rbbt-image 0.1.12 → 0.1.13

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: d78897244f68a6aa7c85ea793a621f981ef8a023
+  metadata.gz: 8123bdaafa5d69e42309938c73c1b4a5a0be39ef
+  data.tar.gz: aa239fa5e61c0545b9c13fe05e7f80aaaf24f807
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-  data.tar.gz: 2e2c08b1370befbb1fda04ac5c5d157753efc7ff4f56f502e2987276a7bad99e4652eb50857901e0962014c7433d19559ef2d44bf125bcbafdcc0f84f85bb49e
+  metadata.gz: 399d4d94aef56aad6dfb58b9e8a4683056495883cf1172b67b047649f181d44a673a162be65c027cb0bb96d3ff8d361baaad29b4e9748de48f2e922a4bbe0de7
+  data.tar.gz: afe7f9ce536106b0daa72f6f567dd66321c794fa741b5d9bba4fa8ca16b763cae9a7e8063f5fbfb5d53df437a2fe44d54b43e482621bc121ea20863155ca1ebf

data/bin/run_rbbt_docker.rb

@@ -2,6 +2,7 @@
 
 require 'rbbt-util'
 require 'rbbt/util/simpleopt'
+require 'rbbt/docker'
 
 $0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
 
@@ -11,13 +12,15 @@ Runs a docker image from an infrastructure definition file
 
 $ #{ $0 } [<options>] <infrastructure.yaml> <command> <args> [-- <extra docker options>]
 
-Infrastruture definition comes in YAML
+Infrastruture definition comes in YAML. 
 
 -h--help Print this help
 --log* Log level
-
+-d--dry_run Dry run
+-n--name* Container name
 EOF
 
+
 Log.severity = options[:log].to_i if options[:log]
 
 module Log
@@ -31,10 +34,15 @@ infrastructure_file, cmd, *args = ARGV
 
 
 if options[:help] or infrastructure_file.nil?
-  if defined? rbbt_usage
+  if false and defined? rbbt_usage
     rbbt_usage 
+    puts Log.color :magenta, "##Example infrastructure.yaml"
+    puts DATA.read
   else
-    puts SOPT.usage
+    puts SOPT.doc
+    puts
+    puts Log.color(:magenta, "##Example infrastructure.yaml")
+    puts DATA.read
   end
   exit 0
 end
@@ -47,42 +55,78 @@ end
 docker_args = args[1..-1] || []
 
 cmd_args.collect!{|a| '"' << a << '"' }
-docker_args.collect!{|a| '"' << a << '"' }
 
+infrastructure_file = Rbbt.etc.infrastructure[infrastructure_file+'.yaml'].find unless File.exists? infrastructure_file
 infrastructure = File.open(infrastructure_file){|io| YAML.load io }
-IndiferentHash.setup(infrastructure)
-
-image = infrastructure[:image]
-
-if user = infrastructure[:user]
-  user_conf = "-u #{user} -e HOME=/home/#{user}/ -e USER=#{user}"
-  user_conf = "-e HOME=/home/#{user}/ -e USER=#{user}"
-else
-  user_conf = ""
-end
-
-mount_conf = ""
-if infrastructure[:mounts]
-  infrastructure[:mounts].each do |target,source|
-    target = target.gsub("USER", user) if target.include? "USER"
-    if source.nil? or source.empty?
-      mount_conf << " -v #{target}"
-    else
-      FileUtils.mkdir_p source unless File.directory? source
-      #FileUtils.chmod 0777, source
-      mount_conf << " -v #{File.expand_path(source)}:#{target}"
-    end
-  end
-end
-
-if infrastructure[:workflow_autoinstall] and infrastructure[:workflow_autoinstall].to_s == 'true' and cmd =~ /rbbt/
-  cmd = "env RBBT_WORKFLOW_AUTOINSTALL=true " + cmd
-end
-
-umask = infrastructure[:umask] ? 'umask 000; ' : ''
-cmd_str = "docker run #{mount_conf} #{user_conf} #{docker_args*" "} #{image} /bin/bash --login -c '#{umask}#{cmd} #{cmd_args*" "}"
-cmd_str += " --log #{Log.severity} " if cmd =~  /\brbbt$/
-cmd_str += "'" 
 
-Log.info "Docker: \n" << cmd_str
-exec(cmd_str)
+RbbtDocker.load_infrastructure(infrastructure, cmd, cmd_args, docker_args, options)
+
+#docker_args.collect!{|a| '"' << a << '"' }
+#
+#infrastructure = File.open(infrastructure_file){|io| YAML.load io }
+#IndiferentHash.setup(infrastructure)
+#
+#image = infrastructure[:image]
+#
+#if user = infrastructure[:user]
+#  user_conf = "-u #{user} -e HOME=/home/#{user}/ -e USER=#{user}"
+#  user_conf = "-e HOME=/home/#{user}/ -e USER=#{user}"
+#else
+#  user_conf = ""
+#end
+#
+#mount_conf = ""
+#seen_mounts = {}
+#if infrastructure[:mounts]
+#  infrastructure[:mounts].each do |target,source|
+#    target = target.gsub("USER", user) if target.include? "USER"
+#    if source.nil? or source.empty?
+#      mount_conf << " -v #{target}"
+#    else
+#      matches = seen_mounts.select{|starget,ssource| Misc.path_relative_to starget, target }
+#
+#      if matches.any?
+#        matches.each do |starget,ssource|
+#          subdir = Misc.path_relative_to starget, target
+#          dir = File.join(ssource, File.dirname(subdir))
+#          if not File.directory? dir
+#            FileUtils.mkdir_p dir 
+#            FileUtils.chmod 0777, dir
+#          end
+#        end
+#
+#      end
+#
+#      if not File.directory? source
+#        FileUtils.mkdir_p source 
+#        FileUtils.chmod 0777, source
+#      end
+#      seen_mounts[target] = source
+#      mount_conf << " -v #{File.expand_path(source)}:#{target}"
+#    end
+#  end
+#end
+#
+#if infrastructure[:workflow_autoinstall] and infrastructure[:workflow_autoinstall].to_s == 'true' and cmd =~ /rbbt/
+#  cmd = "env RBBT_WORKFLOW_AUTOINSTALL=true " + cmd
+#end
+#
+#umask = infrastructure[:umask] ? 'umask 000; ' : ''
+#cmd_str = "docker run #{mount_conf} #{user_conf} #{docker_args*" "} #{image} /bin/bash --login -c '#{umask}#{cmd} #{cmd_args*" "}"
+#cmd_str += " --log #{Log.severity} " if cmd =~  /\brbbt$/
+#cmd_str += "'" 
+#
+#Log.info "Docker: \n" << cmd_str
+#exec(cmd_str) unless options[:dry_run]
+
+__END__
+image: mikisvaz/rbbt-basic
+user: rbbt
+umask: true
+workflow_autoinstall: true
+mounts:
+    /home/USER/.rbbt/: ./.rbbt
+    /home/USER/.rbbt/share/databases: /data3/rbbt/share/databases
+    /home/USER/.rbbt/share/organisms: /data3/rbbt/share/organisms
+    /home/USER/.rbbt/var/dbNSFP: /data3/rbbt/var/dbNSFP
+    /home/USER/.rbbt/var/DbSNP: /data3/rbbt/var/DbSNP

data/lib/rbbt/docker.rb

@@ -0,0 +1,66 @@
+module RbbtDocker
+  def self.load_infrastructure(infrastructure, cmd, cmd_args = [], docker_args = [], options = {})
+    cmd_args.collect!{|a| '"' << a << '"' }
+    docker_args.collect!{|a| '"' << a << '"' }
+
+
+    IndiferentHash.setup(infrastructure)
+
+    image = infrastructure[:image]
+
+    if user = infrastructure[:user]
+      user_conf = "-u #{user} -e HOME=/home/#{user}/ -e USER=#{user}"
+      user_conf = "-e HOME=/home/#{user}/ -e USER=#{user}"
+    else
+      user_conf = ""
+    end
+
+    mount_conf = ""
+    seen_mounts = {}
+    if infrastructure[:mounts]
+      infrastructure[:mounts].each do |target,source|
+        target = target.gsub("USER", user) if target.include? "USER"
+        if source.nil? or source.empty?
+          mount_conf << " --volumes-from #{target}"
+        else
+          matches = seen_mounts.select{|starget,ssource| Misc.path_relative_to starget, target }
+
+          if matches.any?
+            matches.each do |starget,ssource|
+              subdir = Misc.path_relative_to starget, target
+              dir = File.join(ssource, File.dirname(subdir))
+              if not File.directory? dir
+                FileUtils.mkdir_p dir 
+                FileUtils.chmod 0777, dir
+              end
+            end
+
+          end
+
+          if not File.directory? source
+            FileUtils.mkdir_p source 
+            FileUtils.chmod 0777, source
+          end
+          seen_mounts[target] = source
+          mount_conf << " -v #{File.expand_path(source)}:#{target}"
+        end
+      end
+    end
+
+    if infrastructure[:workflow_autoinstall] and infrastructure[:workflow_autoinstall].to_s == 'true' and cmd =~ /rbbt/
+      cmd = "env RBBT_WORKFLOW_AUTOINSTALL=true " + cmd
+    end
+
+    umask = infrastructure[:umask] ? 'umask 000; ' : ''
+    name_conf = options[:name]
+    name_conf = "--name " << name_conf if name_conf
+    name_conf ||= ""
+    cmd_str = "docker run #{name_conf} #{mount_conf} #{user_conf} #{docker_args*" "} #{image} /bin/bash --login -c '#{umask}#{cmd} #{cmd_args*" "}"
+    cmd_str += " --log #{Log.severity} " if cmd =~  /\brbbt$/
+    cmd_str += "'" 
+
+    Log.info "Docker: \n" << cmd_str
+
+    exec(cmd_str) unless options[:dry_run]
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-image
 version: !ruby/object:Gem::Version
-  version: 0.1.12
+  version: 0.1.13
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-06-20 00:00:00.000000000 Z
+date: 2016-09-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -38,7 +38,7 @@ files:
 - Vagrantfile
 - bin/build_rbbt_provision_sh.rb
 - bin/run_rbbt_docker.rb
-- lib/.keep
+- lib/rbbt/docker.rb
 - share/provision_scripts/bootstrap.sh
 - share/provision_scripts/gem_setup.sh
 - share/provision_scripts/ruby_setup.sh