rbbt-image 0.1.14 → 0.1.16

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 333ed8343fe35a750c1b7c35245987b6c0ba2d27
-  data.tar.gz: 7d44691b0cf8ec502e38d4eaadf021521b3d0d52
+  metadata.gz: d807a8cb86f34b8de5d2da2ace7f1c22d2790d37
+  data.tar.gz: 88982fb26b4b6c3f4f285f420caf9565d3a7e7c8
 SHA512:
-  metadata.gz: 4ae0bb951df2edcd31c800470165f8df8205f5a33ff32fea2c27059c241077d17bc7cafb630650c7060edc3cace6d934ec08841d0fe57b64ef1a4ecd69d7a6fd
-  data.tar.gz: 112c761df3151f9482eaf4a77ea4561c21dee2805fbeeafac085c5a4ecb3e022b065e20445e8762f9c62363a5ab006ac8900bba07e9f3f7b50d6fae09e2819ef
+  metadata.gz: e58c39fe63206371bd873c3f9ffd1cabefd6b03a9d9173c9ffb6d1b65f55a16ed0d424f22c58e52ecb139cbb8684b4ae58ee3918db93c7e3d2d2e5697c25d430
+  data.tar.gz: 1832621e353e35c2e90c95ebfdab605800c16a1ee40365cdcc10f3641c5bde481f5847ca84822c881e6d5146809d4fa9c4746e2c3ae00852f0a30611cea49e53

data/bin/run_rbbt_docker.rb

@@ -27,7 +27,7 @@ Log.severity = options[:log].to_i if options[:log]
 module Log
   def self.log(msg,level)
     msg = "" if msg.nil?
-    puts msg
+    puts msg if level >= Log.severity
   end
 end
 
@@ -57,7 +57,19 @@ docker_args = args[1..-1] || []
 
 cmd_args.collect!{|a| '"' << a << '"' }
 
-infrastructure_file = Rbbt.etc.infrastructure[infrastructure_file+'.yaml'].find unless File.exists? infrastructure_file
+if not File.exists? infrastructure_file
+  name = infrastructure_file
+  infrastructure_file = Rbbt.root.etc.infrastructure[name+'.yaml'].find
+  if not File.exists? infrastructure_file
+    docker_dir = Path.setup("~/Docker").find
+    infrastructure_file = docker_dir.infrastructure[name + '.yaml'].find
+    raise "Not found: #{name}" unless infrastructure_file.exists?
+    directory = docker_dir[name].find
+    FileUtils.mkdir_p directory unless File.directory? directory
+    FileUtils.cd directory 
+  end
+end
+
 infrastructure = File.open(infrastructure_file){|io| YAML.load io }
 
 IndiferentHash.setup(infrastructure)
@@ -71,76 +83,4 @@ if options[:extra_mounts]
   end
 end
 
-
-
 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

@@ -31,7 +31,7 @@ module RbbtDocker
               dir = File.join(ssource, File.dirname(subdir))
               if not File.directory? dir
                 FileUtils.mkdir_p dir 
-                FileUtils.chmod 0777, dir
+                FileUtils.chmod_R 0777, File.join(ssource,subdir.split("/").first)
               end
             end
 
@@ -55,11 +55,11 @@ module RbbtDocker
     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 = "docker run #{name_conf} #{mount_conf} #{user_conf} #{docker_args.select{|arg| arg != '"--"'}*" "} #{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
+    Log.debug "Docker: \n\n" << cmd_str << "\n\n"
 
     exec(cmd_str) unless options[:dry_run]
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-image
 version: !ruby/object:Gem::Version
-  version: 0.1.14
+  version: 0.1.16
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-09-06 00:00:00.000000000 Z
+date: 2016-09-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util