rbbt-image 0.1.30 → 0.1.31

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 8084bb0585881a3b624ecd23ab740c0233ccdab8
-  data.tar.gz: c23a657d12a08b4d301b6af434de0db25eae4597
+  metadata.gz: 2f5da609f8fa4562cab537c772c2d5ab54ad9ceb
+  data.tar.gz: 572c62f906ca0362b81dee105a78d656a565ab9b
 SHA512:
-  metadata.gz: 52e7e5366d7d6bdebd73e033d92fa218c136d8bad3d85884554e364ba79dfd6686519022180202624112f50ef33ee404501fa0ab55e8ffe2c977ff7449e91c62
-  data.tar.gz: 7e805772d6d113961bbb1eee05b33b7fa74334e01c192ca1aa00efe377dc5775f8143cb6cef662dfdacaa2805bf574f74fea1d15b02339a93d6d8d6052371188
+  metadata.gz: f6bb4c57a895feb6685d24d54d102acdbfda92587d97d151e82d4b1f6ddd9c032119092aa62f0a74fd098bf3beed1b1e0ee483d4d67abcf63ae53b9890328416
+  data.tar.gz: 0d595c94b87f1f460ffb56de9ec9dfc6ec1aa3a69a0a61f236ccd4d6f2eaa9f2d871463f7d2ea3e1b4389456337f5ce4433284effc1f5d88109f92930a25a92c

data/bin/build_rbbt_provision_sh.rb

@@ -28,6 +28,8 @@ $ #{$0} [options]
 -ss--skip_base_system Skip base system installation
 -st--skip_tokyocabinet Skip tokyocabinet setup installation
 -sr--skip_ruby Skip ruby setup installation
+-sp--skip_perl Skip perl setup installation
+-spy--skip_python Skip python setup installation
 -sg--skip_gem Skip ruby gem installation
 -sR--skip_R Skip R setup
 -su--skip_user_setup Skip user setup
@@ -68,6 +70,8 @@ USER = options[:user] || 'rbbt'
 SKIP_BASE_SYSTEM = options[:skip_base_system]
 SKIP_TOKYOCABINET= options[:skip_tokyocabinet]
 SKIP_RUBY = options[:skip_ruby]
+SKIP_PERL = options[:skip_perl]
+SKIP_PYTHON = options[:skip_python]
 R_CUSTOM = options[:R_custom]
 SKIP_R = options[:skip_R]
 SKIP_BOOT = options[:skip_bootstrap]
@@ -150,6 +154,7 @@ else
 end 
 }
 
+
 echo "3.1. Setting up gems"
 #{
 if not SKIP_GEM
@@ -159,6 +164,24 @@ else
 end 
 }
 
+echo "4 Setting up other stuff"
+echo "4.1 Setting up perl"
+#{
+if not SKIP_PERL
+  File.read(script_dir + 'perl_setup.sh') 
+else
+  "echo SKIPPED\necho"
+end 
+}
+
+echo "4.2 Setting up python"
+#{
+if not SKIP_PYTHON
+  File.read(script_dir + 'python_setup.sh') 
+else
+  "echo SKIPPED\necho"
+end 
+}
 EOF
 
 provision_script +=<<-EOF
@@ -346,7 +369,7 @@ EOF
 
     puts "RUN"
     puts "==="
-    singularity_size = options[:singularity_size] || 2048
+    singularity_size = options[:singularity_size] || 3072
     cmd_create =  "singularity create -s #{singularity_size} #{singularity_image}"
     cmd_boot =  "singularity bootstrap #{singularity_image} '#{dir["singularity_bootstrap"]}'"
     puts cmd_create

data/share/provision_scripts/perl_setup.sh

@@ -0,0 +1,2 @@
+[[ -f /usr/bin/gzip ]] || ln -s /bin/gzip /usr/bin/gzip # Fix for cpan
+cpan -i App::cpanminus

data/share/provision_scripts/python_setup.sh

@@ -0,0 +1,15 @@
+wget "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh" -O /tmp/miniconda.sh
+bash /tmp/miniconda.sh -b -p /opt/miniconda3
+
+[ -d /opt/bin/conda ] || mkdir -p /opt/bin/conda
+ln -s /opt/miniconda3/bin/conda /opt/bin/conda
+
+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
+
+source /etc/rbbt_environment

data/share/provision_scripts/ubuntu_setup.sh

@@ -5,9 +5,8 @@
 
 # Basic system requirements
 # -------------------------
+apt-get -y update
 apt-get -y install software-properties-common
-add-apt-repository ppa:george-edison55/cmake-3.x
-apt-get -y install cmake
 
 apt-get -y update
 apt-get -y update
@@ -19,12 +18,18 @@ apt-get -y install \
   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 \
+  python3 python \
+  tcsh gawk \
   libtbb-dev
 
+add-apt-repository ppa:george-edison55/cmake-3.x
+apt-get -y update
+apt-get -y update
+apt-get -y install cmake
+
 # For paradigm/libdai
 apt-get -y install \
-  libgmp-dev libboost-dev libboost-program-options-dev libboost-test-dev
+  libgmp-dev libboost-all-dev 
 
 # This link was broken for some reason
 rm /usr/lib/R/bin/Rserve

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-image
 version: !ruby/object:Gem::Version
-  version: 0.1.30
+  version: 0.1.31
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-01-24 00:00:00.000000000 Z
+date: 2019-02-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -45,6 +45,8 @@ files:
 - share/provision_scripts/bootstrap.sh
 - share/provision_scripts/gem_setup.sh
 - share/provision_scripts/hacks.sh
+- share/provision_scripts/perl_setup.sh
+- share/provision_scripts/python_setup.sh
 - share/provision_scripts/ruby_setup.sh
 - share/provision_scripts/tokyocabinet_setup.sh
 - share/provision_scripts/ubuntu_setup.sh