cagnut_core 0.3.1 → 0.3.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: a3043c0169386288bb33ba28308bc79a662bfb06
-  data.tar.gz: d53e358ea09299895646b483dc43507545ac94a9
+  metadata.gz: 45208b3f586da65477c5b699d8626bce76ecc66d
+  data.tar.gz: cfc256daa53bc7daaa98031c49296c0164772857
 SHA512:
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+  metadata.gz: e9c058af090d0e6d622524c239d81f8cb3b2ff3739a7aa52ab58e0c92d0924761a1d72ab1d0ee72a65d1b79adda86882775ebd01655f5abc2627feb4c336526c
+  data.tar.gz: 2f1001b6c10b2089d159c8686ce63cb3e705a6cbc9edb0dc4560681847572f84ba6915bcbb5840d5475f701eda546a9bfbbbd66b03fa2a2164ef650347d508f9

data/lib/cagnut/cli/new_project.rb

@@ -25,6 +25,7 @@ module Cagnut
     private
 
     def new_project name, options
+      check_pipeline options[:pipelines]
       empty_directory name
       copy_file 'Gemfile', "#{name}/Gemfile"
       inside name, verbose: true do
@@ -37,6 +38,11 @@ module Cagnut
       load_bundle_env name
       after_new_project name
       generate_pipeline_tools_config name, options[:pipelines], options[:cluster]
+      append_pipeline_dependency_gems_to_gemfile name, options[:pipelines]
+    end
+
+    def check_pipeline pipelines
+      abort('Please select at least one pipeline.') if pipelines.blank?
     end
 
     def add_queue_setting name, pipeline
@@ -55,6 +61,17 @@ module Cagnut
       end
     end
 
+    def append_pipeline_dependency_gems_to_gemfile folder, pipelines
+      return if pipelines.blank?
+      inside folder, verbose: true do
+        pipelines.each do |pipeline_name|
+          gems = send "#{pipeline_name}_pipeline_dependency_gems"
+          gems.each { |gem_name| append_to_file 'Gemfile', "gem #{gem_name}\n" }
+        end
+        bundle 'update'
+      end
+    end
+
     def generate_pipeline_tools_config name, pipelines, cluster=nil
       return if pipelines.blank?
       pipelines.each do |pipeline_name|

data/lib/cagnut/job_manage.rb

@@ -23,12 +23,11 @@ module Cagnut
     end
 
     def full_command job_script, job_name, opts
-      super if defined?(super)
-      return unless local_run?
-      command = local job_script
+      return super if defined?(super) && !run_local?
+      local job_script
     end
 
-    def local_run?
+    def run_local?
       cluster.blank? || cluster['system'] == 'Local'
     end
 
@@ -50,13 +49,13 @@ module Cagnut
     end
 
     def run_local
-      return unless local_run?
+      return unless run_local?
       %(& echo $! >> #{jobs_dir}/submit_job_#{sample_name}.ids
         wait $!)
     end
 
     def wait_local
-      return unless local_run?
+      return unless run_local?
       'wait $!'
     end
   end

data/lib/cagnut/version.rb

@@ -1,3 +1,3 @@
 module CagnutCore
-  VERSION = "0.3.1"
+  VERSION = "0.3.2"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: cagnut_core
 version: !ruby/object:Gem::Version
-  version: 0.3.1
+  version: 0.3.2
 platform: ruby
 authors:
 - Shi-Gang Wang
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2016-11-07 00:00:00.000000000 Z
+date: 2016-11-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activesupport