 +11,7 @@ gem install --force --no-ri --no-rdoc ZenTest
 gem install --force --no-ri --no-rdoc RubyInline
 
 # R (extra config in gem)
-. /etc/profile
+. /etc/rbbt_environment
 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"
@@ -27,7 +27,7 @@ gem install --no-ri --no-rdoc --force \
     rbbt-util rbbt-rest rbbt-dm rbbt-text rbbt-sources rbbt-phgx rbbt-GE \
     rserve-client \
     uglifier therubyracer kramdown\
-    puma
+    puma prawn
 
 # Get good version of lockfile
 wget http://ubio.bioinfo.cnio.es/people/mvazquezg/lockfile-2.1.4.gem -O /tmp/lockfile-2.1.4.gem

data/share/provision_scripts/ruby_setup.sh

@@ -13,8 +13,8 @@ make && make install
 
 unset _small_version
 
-grep '#Ruby2' /etc/profile || echo 'export PATH="/usr/local/bin:$PATH" #Ruby2' >> /etc/profile
-. /etc/profile
+echo 'export PATH="/usr/local/bin:$PATH" #Ruby2' >> /etc/rbbt_environment
+. /etc/rbbt_environment
 
 #\curl -sSL https://get.rvm.io | bash -s stable
 #source /etc/profile.d/rvm.sh

data/share/provision_scripts/ubuntu_setup.sh

@@ -5,6 +5,10 @@
 
 # Basic system requirements
 # -------------------------
+apt-get -y install software-properties-common
+add-apt-repository ppa:george-edison55/cmake-3.x
+apt-get -y install cmake
+
 apt-get -y update
 apt-get -y update
 apt-get -y install \
@@ -15,12 +19,15 @@ apt-get -y install \
   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
+echo "export R_HOME='/usr/lib/R' # For Ruby's RSRuby gem" >> /etc/rbbt_environment
+echo "export PATH='$R_HOME/bin/:$PATH' # Rserver" >> /etc/rbbt_environment
+
+. /etc/rbbt_environment
 
 apt-get clean
 rm -rf /var/lib/apt/lists/* 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-image
 version: !ruby/object:Gem::Version
-  version: 0.1.24
+  version: 0.1.25
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-12-20 00:00:00.000000000 Z
+date: 2018-08-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -40,6 +40,7 @@ files:
 - bin/run_rbbt_docker.rb
 - lib/rbbt/docker.rb
 - share/provision_scripts/Dockerfile.R-packages
+- share/provision_scripts/R_packages.sh
 - share/provision_scripts/R_setup.sh
 - share/provision_scripts/bootstrap.sh
 - share/provision_scripts/gem_setup.sh