rbbt-image 0.1.36 → 0.1.37

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: b6ed0fbc0b9b6ea6d4f6b7f1cd9931bebd8e5438ec37b5c73ecdaf545ffde7b2
-  data.tar.gz: 68e3073a6bd603fa0404fb3403ecf87c22c0731546b24afc4e2ea059b73a2acf
+  metadata.gz: 45c46d847d1522d0d774cbdad29d9ba70bb1cc42036234dc53de6d0723403e02
+  data.tar.gz: eef195a183125dbb8f9c3d3f12157a3bff0c4ed12ef1118cd88acf3878d7bba4
 SHA512:
-  metadata.gz: 288e7e36fed3c08d32416a88af59caffe684d5fdefdf22b5a9b5e1ea051f825c3b1e138932d787d797ff8aa142ff2d5b8a5d1481a28f6f4ca5388df956f231e8
-  data.tar.gz: 5910cee842328c52a9057b85184aaba2149d6d8427efd4e164448af75651ca2783a881e612b6517baba7dce920a3389236a04d1bc45b17bac9ff0770a0d6fcda
+  metadata.gz: e3d2cac785c2cd0d192f2913af0f40e6a1abb65b3daa8efd8a2e4f4c97aba672c6421e2e1a8222f753694ac7e52493de3be2af7080943e3bcaf3faec16e44aa2
+  data.tar.gz: 90c007ee52794941a8c421882779d2e6a1e147e83e9c77e59a1dd4e57e248bed87e4fd20165d530a71933e783b1e929eaa652aec86b6dc1afb176cd01a3984db

data/bin/build_rbbt_provision_sh.rb

@@ -94,7 +94,7 @@ 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"
+options[:ruby_version] ||= "2.6.4"
 
 
 provision_script =<<-EOF
@@ -290,7 +290,7 @@ provision_script +=<<-EOF
 # ====
 
 apt-get clean
-rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /usr/share/doc /usr/share/man /usr/local/share/ri
+rm -rf /var/lib/apt/lists/* /var/tmp/* /usr/share/doc /usr/share/man /usr/local/share/ri
 
 #{ "su -l -c 'rbbt system optimize /home/#{USER}/.rbbt ' #{USER}" if OPTIMIZE}
 
@@ -300,9 +300,9 @@ date
 
 EOF
 
-container_dependency = options[:container_dependency] || 'ubuntu:cosmic'
 
 if docker_image = options[:docker]
+  container_dependency = options[:container_dependency] || 'ubuntu:disco'
   dockerfile = options[:dockerfile] || File.join(root_dir, 'Dockerfile')
   dockerfile_text = Open.read(dockerfile)
   dockerfile_text.sub!(/^FROM.*/,'FROM ' + container_dependency) if container_dependency
@@ -339,6 +339,7 @@ end
 
 if singularity_image = options[:singularity]
 
+  container_dependency = options[:container_dependency] || 'ubuntu:disco'
   TmpFile.with_file(nil, false) do |dir|
     Path.setup(dir)
 
@@ -349,10 +350,10 @@ Bootstrap: docker
 From: #{container_dependency}
 
 %post
-  cat > /tmp/rbbt_provision.sh <<"EOS"
+  cat > /image_provision.sh <<"EOS"
   #{provision_script}
 EOS
-  bash -x /tmp/rbbt_provision.sh
+  bash -x /image_provision.sh 2>&1 | tee /image_provision.log
   ln -s /etc/rbbt_environment /.singularity.d/env/99-rbbt_environment.sh 
   chmod +x /.singularity.d/env/99-rbbt_environment.sh
   bash -c '[ -d /usr/local/share ] || mkdir -p /usr/local/share' 
@@ -368,22 +369,22 @@ EOF
     Open.write(dir["singularity_bootstrap"].find, bootstrap_text)
     Open.write(provision_file, provision_script)
 
-    puts "RUN"
-    puts "==="
     singularity_size = options[:singularity_size] || 3072
     cmd_create =  "singularity create -s #{singularity_size} #{singularity_image}"
     cmd_boot =  "singularity build #{singularity_image} '#{dir["singularity_bootstrap"]}'"
+
+
+    puts "**************"
+    puts "CREATING IMAGE: #{dir["singularity_bootstrap"].find}"
+    puts "**************"
     puts cmd_create
-    io = CMD.cmd(cmd_create, :pipe => true, :log => true)
-    while line = io.gets
-      puts line
-    end
+    CMD.cmd_log(cmd_create, :log => 4)
 
+    puts "**************"
+    puts "BUILDING IMAGE: #{dir["singularity_bootstrap"].find}"
+    puts "**************"
     puts cmd_boot
-    io = CMD.cmd(cmd_boot, :pipe => true, :log => true)
-    while line = io.gets
-      puts line
-    end
+    CMD.cmd_log(cmd_boot, :log => 4)
   end
 
 end

data/share/provision_scripts/R_packages.sh

@@ -38,7 +38,8 @@ 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_install_packages NMF Cairo drc Rserve gridSVG ggthemes mclust randomForest viper
-R_install_packages pheatmap VennDiagram Hmisc pls
+R_install_packages pheatmap VennDiagram Hmisc pls gridSVG
+R_install_packages tidyverse
 
 R_biocLite limma viper
 

data/share/provision_scripts/R_setup.sh

@@ -7,7 +7,7 @@ cd /tmp
 
 apt-get remove r-base-core
 
-wget https://ftp.gwdg.de/pub/misc/cran/src/base/R-3/R-3.4.2.tar.gz -O R.tar.gz
+wget https://cran.rediris.es/src/base/R-3/R-3.6.1.tar.gz -O R.tar.gz
 tar -xvzf R.tar.gz
 
 cd R-*/

data/share/provision_scripts/bootstrap.sh

@@ -3,7 +3,7 @@
 # USER RBBT BOOTSTRAP
 # ===================
 
-for workflow in $WORKFLOWS; do
+for workflow in $BOOTSTRAP_WORKFLOWS; do
     rbbt workflow install $workflow 
 done
 

data/share/provision_scripts/gem_setup.sh

@@ -29,8 +29,6 @@ gem install --no-document --force \
     ruby-prof \
     rbbt-util rbbt-rest rbbt-dm rbbt-text rbbt-sources rbbt-phgx rbbt-GE \
     rserve-client \
-    uglifier therubyracer kramdown\
-    puma prawn prawn-svg
 
 # 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
@@ -39,4 +37,10 @@ wget http://github.com/mikisvaz/lockfile/raw/master/lockfile-2.1.5.gem -O /tmp/l
 gem install --no-document /tmp/lockfile-2.1.5.gem
 
 # Extra things for web interface
-gem install --no-document bio-svgenes mimemagic
+gem install --no-document --force \
+    tokyocabinet \
+    ruby-prof \
+    rbbt-util rbbt-rest rbbt-dm rbbt-text rbbt-sources rbbt-phgx rbbt-GE \
+    rserve-client \
+    uglifier therubyracer kramdown pandoc pandoc-ruby\
+    puma prawn prawn-svg

data/share/provision_scripts/ruby_setup.sh

@@ -4,7 +4,12 @@
 # ============
 
 _small_version=`echo $RUBY_VERSION | cut -f 1,2 -d.`
-cd /tmp
+
+[ -d /tmp/ruby-install ] || mkdir /tmp/ruby-install
+
+_prewd="$(pwd)"
+cd /tmp/ruby-install
+
 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-*/
@@ -13,7 +18,8 @@ make && make install
 
 unset _small_version
 
-. /etc/rbbt_environment
+cd "$_prewd"
+rm -Rf /tmp/ruby-install
 
 #\curl -sSL https://get.rvm.io | bash -s stable
 #source /etc/profile.d/rvm.sh

data/share/provision_scripts/ubuntu_setup.sh

@@ -15,7 +15,7 @@ _append_with_colon(){
 
     current=`_var_content $var`
 
-    if ! echo $current | grep "\(^\|:\)$value\(:\|$\)" &> /dev/null; then
+    if ! echo $current | grep "\(^\|:\)$value\(:\|$\)" >/dev/null 2>&1; then
         eval $(echo $var)="\"$current:$value\""
     fi
 }
@@ -26,7 +26,7 @@ _append_with_space(){
 
     current=`_var_content $var`
 
-    if ! echo $current | grep "\(^\| \)$value\( \|$\)" &> /dev/null; then
+    if ! echo $current | grep "\(^\| \)$value\( \|$\)" >/dev/null 2>&1; then
         eval $(echo $var)="\"$current:$value\""
     fi
 }
@@ -37,7 +37,7 @@ _prepend_with_colon(){
 
     current=`_var_content $var`
 
-    if ! echo $current | grep "\(^\|:\)$value\(:\|$\)" &> /dev/null; then
+    if ! echo $current | grep "\(^\|:\)$value\(:\|$\)" >/dev/null 2>&1; then
         eval $(echo $var)="\"$value:$current\""
     fi
 }
@@ -48,18 +48,18 @@ _prepend_with_space(){
 
     current=`_var_content $var`
 
-    if ! echo $current | grep "\(^\| \)$value\( \|$\)" &> /dev/null; then
+    if ! echo $current | grep "\(^\| \)$value\( \|$\)" >/dev/null 2>&1; then
         eval $(echo $var)="\"$value $current\""
     fi
 }
 
 _add_path(){
-  _prepend_with_colon PATH "$1"
+  _prepend_with_colon PATH "${1%/}"
 }
 
 _add_libpath(){
-  _prepend_with_colon LD_LIBRARY_PATH "$1"
-  _prepend_with_colon LD_RUN_PATH "$1"
+  _prepend_with_colon LD_LIBRARY_PATH "${1%/}"
+  _prepend_with_colon LD_RUN_PATH "${1%/}"
 }
 EOF
 
@@ -72,16 +72,19 @@ apt-get -y install software-properties-common
 
 apt-get -y update
 apt-get -y update
-apt-get -y install \
+DEBIAN_FRONTEND=noninteractive apt-get -y install \
   vim \
+  wget \
+  libc6 \
   bison autoconf g++ libxslt1-dev make \
   zlib1g-dev libbz2-dev libreadline-dev \
-  wget curl git openssl libyaml-0-2 libyaml-dev \
+  rsync wget curl git openssl libyaml-0-2 libyaml-dev \
   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 libyaml-dev libffi-dev \
   python3 python \
   tcsh gawk \
+  pandoc \
   libtbb-dev
 
 #add-apt-repository ppa:george-edison55/cmake-3.x
@@ -99,6 +102,7 @@ ln -s /usr/lib/R/site-library/Rserve/libs/Rserve /usr/lib/R/bin/Rserve
 
 echo "export R_HOME='/usr/lib/R' # For Ruby's RSRuby gem" >> /etc/rbbt_environment
 echo '_add_path "$R_HOME/bin/" # Rserver' >> /etc/rbbt_environment
+echo 'export R_LIBS_USER="~/container_R/lib" # Avoid collision with host system' >> /etc/rbbt_environment
 
 [ -d /opt/bin ] || mkdir -p /opt/bin
 echo '_add_path "/opt/bin/"' >> /etc/rbbt_environment
@@ -106,6 +110,9 @@ echo '_add_path "/opt/bin/"' >> /etc/rbbt_environment
 [ -d /usr/local/bin ] || mkdir -p /usr/local/bin
 echo '_add_path "/usr/local/bin/"' >> /etc/rbbt_environment
 
+echo 'export LC_ALL=C.UTF-8' >> /etc/rbbt_environment
+
+
 . /etc/rbbt_environment
 
 apt-get clean

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-image
 version: !ruby/object:Gem::Version
-  version: 0.1.36
+  version: 0.1.37
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-08-07 00:00:00.000000000 Z
+date: 2020-03-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -71,7 +71,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.0.3
+rubygems_version: 3.0.6
 signing_key: 
 specification_version: 4
 summary: Build docker and Vagrant (VM) images