rbbt-image 0.1.27 → 0.1.28

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 4a34563591892148b42e8293da580a69ba0fdf22
-  data.tar.gz: f9a24f57bdac10fa46b66ef711657bd3b617c9a7
+  metadata.gz: 1cb89f08075de1b263ebc22095ae3a0b8c9973b6
+  data.tar.gz: 24b81127c036dcb78571b520d20a66cb25229b3a
 SHA512:
-  metadata.gz: c54d3107cec5c2db856f15c74928710185ab545831901f4c9e22f535ef0bad1fb2b54dde03ea23436061da5128a300905de1e08a9b21976ca5dac0c00efb4505
-  data.tar.gz: 557fd9677bea9dd009648b8e9661239a4a787f89302b27415fe53693bf8bbd9f6fd4f58ab6d5933d4ea7ff2f82beffd5dd23de4236c8b94a45816d2002be4e34
+  metadata.gz: f28ab3cc789221ee988581e041f27b7fb34c8e7abb5b3e9444909ad2b00ac44fffa03b5a8f3150782a9f58ce902aa1dc0bf62fb1048ccecf12b39f01e0ad3efc
+  data.tar.gz: 0f5bfb7debcfb0784bac11903f94d97fd79e1ca774c6df66e50e723b09df751ab3313f6ac09624094ff2d7a188c5c57c94cd02023e984780ce372604831800da

data/bin/build_rbbt_provision_sh.rb

@@ -34,12 +34,12 @@ $ #{$0} [options]
 -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
 -dep--container_dependency* Use a different image in Dockerfile, Singularity and Virtualbox
 -dt--docker* Build docker image using the provided name
 -si--singularity* Build singularity image using the provided name
+-sis--singularity_size* Singularity image size (default 2024)
 -vb--virtualbox Build virtualbox image
 -df--docker_file* Use a Dockerfile different than the default
 -dv--docker_volumnes* List of volumes to set-up in Docker
@@ -59,10 +59,10 @@ 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
+#if options[:singularity]
+#  options[:skip_user_setup] = true
+#  options[:skip_bootstrap] = true
+#end
 
 USER = options[:user] || 'rbbt'
 SKIP_BASE_SYSTEM = options[:skip_base_system]
@@ -83,7 +83,6 @@ VARIABLES={
 
 VARIABLES[:BOOTSTRAP_WORKFLOWS] = "" if VARIABLES[:BOOTSTRAP_WORKFLOWS] == 'none'
 
-VARIABLES[:RBBT_NO_LOCKFILE_ID] = "true" if options[:concurrent]
 VARIABLES[:RBBT_SERVER] = options[:server] if options[:server]
 VARIABLES[:RBBT_FILE_SERVER] = options[:file_server] if options[:file_server]
 VARIABLES[:RBBT_WORKFLOW_SERVER] = options[:workflow_server] if options[:workflow_server]
@@ -330,9 +329,16 @@ From: #{container_dependency}
   cat > /tmp/rbbt_provision.sh <<"EOS"
   #{provision_script}
 EOS
-  bash /tmp/rbbt_provision.sh
+  bash -x /tmp/rbbt_provision.sh
   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'
+  bash -c '[ -d /software/rbbt ] || mkdir -p /software/rbbt'
+  bash -c '[ -d /home/#{USER}/.rbbt/var/ ] && mv /home/#{USER}/.rbbt/var/ /var/rbbt'
+  bash -c '[ -d /home/#{USER}/.rbbt/share/ ] && mv /home/#{USER}/.rbbt/share/ /usr/local/share/rbbt'
+  bash -c '[ -d /home/#{USER}/.rbbt/software/opt ] && mv /home/#{USER}/.rbbt/software/opt /software/rbbt/opt'
+  bash -c '[ -d /home/#{USER}/.rbbt/software/src ] && mv /home/#{USER}/.rbbt/software/src /software/rbbt/src'
+  bash -c '[ -d /home/#{USER}/.rbbt/software/scm ] && mv /home/#{USER}/.rbbt/software/scm /software/rbbt/scm'
 EOF
     FileUtils.mkdir_p dir
     Open.write(dir["singularity_bootstrap"].find, bootstrap_text)
@@ -340,7 +346,8 @@ EOF
 
     puts "RUN"
     puts "==="
-    cmd_create =  "singularity create -s 2048 #{singularity_image}"
+    singularity_size = options[:singularity_size]
+    cmd_create =  "singularity create -s #{singularity_size} #{singularity_image}"
     cmd_boot =  "singularity bootstrap #{singularity_image} '#{dir["singularity_bootstrap"]}'"
     puts cmd_create
     io = CMD.cmd(cmd_create, :pipe => true, :log => true)

data/share/provision_scripts/R_packages.sh

@@ -33,7 +33,7 @@ function R_CMD_install(){
 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_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
 

data/share/provision_scripts/bootstrap.sh

@@ -7,10 +7,11 @@ for workflow in $WORKFLOWS; do
     rbbt workflow install $workflow 
 done
 
-export RBBT_WORKFLOW_AUTOINSTALL
+export RBBT_WORKFLOW_AUTOINSTALL=true
 export RBBT_LOG
 
 for workflow in $BOOTSTRAP_WORKFLOWS; do
     echo "Bootstrapping $workflow on $BOOTSTRAP_CPUS CPUs"
-    rbbt workflow cmd $workflow bootstrap --cpus $BOOTSTRAP_CPUS
+    [ -d $HOME/.rbbt/tmp/ ] || mkdir -p $HOME/.rbbt/tmp/
+    rbbt workflow cmd $workflow bootstrap --cpus $BOOTSTRAP_CPUS &> $HOME/.rbbt/tmp/${workflow}.bootstrap.log
 done

data/share/provision_scripts/gem_setup.sh

@@ -5,23 +5,26 @@
 
 . /etc/rbbt_environment
 
+echo "* Updating RubyGem"
 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
+env REALLY_GEM_UPDATE_SYSTEM=true gem update --no-document --system
+
+echo "* Installing difficult gems: ZenTest, RubyInline, rsruby and rjb"
+gem install --force --no-document ZenTest
+gem install --force --no-document RubyInline
 
 # R (extra config in gem)
-. /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" \
+gem install --conservative --no-document 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-?-openjdk-*)
-gem install --conservative --force --no-ri --no-rdoc rjb
+gem install --conservative --force --no-document rjb
 
+echo "* Installing bulk gems and Rbbt"
 # Rbbt and some optional gems
-gem install --no-ri --no-rdoc --force \
+gem install --no-document --force \
     tokyocabinet \
     ruby-prof \
     rbbt-util rbbt-rest rbbt-dm rbbt-text rbbt-sources rbbt-phgx rbbt-GE \
@@ -31,8 +34,9 @@ gem install --no-ri --no-rdoc --force \
 
 # 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
+echo "* Installing our version of lockfile"
 wget http://github.com/mikisvaz/lockfile/raw/master/lockfile-2.1.5.gem -O /tmp/lockfile-2.1.5.gem
-gem install --no-ri --no-rdoc /tmp/lockfile-2.1.5.gem
+gem install --no-document /tmp/lockfile-2.1.5.gem
 
 # Extra things for web interface
-gem install --no-ri --no-rdoc bio-svgenes mimemagic
+gem install --no-document bio-svgenes mimemagic

data/share/provision_scripts/ubuntu_setup.sh

@@ -18,7 +18,8 @@ apt-get -y install \
   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 libreadline6-dev libyaml-dev libffi-dev
+  build-essential zlib1g-dev libssl-dev libreadline6-dev libyaml-dev libffi-dev \
+  libtbb-dev
 
 # For paradigm/libdai
 apt-get -y install \

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-image
 version: !ruby/object:Gem::Version
-  version: 0.1.27
+  version: 0.1.28
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-11-20 00:00:00.000000000 Z
+date: 2019-01-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util