rbbt-util 5.0.0 → 5.0.1

data/README.rdoc

@@ -39,7 +39,28 @@
     mv tmp.bash_profile .bash_profile
     . .bash_profile
     
-3 - install gems rbbt-util rbbt-sources rbbt-text rbbt-phgx
+3.pre1 - If using ruby 1.9 install these gems from github so that some issues with 1.9 are fixed
+
+   :script
+
+   gem install specific_install
+   gem specific_install -l https://github.com/bensomers/png.git
+   gem specific_install -l https://github.com/felipec/soap4r.git
+   gem specific_install -l https://github.com/mikisvaz/tokyocabinet_19_fix.git
+
+3.pre2 - A couple of gems are better installed beforehand, since they require some configuration
+
+   :script
+
+   # RSRuby
+   R_HOME='full_path_to_R_dir' # Example in ubuntu
+   gem install rsruby -- --with-R-dir=/usr/lib/R/lib/ --with-R-include=/usr/share/R/include
+
+   # JRB
+   export JAVA_HOME="full_path_to_jdk"
+   gem install rjb
+
+3 - install gems rbbt-util rbbt-sources rbbt-text rbbt-phgx. 
 
     :script
     
@@ -75,6 +96,3 @@
     mkdir -p ~/git/workflows
     echo "~/git/workflows/" > ~/.rbbt/etc/workflow_dir
 
-6- - Place some other files
-
-    /home/mvazquezg/.rbbt/share/databases/InterPro/pfam_names

data/lib/rbbt/resource.rb

@@ -81,8 +81,13 @@ module Resource
           when :url
             Open.write(final_path, Open.open(content))
           when :proc
-            data = content.call
-            Open.write(final_path, data) 
+            data = case content.arity
+                   when 0
+                     content.call
+                   when 1
+                     content.call final_path
+                   end
+            Open.write(final_path, data) unless data.nil?
           when :rake
             run_rake(path, content, rake_dir)
           when :install

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.0.0
+  version: 5.0.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-12-21 00:00:00.000000000 Z
+date: 2013-01-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -215,34 +215,34 @@ files:
 - share/install/software/lib/install_helpers
 - share/lib/R/util.R
 - README.rdoc
-- test/test_helper.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_R.rb
-- test/rbbt/util/test_open.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/test_simpleopt.rb
-- test/rbbt/resource/test_path.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/test_fix_width_table.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_tsv.rb
-- test/rbbt/test_workflow.rb
 - test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_attach.rb
-- test/rbbt/tsv/test_filter.rb
 - test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_manipulate.rb
 - test/rbbt/tsv/test_util.rb
-- test/rbbt/workflow/test_soap.rb
+- test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_attach.rb
+- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/test_fix_width_table.rb
+- test/rbbt/test_workflow.rb
 - test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_task.rb
+- test/rbbt/workflow/test_soap.rb
+- test/rbbt/resource/test_path.rb
+- test/rbbt/test_tsv.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_annotations.rb
 - test/rbbt/test_persist.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/test_tmpfile.rb
+- test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/test_misc.rb
+- test/rbbt/util/test_open.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/test_chain_methods.rb
+- test/rbbt/util/test_R.rb
+- test/rbbt/util/test_simpleDSL.rb
 - test/test_rbbt.rb
+- test/test_helper.rb
 - bin/tsv.rb
 - bin/tchash.rb
 - bin/run_workflow.rb
@@ -275,31 +275,31 @@ signing_key:
 specification_version: 3
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/test_helper.rb
-- test/rbbt/util/test_tmpfile.rb
-- test/rbbt/util/test_filecache.rb
-- test/rbbt/util/test_misc.rb
-- test/rbbt/util/test_R.rb
-- test/rbbt/util/test_open.rb
-- test/rbbt/util/test_cmd.rb
-- test/rbbt/util/test_simpleDSL.rb
-- test/rbbt/util/test_chain_methods.rb
-- test/rbbt/util/test_excel2tsv.rb
-- test/rbbt/util/test_simpleopt.rb
-- test/rbbt/resource/test_path.rb
-- test/rbbt/test_annotations.rb
-- test/rbbt/test_fix_width_table.rb
-- test/rbbt/test_resource.rb
-- test/rbbt/test_tsv.rb
-- test/rbbt/test_workflow.rb
 - test/rbbt/tsv/test_accessor.rb
-- test/rbbt/tsv/test_attach.rb
-- test/rbbt/tsv/test_filter.rb
 - test/rbbt/tsv/test_index.rb
-- test/rbbt/tsv/test_manipulate.rb
 - test/rbbt/tsv/test_util.rb
-- test/rbbt/workflow/test_soap.rb
+- test/rbbt/tsv/test_filter.rb
+- test/rbbt/tsv/test_attach.rb
+- test/rbbt/tsv/test_manipulate.rb
+- test/rbbt/test_fix_width_table.rb
+- test/rbbt/test_workflow.rb
 - test/rbbt/workflow/test_step.rb
 - test/rbbt/workflow/test_task.rb
+- test/rbbt/workflow/test_soap.rb
+- test/rbbt/resource/test_path.rb
+- test/rbbt/test_tsv.rb
+- test/rbbt/test_resource.rb
+- test/rbbt/test_annotations.rb
 - test/rbbt/test_persist.rb
+- test/rbbt/util/test_filecache.rb
+- test/rbbt/util/test_tmpfile.rb
+- test/rbbt/util/test_excel2tsv.rb
+- test/rbbt/util/test_simpleopt.rb
+- test/rbbt/util/test_misc.rb
+- test/rbbt/util/test_open.rb
+- test/rbbt/util/test_cmd.rb
+- test/rbbt/util/test_chain_methods.rb
+- test/rbbt/util/test_R.rb
+- test/rbbt/util/test_simpleDSL.rb
 - test/test_rbbt.rb
+- test/test_helper.rb