rbbt-image 0.1.25 → 0.1.26

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 0537ca8e50ce927886c8a21afbe078059aa75c09
-  data.tar.gz: 97cd46d82ff5951459fa3e5a144b409ad7f8b5e8
+  metadata.gz: 5ede89962854413ae2565fde3f030fc21a95b396
+  data.tar.gz: db2c48b96ffe082dd5e2fb2142e938ac8b18fd08
 SHA512:
-  metadata.gz: 1418697fc48d5fc3a863801a56f3e40c8b711db2f914569d952e2c16efe276ecac4419e0cad85b91757ab2e08ec05a36acb5d397a1437e28e6338674e4141a2d
-  data.tar.gz: 8dadc56b89c8cb4de7f6720f35a4ee3fdfed10eef8fad619d4253e43ac6bc7b43ad39b108e253a88df070c9ea372124e9682dff9c10501b1d3c70ab9b2bc9ab9
+  metadata.gz: 7ba3e545a8ba417fe23e54209d54147b3436a902eaf1801437e434118726147941784cac9714e97d8db5784cc66880a86e593c94356d9ed043b0e39f04bb6e8c
+  data.tar.gz: f9d1dbc5c0a1e326f4b3d48fb2f52519f590b1384a8f7bfca08907fdfa20f3565db78f7cfe319049ac29e718897c0d9eda595a88cc1190e92aa6477e708846a4

data/bin/build_rbbt_provision_sh.rb

@@ -116,6 +116,7 @@ else
 end 
 }
 
+echo "[ -f ~/.rbbt/etc/environtment ] && . ~/.rbbt/etc/environtment" >> "/etc/rbbt_environment"
 echo "source /etc/rbbt_environment" >> /etc/profile
 
 #{
@@ -255,6 +256,13 @@ else
   provision_script += "echo SKIPPED\necho\n\n"
 end
 
+provision_script +=<<-EOF
+# HACKS
+# =====
+
+#{File.read(script_dir + 'hacks.sh')}
+EOF
+
 provision_script +=<<-EOF
 # CODA
 # ====
@@ -265,7 +273,7 @@ rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /usr/share/doc /usr/share/man /usr
 #{ "su -l -c 'rbbt system optimize /home/#{USER}/.rbbt ' #{USER}" if OPTIMIZE}
 
 echo
-echo "Installation done."
+echo -n "Installation done: "
 date
 
 EOF
@@ -320,10 +328,11 @@ 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
+  ln -s /etc/rbbt_environment /.singularity.d/env/99-rbbt_environment.sh
+  chmod +x /.singularity.d/env/99-rbbt_environment.sh
 EOF
     FileUtils.mkdir_p dir
     Open.write(dir["singularity_bootstrap"].find, bootstrap_text)

data/share/provision_scripts/R_packages.sh

@@ -15,6 +15,14 @@ function R_install_packages(){
   echo "install.packages(c($pkgs), repos='http://cran.us.r-project.org')" | R --vanilla
 }
 
+function R_biocLite(){
+  pkgs="'$1'"
+  shift
+  for p in $@; do
+    echo "source('http://bioconductor.org/biocLite.R'); biocLite('$p')" | R --vanilla
+  done
+}
+
 function R_CMD_install(){
   url=$1
   name=$2
@@ -28,12 +36,12 @@ R_CMD_install 'https://cran.r-project.org/src/contrib/Archive/car/car_2.0-22.tar
 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 NMF Cairo drc Rserve gridSVG ggthemes mclust randomForest viper
 R_install_packages pheatmap VennDiagram Hmisc pls
 
+R_biocLite limma viper
+
+R_install_packages pROC
+
 rm /tmp/R-pkg-*.tar.gz

data/share/provision_scripts/gem_setup.sh

@@ -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 prawn
+    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

data/share/provision_scripts/hacks.sh

@@ -0,0 +1,2 @@
+# For BNReduction work
+ln -s /bin/sed /usr/bin/sed

data/share/provision_scripts/ruby_setup.sh

@@ -13,7 +13,7 @@ make && make install
 
 unset _small_version
 
-echo 'export PATH="/usr/local/bin:$PATH" #Ruby2' >> /etc/rbbt_environment
+echo 'export PATH="/usr/local/bin:/opt/bin:$PATH" #Ruby2' >> /etc/rbbt_environment
 . /etc/rbbt_environment
 
 #\curl -sSL https://get.rvm.io | bash -s stable

data/share/provision_scripts/ubuntu_setup.sh

@@ -12,6 +12,7 @@ apt-get -y install cmake
 apt-get -y update
 apt-get -y update
 apt-get -y install \
+  vim \
   bison autoconf g++ libxslt1-dev make \
   zlib1g-dev libbz2-dev libreadline6 libreadline6-dev \
   wget curl git openssl libyaml-0-2 libyaml-dev \
@@ -19,13 +20,16 @@ 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
 
+# For paradigm/libdai
+apt-get -y install \
+  libgmp-dev libboost-dev libboost-program-options-dev libboost-test-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
 
 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 'export PATH="$R_HOME/bin/:$PATH" # Rserver' >> /etc/rbbt_environment
 
 . /etc/rbbt_environment
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-image
 version: !ruby/object:Gem::Version
-  version: 0.1.25
+  version: 0.1.26
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-08-05 00:00:00.000000000 Z
+date: 2018-08-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -44,6 +44,7 @@ files:
 - share/provision_scripts/R_setup.sh
 - share/provision_scripts/bootstrap.sh
 - share/provision_scripts/gem_setup.sh
+- share/provision_scripts/hacks.sh
 - share/provision_scripts/ruby_setup.sh
 - share/provision_scripts/tokyocabinet_setup.sh
 - share/provision_scripts/ubuntu_setup.sh