crb-blast 0.4.2 → 0.4.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: fca3c14697b93c5e9448b78a2ede132d986fd53d
-  data.tar.gz: 943aa5b9c759f3ae2322cba50d161b3d6b11c8d6
+  metadata.gz: 8cddd4963085fc1c0eadbb17f900f146792770f4
+  data.tar.gz: 6f68c6fb69f679d93a99385d376615f11a8288d2
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+  metadata.gz: f5aa6f4dc288009229dd004f03b131bb6d1ef61fdd1a917f91f06676c50fdd9b9cf9707eb69aff35bd286b7e76e5f3a94e00a26b4c9ccbbc34c3dc17b97bd3fe
+  data.tar.gz: d4f63f98ca4c5dec3625894fd9a6439cc421c8e891e88366dbdb31e44d398fad4243106d4207da84a3f0d91ae7e8942d7113187708506d587b875c0e9fa6466f

data/crb-blast.gemspec

@@ -1,6 +1,6 @@
 Gem::Specification.new do |gem|
   gem.name        = 'crb-blast'
-  gem.version     = '0.4.2'
+  gem.version     = '0.4.3'
   gem.date        = '2014-07-23'
   gem.summary     = "Run conditional reciprocal best blast"
   gem.description = "See summary"
@@ -16,7 +16,7 @@ Gem::Specification.new do |gem|
   gem.add_dependency 'bio', '~> 1.4', '>= 1.4.3'
   gem.add_dependency 'which', '0.0.2'
   gem.add_dependency 'threach', '~> 0.2', '>= 0.2.0'
-  gem.add_dependency 'bindeps', '~> 0.0', '>= 0.0.7'
+  gem.add_dependency 'bindeps', '~> 0.1', '>= 0.1.3'
 
   gem.add_development_dependency 'rake', '~> 10.3', '>= 10.3.2'
   gem.add_development_dependency 'turn', '~> 0.9', '>= 0.9.7'

data/lib/crb-blast/crb-blast.rb

@@ -111,7 +111,10 @@ module CRB_Blast
         make_db = Cmd.new(make_query_db_cmd)
         make_db.run
         if !make_db.status.success?
-          raise RuntimeError.new("BLAST Error creating database")
+          msg = "BLAST Error creating database:\n" +
+                make_db.stdout + "\n" +
+                make_db.stderr
+          raise RuntimeError.new(msg)
         end
       end
 
@@ -316,8 +319,8 @@ module CRB_Blast
       output_files=[]
       pieces = [pieces, sequences].min
       pieces.times do |n|
-        outfile = "#{filename}_chunk_#{n}.fasta"
-        outfile = File.expand_path(outfile)
+        outfile = File.basename("#{filename}_chunk_#{n}.fasta")
+        outfile = "#{@working_dir}/#{outfile}"
         outputs[n] = File.open("#{outfile}", "w")
         output_files[n] = "#{outfile}"
       end
@@ -521,4 +524,4 @@ module CRB_Blast
     end
   end
 
-end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: crb-blast
 version: !ruby/object:Gem::Version
-  version: 0.4.2
+  version: 0.4.3
 platform: ruby
 authors:
 - Chris Boursnell
@@ -85,20 +85,20 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.0'
+        version: '0.1'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.0.7
+        version: 0.1.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.0'
+        version: '0.1'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.0.7
+        version: 0.1.3
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement