aai 0.2.0 → 0.2.1

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 2bdc68dc8d289e3d9770373f856d9e05d6c1a0b0
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+  data.tar.gz: 74c4793c46883e92fab311837cf8b9ffd74b116d
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data/lib/aai.rb

@@ -48,12 +48,7 @@ module Aai
     end
 
     title = "Running blast jobs"
-    cmd = "parallel --link blastp -outfmt 6 " +
-          "-query {1} -db {2} " +
-          "-out {3} -evalue 1e-3 " +
-          "::: #{first_files.join " "} ::: " +
-          "#{second_files.join " "} ::: " +
-          "#{outf_names.join " "}"
+    cmd = %Q{parallel --xapply "blastp -outfmt 6 -query {1} -db {2} -out {3} -evalue 1e-3" ::: #{first_files.join " "} ::: #{second_files.join " "} ::: #{outf_names.join " "}}
 
     Process.run_and_time_it! title, cmd
 
@@ -70,9 +65,7 @@ module Aai
     outfiles = fnames.map { |fname| fname + suffix }
 
     title = "Making blast databases"
-    cmd = "parallel makeblastdb -in {} " +
-          "-out {}#{BLAST_DB_SUFFIX} -dbtype prot " +
-          "::: #{fnames.join " "}"
+    cmd = %Q{parallel "makeblastdb -in {} -out {}#{BLAST_DB_SUFFIX} -dbtype prot" ::: #{fnames.join " "}}
 
     Process.run_and_time_it! title, cmd
 

data/lib/aai/utils.rb

@@ -51,7 +51,8 @@ module Aai
       path = command? cmd
 
       AbortIf.abort_unless path,
-                           "MIssing #{cmd} command. Is it on your path?"
+                           "Missing #{cmd} command. " +
+                           "Is it executable and on your path?"
 
       path
     end

data/lib/aai/version.rb

@@ -1,5 +1,5 @@
 module Aai
-  VERSION = "0.2.0"
+  VERSION = "0.2.1"
   COPYRIGHT = "2017 Ryan Moore"
   CONTACT   = "moorer@udel.edu"
   WEBSITE   = "https://github.com/mooreryan/aai"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: aai
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.2.1
 platform: ruby
 authors:
 - Ryan Moore