rbbt-image 0.1.33 → 0.1.38

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: 9a36cc9035c5e5ed455f5f2702a783b4b808a417
-  data.tar.gz: f46782d2b990fc20dfdaf4801f7217ff9683f796
+SHA256:
+  metadata.gz: 217c640720936293815a4871cdef2c80d44a53f981ab3fa549401f826145206b
+  data.tar.gz: 25cd8cfb00abddde8d8047b2b7f46d512ae65d0eed1551a4e9974b986d27f27e
 SHA512:
-  metadata.gz: c16da78e9abf7471528822e04cfddd521ccf420300a7ef307988cd7eb8c2a7a3e34ebed1618dc5cbcc0301d0cf933328a84e009f78a3fdb23f65d4a3ac6aa9b5
-  data.tar.gz: 632bdf10e05f6bf26417ddcec3a7c7b4686c5a3e6b16b7ab496d34e3cb9867645e9200507a0fc03f7a7a33f4181c0fc4211bc529355c6814fa0ee81ed9eca415
+  metadata.gz: e31fc043b5db3d46e82cb75ccf7776b6e6e1fd276b73032608fccad466d24d2cc58edbe2836626da28cb0614b705718d748edb2517fe38601238cf119288ccc3
+  data.tar.gz: 26a90fd5f55b334c1ca7892d28e4fcb94852e74da89077866f3193c53a580be147892585c568b6077a8e0a24b60e4815d174229031031aa703353e3eb4e0f3f7

data/bin/build_rbbt_provision_sh.rb

@@ -81,7 +81,7 @@ OPTIMIZE = options[:optimize]
 
 VARIABLES={
  :RBBT_LOG => 0,
- :BOOTSTRAP_WORKFLOWS => (options[:workflow] || "Enrichment Translation Sequence MutationEnrichment").split(/[\s,]+/)*" ",
+ :BOOTSTRAP_WORKFLOWS => (options[:workflow] || "").split(/[\s,]+/)*" ",
  :REMOTE_RESOURCES => (options[:remote_resources] || "KEGG").split(/[\s,]+/)*" "
 }
 
@@ -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
@@ -119,9 +119,6 @@ else
 end 
 }
 
-echo "[ -f ~/.rbbt/etc/environment ] && . ~/.rbbt/etc/environment" >> "/etc/rbbt_environment"
-echo "source /etc/rbbt_environment" >> /etc/profile
-
 #{
 if not SKIP_BASE_SYSTEM and R_CUSTOM
   "echo 1.1 Setting custom R"
@@ -182,6 +179,9 @@ else
   "echo SKIPPED\necho"
 end 
 }
+
+echo "[ -f ~/.rbbt/etc/environment ] && . ~/.rbbt/etc/environment" >> "/etc/rbbt_environment"
+echo "source /etc/rbbt_environment" >> /etc/profile
 EOF
 
 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:focal'
   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:focal'
   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 bootstrap #{singularity_image} '#{dir["singularity_bootstrap"]}'"
+    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

@@ -37,8 +37,12 @@ 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 NMF Cairo drc gridSVG ggthemes mclust randomForest viper
+
+echo 'install.packages("Rserve", repos="http://www.rforge.net/")' | R --vanilla
+
+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-*/
@@ -15,9 +15,8 @@ cd R-*/
 make && make install
 
 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
+echo 'export R_HOME="/usr/local/lib/R"' >> /etc/rbbt_environment
+echo '_add_path "$R_HOME/bin/" # Rserver' >> /etc/rbbt_environment
+echo '_add_lib_path "$R_HOME/lib/" # Rserver' >> /etc/rbbt_environment
 
 . /etc/rbbt_environment

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/python_setup.sh

@@ -1,15 +1,16 @@
 wget "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" -O /tmp/miniconda.sh
-bash /tmp/miniconda.sh -b -p /opt/miniconda3
+echo "# Python conda " >> /etc/rbbt_environment
 
-[ -d /opt/bin/conda ] || mkdir -p /opt/bin/conda
-ln -s /opt/miniconda3/bin/conda /opt/bin/conda
+bash /tmp/miniconda.sh -b -p /usr/local/miniconda3
+ln -s /usr/local/miniconda3/bin/conda /usr/local/bin/conda
+echo '_add_path "/usr/local/miniconda3/bin/"' >> /etc/rbbt_environment
 
-conda create --yes -n python3 python=3.6.1 pip
-rm -Rf /opt/miniconda3/pkgs
 conda create --yes -n python2 python=2.7 pip
-rm -Rf /opt/miniconda3/pkgs
 
-echo "# Python conda " >> /etc/rbbt_environment
-echo 'export PATH="/opt/bin/:/opt/miniconda3/envs/python3/bin/:$PATH"' >> /etc/rbbt_environment
+conda create --yes -n python3 python=3 pip
+
+echo '_add_path "/usr/local/miniconda3/envs/python2/bin/"' >> /etc/rbbt_environment
+echo '_add_path "/usr/local/miniconda3/envs/python3/bin/"' >> /etc/rbbt_environment
 
+rm -Rf /usr/local/miniconda3/pkgs
 source /etc/rbbt_environment

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-*/
@@ -13,8 +18,8 @@ make && make install
 
 unset _small_version
 
-echo 'export PATH="/usr/local/bin:/opt/bin:$PATH" #Ruby2' >> /etc/rbbt_environment
-. /etc/rbbt_environment
+cd "$_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

@@ -3,6 +3,68 @@
 # INSTALL
 # =======
 
+cat << 'EOF' > /etc/rbbt_environment 
+_var_content(){
+    var=$1
+    eval echo "$"$(echo $var)
+}
+
+_append_with_colon(){
+    var=$1
+    value=$2
+
+    current=`_var_content $var`
+
+    if ! echo $current | grep "\(^\|:\)$value\(:\|$\)" >/dev/null 2>&1; then
+        eval $(echo $var)="\"$current:$value\""
+    fi
+}
+
+_append_with_space(){
+    var=$1
+    value=$2
+
+    current=`_var_content $var`
+
+    if ! echo $current | grep "\(^\| \)$value\( \|$\)" >/dev/null 2>&1; then
+        eval $(echo $var)="\"$current:$value\""
+    fi
+}
+
+_prepend_with_colon(){
+    var=$1
+    value=$2
+
+    current=`_var_content $var`
+
+    if ! echo $current | grep "\(^\|:\)$value\(:\|$\)" >/dev/null 2>&1; then
+        eval $(echo $var)="\"$value:$current\""
+    fi
+}
+
+_prepend_with_space(){
+    var=$1
+    value=$2
+
+    current=`_var_content $var`
+
+    if ! echo $current | grep "\(^\| \)$value\( \|$\)" >/dev/null 2>&1; then
+        eval $(echo $var)="\"$value $current\""
+    fi
+}
+
+_add_path(){
+  _prepend_with_colon PATH "${1%/}"
+}
+
+_add_libpath(){
+  _prepend_with_colon LD_LIBRARY_PATH "${1%/}"
+  _prepend_with_colon LD_RUN_PATH "${1%/}"
+}
+EOF
+
+. /etc/rbbt_environment
+
 # Basic system requirements
 # -------------------------
 apt-get -y update
@@ -10,19 +72,23 @@ 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 \
+  time numactl \
   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
+#add-apt-repository ppa:george-edison55/cmake-3.x
 apt-get -y update
 apt-get -y update
 apt-get -y install cmake
@@ -36,12 +102,19 @@ rm /usr/lib/R/bin/Rserve
 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 'export PATH="$R_HOME/bin/:$PATH" # Rserver' >> /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
 
-. /etc/rbbt_environment
+[ -d /opt/bin ] || mkdir -p /opt/bin
+echo '_add_path "/opt/bin/"' >> /etc/rbbt_environment
 
-apt-get clean
-rm -rf /var/lib/apt/lists/* 
+[ -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
+rm -rf /var/lib/apt/lists/* 

data/share/provision_scripts/variables.sh

@@ -1,6 +1,6 @@
 #!/bin/bash -x
 
-test -z ${RBBT_SERVER+x}           && RBBT_SERVER=http://rbbt.bioinfo.cnio.es/ 
+test -z ${RBBT_SERVER+x}           && RBBT_SERVER=http://rbbt.bsc.es/ 
 test -z ${RBBT_FILE_SERVER+x}      && RBBT_FILE_SERVER="$RBBT_SERVER"
 test -z ${RBBT_WORKFLOW_SERVER+x}  && RBBT_WORKFLOW_SERVER="$RBBT_SERVER"
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-image
 version: !ruby/object:Gem::Version
-  version: 0.1.33
+  version: 0.1.38
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-02-28 00:00:00.000000000 Z
+date: 2020-11-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -71,8 +71,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.6.13
+rubygems_version: 3.0.6
 signing_key: 
 specification_version: 4
 summary: Build docker and Vagrant (VM) images