rbbt-image 0.1.7 → 0.1.10
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- checksums.yaml +4 -4
- data/share/provision_scripts/bootstrap.sh +16 -0
- data/share/provision_scripts/gem_setup.sh +30 -0
- data/share/provision_scripts/ruby_setup.sh +15 -0
- data/share/provision_scripts/ubuntu_setup.sh +26 -0
- data/share/provision_scripts/user_setup.sh +16 -0
- data/share/provision_scripts/variables.sh +18 -0
- metadata +8 -2
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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-
metadata.gz:
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-
data.tar.gz:
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3
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metadata.gz: 4315b3197e42bc7bc251c929639ba3305a94b05e
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4
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data.tar.gz: 850d49ad2942e9fc5ca9d30a196145dffd12bcf5
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SHA512:
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6
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metadata.gz:
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7
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data.tar.gz:
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metadata.gz: 3b6b9dfc32521fc1c23074129d13d8f0b9e5c89c1d38440d24d01533d245439e50bc1adb0480fd1171e2d9593094abbbd418210a871c8e6141e37379d64e713a
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7
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data.tar.gz: ff3cee902de1d1296c991f67fef69c7447a0e8d970cadac8bb60f1c2c096e0a5d9e6dd48a913692fdc75c5ab05589bc9e1ba7f87ca44e6497a4e500c0dc859c6
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@@ -0,0 +1,16 @@
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1
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#!/bin/bash -x
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# USER RBBT BOOTSTRAP
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# ===================
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for workflow in $WORKFLOWS; do
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rbbt workflow install $workflow
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done
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export RBBT_WORKFLOW_AUTOINSTALL
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export RBBT_LOG
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for workflow in $BOOTSTRAP_WORKFLOWS; do
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echo "Bootstrapping $workflow on $BOOTSTRAP_CPUS CPUs"
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rbbt workflow cmd $workflow bootstrap --cpus $BOOTSTRAP_CPUS
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done
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@@ -0,0 +1,30 @@
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1
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#!/bin/bash -x
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# RUBY GEMS and RBBT
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# =================
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export REALLY_GEM_UPDATE_SYSTEM=true
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env REALLY_GEM_UPDATE_SYSTEM=true gem update --no-ri --no-rdoc --system
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gem install --force --no-ri --no-rdoc ZenTest
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gem install --force --no-ri --no-rdoc RubyInline
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# R (extra config in gem)
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gem install --conservative --no-ri --no-rdoc rsruby -- --with-R-dir=/usr/lib/R --with-R-include=/usr/share/R/include --with_cflags="-fPIC -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Wall -fno-strict-aliasing"
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# Java (extra config in gem)
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export JAVA_HOME=$(echo /usr/lib/jvm/java-7-openjdk-*)
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gem install --conservative --force --no-ri --no-rdoc rjb
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# Rbbt and some optional gems
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gem install --no-ri --no-rdoc --force \
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tokyocabinet \
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ruby-prof \
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rbbt-util rbbt-rest rbbt-dm rbbt-text rbbt-sources rbbt-phgx rbbt-GE \
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rserve-client \
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uglifier therubyracer kramdown\
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puma
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# Get good version of lockfile
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wget http://ubio.bioinfo.cnio.es/people/mvazquezg/lockfile-2.1.4.gem -O /tmp/lockfile-2.1.4.gem
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gem install --no-ri --no-rdoc /tmp/lockfile-2.1.4.gem
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@@ -0,0 +1,15 @@
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1
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#!/bin/bash -x
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# RUBY INSTALL
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# ============
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cd /tmp
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7
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wget https://cache.ruby-lang.org/pub/ruby/2.3/ruby-2.3.0.tar.gz
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8
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tar -xvzf ruby-2.3.0.tar.gz
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cd ruby-2.3.0/
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./configure --prefix=/usr/local
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make && make install
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grep "#Ruby2" /etc/profile || echo 'export PATH="/usr/local/bin:$PATH" #Ruby2' >> /etc/profile
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. /etc/profile
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@@ -0,0 +1,26 @@
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1
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#!/bin/bash -x
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# INSTALL
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# =======
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# Basic system requirements
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# -------------------------
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8
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apt-get -y update
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apt-get -y update
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apt-get -y install \
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bison autoconf g++ libxslt1-dev make \
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zlib1g-dev libbz2-dev libreadline6 libreadline6-dev \
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wget curl git openssl libyaml-0-2 libyaml-dev \
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ruby2.0 ruby-dev \
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r-base-core r-base-dev r-cran-rserve \
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openjdk-7-jdk \
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libtokyocabinet-dev tokyocabinet-bin \
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build-essential zlib1g-dev libssl-dev libreadline6-dev libyaml-dev libffi-dev
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grep R_HOME /etc/profile || echo "export R_HOME='/usr/lib/R' # For Ruby's RSRuby gem" >> /etc/profile
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. /etc/profile
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# This link was broken for some reason
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rm /usr/lib/R/bin/Rserve
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ln -s /usr/lib/R/site-library/Rserve/libs/Rserve /usr/lib/R/bin/Rserve
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@@ -0,0 +1,16 @@
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#!/bin/bash -x
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# USER RBBT CONFIG
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# ================
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# File servers: to speed up the production of some resources
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for resource in $REMOTE_RESOURCES; do
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echo "Adding remote file server: $resource -- $RBBT_FILE_SERVER"
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rbbt file_server add $resource $RBBT_FILE_SERVER
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done
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11
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12
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# Remote workflows: avoid costly cache generation
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for workflow in $REMOTE_WORKFLOWS; do
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echo "Adding remote workflow: $workflow -- $RBBT_WORKFLOW_SERVER"
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rbbt workflow remote add $workflow $RBBT_WORKFLOW_SERVER
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done
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@@ -0,0 +1,18 @@
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1
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#!/bin/bash -x
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2
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3
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test -z ${RBBT_SERVER+x} && RBBT_SERVER=http://rbbt.bioinfo.cnio.es/
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4
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test -z ${RBBT_FILE_SERVER+x} && RBBT_FILE_SERVER="$RBBT_SERVER"
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test -z ${RBBT_WORKFLOW_SERVER+x} && RBBT_WORKFLOW_SERVER="$RBBT_SERVER"
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test -z ${REMOTE_RESOURCES+x} && REMOTE_RESOURCES="Organism ICGC COSMIC KEGG InterPro"
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test -z ${REMOTE_WORFLOWS+x} && REMOTE_WORFLOWS=""
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test -z ${RBBT_WORKFLOW_AUTOINSTALL+x} && RBBT_WORKFLOW_AUTOINSTALL="true"
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test -z ${WORKFLOWS+x} && WORKFLOWS=""
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test -z ${BOOTSTRAP_WORKFLOWS+x} && BOOTSTRAP_WORKFLOWS=""
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test -z ${BOOTSTRAP_CPUS+x} && BOOTSTRAP_CPUS="2"
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test -z ${RBBT_LOG+x} && RBBT_LOG="LOW"
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metadata
CHANGED
@@ -1,14 +1,14 @@
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1
1
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--- !ruby/object:Gem::Specification
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2
2
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name: rbbt-image
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version: !ruby/object:Gem::Version
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-
version: 0.1.
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version: 0.1.10
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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: 2016-
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date: 2016-05-19 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
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@@ -37,6 +37,12 @@ files:
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- bin/build_rbbt_provision_sh.rb
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- bin/run_rbbt_docker.rb
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- lib/.keep
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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/ruby_setup.sh
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- share/provision_scripts/ubuntu_setup.sh
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- share/provision_scripts/user_setup.sh
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- share/provision_scripts/variables.sh
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homepage: http://github.com/mikisvaz/rbbt-image
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licenses:
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- MIT
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