rbbt-sources 3.2.13 → 3.2.14

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 10addbc1c9530276a6af29fe2926ed8ac6eff0fb068f717c1092d31b7dac532e
-  data.tar.gz: b3e9c79df78aaf15976f19c8e151c712ea99c1edbc7fae49421e61aa4051b645
+  metadata.gz: 476a20bf7be9718acce0355dccc7f88105e168247348de1895491bbf7189b7d2
+  data.tar.gz: a434af060363f85fe565f9f394aa0a64acae7bf58bf98859159536c59be51a11
 SHA512:
-  metadata.gz: e4b950bff0261074c04e738f7d852ee713e58419358a7a0cfd79de1b6b5254c8a40f7df3107f8e964feca7ae83889efd90db9823d98f611b14426f8ee18208af
-  data.tar.gz: 8d8db4d53f2b14d7a64e206c6625544b0ee21033e06781b02587297fb96f25c54c0f52e16abacbb1b1e1c3a27bb27d7e5f13189df8e7c8f17c20f0485554cee1
+  metadata.gz: e9f09c7a4514edaf3aabd89a5980d6be18d4761d72676da8be74625617f330b36816f66054fc6af5913ed9d94f6427391dec951307be23a2846225e1c840a813
+  data.tar.gz: 4b07413c9c8e8c6dd64180a1cdbb86407f81b86db8b14c63ff330a17d766b5604014f34dd3346bc6062029dd3c1dd4c1a2bdcaabb3b8cfa96434ba0170da32d6

data/lib/rbbt/sources/organism.rb

@@ -72,10 +72,14 @@ module Organism
     Open.mkdir File.dirname(file) unless File.directory?(file)
     url = "http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver"
     CMD.cmd_log("wget '#{url}' -O '#{file}'")
-    CMD.cmd("chmod 755 '#{file}'")
+    CMD.cmd("chmod 0755 '#{file}'")
     nil
   end
 
+  CMD.tool :liftOver, Rbbt.software.opt.bin.liftOver
+
+  Rbbt.set_software_env
+
   def self.hg_build(organism)
     require 'rbbt/sources/ensembl_ftp'
     organism = organism.strip 
@@ -176,8 +180,7 @@ module Organism
 
           Open.write(map_file, Open.read(map_url))
           new_mutations = TmpFile.with_file do |target_bed|
-            FileUtils.chmod(755, Rbbt.software.opt.bin.liftOver.produce.find)
-            CMD.cmd("#{Rbbt.software.opt.bin.liftOver.find} '#{source_bed}' '#{map_file}' '#{target_bed}' '#{unmapped_file}'").read
+            CMD.cmd_log(:liftOver, "'#{source_bed}' '#{map_file}' '#{target_bed}' '#{unmapped_file}'")
             Open.read(target_bed) do |line|
               chr, position_alt, position, name = line.chomp.split("\t")
               chr.sub! /chr/, ''

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.2.13
+  version: 3.2.14
 platform: ruby
 authors:
 - Miguel Vazquez
@@ -178,24 +178,24 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.4.8
+rubygems_version: 3.3.26
 signing_key: 
 specification_version: 4
 summary: Data sources for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
+- test/rbbt/sources/test_HPRD.rb
+- test/rbbt/sources/test_biomart.rb
+- test/rbbt/sources/test_entrez.rb
 - test/rbbt/sources/test_go.rb
-- test/rbbt/sources/test_pubmed.rb
-- test/rbbt/sources/test_pina.rb
-- test/rbbt/sources/test_pharmagkb.rb
+- test/rbbt/sources/test_gscholar.rb
+- test/rbbt/sources/test_kegg.rb
+- test/rbbt/sources/test_matador.rb
 - test/rbbt/sources/test_organism.rb
-- test/rbbt/sources/test_synapse.rb
-- test/rbbt/sources/test_entrez.rb
+- test/rbbt/sources/test_pharmagkb.rb
+- test/rbbt/sources/test_pina.rb
+- test/rbbt/sources/test_pubmed.rb
 - test/rbbt/sources/test_stitch.rb
-- test/rbbt/sources/test_biomart.rb
-- test/rbbt/sources/test_HPRD.rb
 - test/rbbt/sources/test_string.rb
-- test/rbbt/sources/test_kegg.rb
+- test/rbbt/sources/test_synapse.rb
 - test/rbbt/sources/test_tfacts.rb
-- test/rbbt/sources/test_matador.rb
-- test/rbbt/sources/test_gscholar.rb
 - test/test_helper.rb