rbbt-image 0.1.7 → 0.1.10

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: ef8f85379b89c224a40cd3d62e4c380d26964fce
-  data.tar.gz: 6e9dadd53f2c2eb2c51111518b73611485d3b52e
+  metadata.gz: 4315b3197e42bc7bc251c929639ba3305a94b05e
+  data.tar.gz: 850d49ad2942e9fc5ca9d30a196145dffd12bcf5
 SHA512:
-  metadata.gz: 1101cc47a96e0f31159ee24af74e2673e92c893006a02ef36a4a99c3a100756b123dcde677d97044c7c1d2c04c99d1d07cbcfa212cc567f10f259a9db72fe4f6
-  data.tar.gz: 1b5878c1fcc75eb572d77fb778bf2385add507e16aeaf43d9a7b822582d6d41fdac1d30a8d841ffd1fef194028ae5dd9eabb573952705c94661c74cdc5204fc6
+  metadata.gz: 3b6b9dfc32521fc1c23074129d13d8f0b9e5c89c1d38440d24d01533d245439e50bc1adb0480fd1171e2d9593094abbbd418210a871c8e6141e37379d64e713a
+  data.tar.gz: ff3cee902de1d1296c991f67fef69c7447a0e8d970cadac8bb60f1c2c096e0a5d9e6dd48a913692fdc75c5ab05589bc9e1ba7f87ca44e6497a4e500c0dc859c6

data/share/provision_scripts/bootstrap.sh

@@ -0,0 +1,16 @@
+#!/bin/bash -x
+
+# USER RBBT BOOTSTRAP
+# ===================
+
+for workflow in $WORKFLOWS; do
+    rbbt workflow install $workflow 
+done
+
+export RBBT_WORKFLOW_AUTOINSTALL
+export RBBT_LOG
+
+for workflow in $BOOTSTRAP_WORKFLOWS; do
+    echo "Bootstrapping $workflow on $BOOTSTRAP_CPUS CPUs"
+    rbbt workflow cmd $workflow bootstrap --cpus $BOOTSTRAP_CPUS
+done

data/share/provision_scripts/gem_setup.sh

@@ -0,0 +1,30 @@
+#!/bin/bash -x
+
+# RUBY GEMS and RBBT
+# =================
+
+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
+
+# R (extra config in gem)
+gem install --conservative --no-ri --no-rdoc rsruby -- --with-R-dir=/usr/lib/R --with-R-include=/usr/share/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-7-openjdk-*)
+gem install --conservative --force --no-ri --no-rdoc rjb
+
+# Rbbt and some optional gems
+gem install --no-ri --no-rdoc --force \
+    tokyocabinet \
+    ruby-prof \
+    rbbt-util rbbt-rest rbbt-dm rbbt-text rbbt-sources rbbt-phgx rbbt-GE \
+    rserve-client \
+    uglifier therubyracer kramdown\
+    puma
+
+# 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
+gem install --no-ri --no-rdoc /tmp/lockfile-2.1.4.gem
+

data/share/provision_scripts/ruby_setup.sh

@@ -0,0 +1,15 @@
+#!/bin/bash -x
+
+# RUBY INSTALL
+# ============
+
+cd /tmp
+wget https://cache.ruby-lang.org/pub/ruby/2.3/ruby-2.3.0.tar.gz
+tar -xvzf ruby-2.3.0.tar.gz
+cd ruby-2.3.0/
+./configure --prefix=/usr/local
+make && make install
+
+grep "#Ruby2" /etc/profile || echo 'export PATH="/usr/local/bin:$PATH" #Ruby2' >> /etc/profile
+. /etc/profile
+

data/share/provision_scripts/ubuntu_setup.sh

@@ -0,0 +1,26 @@
+#!/bin/bash -x
+
+# INSTALL
+# =======
+
+# Basic system requirements
+# -------------------------
+apt-get -y update
+apt-get -y update
+apt-get -y install \
+  bison autoconf g++ libxslt1-dev make \
+  zlib1g-dev libbz2-dev libreadline6 libreadline6-dev \
+  wget curl git openssl libyaml-0-2 libyaml-dev \
+  ruby2.0 ruby-dev \
+  r-base-core r-base-dev r-cran-rserve \
+  openjdk-7-jdk \
+  libtokyocabinet-dev tokyocabinet-bin \
+  build-essential zlib1g-dev libssl-dev libreadline6-dev libyaml-dev libffi-dev
+
+
+grep R_HOME /etc/profile || echo "export R_HOME='/usr/lib/R' # For Ruby's RSRuby gem" >> /etc/profile
+. /etc/profile
+
+# 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

data/share/provision_scripts/user_setup.sh

@@ -0,0 +1,16 @@
+#!/bin/bash -x
+
+# USER RBBT CONFIG
+# ================
+
+# File servers: to speed up the production of some resources
+for resource in $REMOTE_RESOURCES; do
+    echo "Adding remote file server: $resource -- $RBBT_FILE_SERVER"
+    rbbt file_server add $resource $RBBT_FILE_SERVER
+done
+
+# Remote workflows: avoid costly cache generation
+for workflow in $REMOTE_WORKFLOWS; do
+    echo "Adding remote workflow: $workflow -- $RBBT_WORKFLOW_SERVER"
+    rbbt workflow remote add $workflow $RBBT_WORKFLOW_SERVER
+done

data/share/provision_scripts/variables.sh

@@ -0,0 +1,18 @@
+#!/bin/bash -x
+
+test -z ${RBBT_SERVER+x}           && RBBT_SERVER=http://rbbt.bioinfo.cnio.es/ 
+test -z ${RBBT_FILE_SERVER+x}      && RBBT_FILE_SERVER="$RBBT_SERVER"
+test -z ${RBBT_WORKFLOW_SERVER+x}  && RBBT_WORKFLOW_SERVER="$RBBT_SERVER"
+
+test -z ${REMOTE_RESOURCES+x}  && REMOTE_RESOURCES="Organism ICGC COSMIC KEGG InterPro"
+test -z ${REMOTE_WORFLOWS+x}   && REMOTE_WORFLOWS=""
+
+test -z ${RBBT_WORKFLOW_AUTOINSTALL+x}  && RBBT_WORKFLOW_AUTOINSTALL="true"
+
+test -z ${WORKFLOWS+x}  && WORKFLOWS=""
+
+test -z ${BOOTSTRAP_WORKFLOWS+x}  && BOOTSTRAP_WORKFLOWS=""
+test -z ${BOOTSTRAP_CPUS+x}       && BOOTSTRAP_CPUS="2"
+
+test -z ${RBBT_LOG+x}  && RBBT_LOG="LOW"
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-image
 version: !ruby/object:Gem::Version
-  version: 0.1.7
+  version: 0.1.10
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-02-04 00:00:00.000000000 Z
+date: 2016-05-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -37,6 +37,12 @@ files:
 - bin/build_rbbt_provision_sh.rb
 - bin/run_rbbt_docker.rb
 - lib/.keep
+- share/provision_scripts/bootstrap.sh
+- share/provision_scripts/gem_setup.sh
+- share/provision_scripts/ruby_setup.sh
+- share/provision_scripts/ubuntu_setup.sh
+- share/provision_scripts/user_setup.sh
+- share/provision_scripts/variables.sh
 homepage: http://github.com/mikisvaz/rbbt-image
 licenses:
 - MIT