rbbt-image 0.1.30 → 0.1.31

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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  SHA1:
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- data.tar.gz: c23a657d12a08b4d301b6af434de0db25eae4597
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+ data.tar.gz: 0d595c94b87f1f460ffb56de9ec9dfc6ec1aa3a69a0a61f236ccd4d6f2eaa9f2d871463f7d2ea3e1b4389456337f5ce4433284effc1f5d88109f92930a25a92c
@@ -28,6 +28,8 @@ $ #{$0} [options]
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  -ss--skip_base_system Skip base system installation
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  -st--skip_tokyocabinet Skip tokyocabinet setup installation
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  -sr--skip_ruby Skip ruby setup installation
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+ -sp--skip_perl Skip perl setup installation
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+ -spy--skip_python Skip python setup installation
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  -sg--skip_gem Skip ruby gem installation
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  -sR--skip_R Skip R setup
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  -su--skip_user_setup Skip user setup
@@ -68,6 +70,8 @@ USER = options[:user] || 'rbbt'
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  SKIP_BASE_SYSTEM = options[:skip_base_system]
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  SKIP_TOKYOCABINET= options[:skip_tokyocabinet]
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  SKIP_RUBY = options[:skip_ruby]
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+ SKIP_PERL = options[:skip_perl]
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+ SKIP_PYTHON = options[:skip_python]
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  R_CUSTOM = options[:R_custom]
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  SKIP_R = options[:skip_R]
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  SKIP_BOOT = options[:skip_bootstrap]
@@ -150,6 +154,7 @@ else
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  end
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  }
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+
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  echo "3.1. Setting up gems"
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  #{
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  if not SKIP_GEM
@@ -159,6 +164,24 @@ else
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  end
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  }
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+ echo "4 Setting up other stuff"
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+ echo "4.1 Setting up perl"
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+ #{
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+ if not SKIP_PERL
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+ File.read(script_dir + 'perl_setup.sh')
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+ else
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+ "echo SKIPPED\necho"
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+ end
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+ }
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+
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+ echo "4.2 Setting up python"
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+ #{
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+ if not SKIP_PYTHON
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+ File.read(script_dir + 'python_setup.sh')
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+ else
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+ "echo SKIPPED\necho"
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+ end
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+ }
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  EOF
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  provision_script +=<<-EOF
@@ -346,7 +369,7 @@ EOF
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  puts "RUN"
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  puts "==="
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- singularity_size = options[:singularity_size] || 2048
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+ singularity_size = options[:singularity_size] || 3072
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  cmd_create = "singularity create -s #{singularity_size} #{singularity_image}"
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  cmd_boot = "singularity bootstrap #{singularity_image} '#{dir["singularity_bootstrap"]}'"
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  puts cmd_create
@@ -0,0 +1,2 @@
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+ [[ -f /usr/bin/gzip ]] || ln -s /bin/gzip /usr/bin/gzip # Fix for cpan
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+ cpan -i App::cpanminus
@@ -0,0 +1,15 @@
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+ wget "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" -O /tmp/miniconda.sh
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+ bash /tmp/miniconda.sh -b -p /opt/miniconda3
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+
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+ [ -d /opt/bin/conda ] || mkdir -p /opt/bin/conda
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+ ln -s /opt/miniconda3/bin/conda /opt/bin/conda
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+
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+ conda create --yes -n python3 python=3.6.1 pip
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+ rm -Rf /opt/miniconda3/pkgs
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+ conda create --yes -n python2 python=2.7 pip
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+ rm -Rf /opt/miniconda3/pkgs
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+
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+ echo "# Python conda " >> /etc/rbbt_environment
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+ echo 'export PATH="/opt/bin/:/opt/miniconda3/envs/python3/bin/:$PATH"' >> /etc/rbbt_environment
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+
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+ source /etc/rbbt_environment
@@ -5,9 +5,8 @@
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  # Basic system requirements
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  # -------------------------
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+ apt-get -y update
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  apt-get -y install software-properties-common
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- add-apt-repository ppa:george-edison55/cmake-3.x
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- apt-get -y install cmake
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  apt-get -y update
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  apt-get -y update
@@ -19,12 +18,18 @@ apt-get -y install \
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  openjdk-8-jdk \
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  libcairo2 libcairo2-dev r-base-core r-base-dev r-cran-rserve liblzma5 liblzma-dev libcurl4-openssl-dev \
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  build-essential zlib1g-dev libssl-dev libyaml-dev libffi-dev \
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- python3 \
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+ python3 python \
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+ tcsh gawk \
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  libtbb-dev
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+ add-apt-repository ppa:george-edison55/cmake-3.x
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+ apt-get -y update
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+ apt-get -y update
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+ apt-get -y install cmake
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+
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  # For paradigm/libdai
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  apt-get -y install \
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- libgmp-dev libboost-dev libboost-program-options-dev libboost-test-dev
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+ libgmp-dev libboost-all-dev
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  # This link was broken for some reason
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  rm /usr/lib/R/bin/Rserve
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: rbbt-image
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  version: !ruby/object:Gem::Version
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- version: 0.1.30
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+ version: 0.1.31
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  platform: ruby
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  authors:
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  - Miguel Vazquez
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2019-01-24 00:00:00.000000000 Z
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+ date: 2019-02-04 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rbbt-util
@@ -45,6 +45,8 @@ files:
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  - share/provision_scripts/bootstrap.sh
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  - share/provision_scripts/gem_setup.sh
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  - share/provision_scripts/hacks.sh
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+ - share/provision_scripts/perl_setup.sh
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+ - share/provision_scripts/python_setup.sh
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  - share/provision_scripts/ruby_setup.sh
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  - share/provision_scripts/tokyocabinet_setup.sh
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  - share/provision_scripts/ubuntu_setup.sh