rbbt-sources 2.0.1 → 2.0.2

data/lib/rbbt/sources/dbSNP.rb

@@ -9,7 +9,7 @@ module DbSNP
 
   URL = "ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/common_all.vcf.gz"
 
-  DbSNP.claim DbSNP.mutations, :proc do
+  DbSNP.claim DbSNP.mutations_ncbi, :proc do
     tsv = TSV.setup({}, :key_field => "RS ID", :fields => ["Genomic Mutation"], :type => :single)
     file = Open.open(URL, :nocache => true) 
     while line = file.gets do
@@ -28,8 +28,9 @@ module DbSNP
     tsv.to_s
   end
 
-  DbSNP.claim DbSNP.mutations_gatk, :proc do
+  DbSNP.claim DbSNP.mutations, :proc do
     ftp = Net::FTP.new('ftp.broadinstitute.org')
+    ftp.passive = true
     ftp.login('gsapubftp-anonymous', 'devnull@nomail.org')
     ftp.chdir('/bundle/2.3/hg19')
 

data/lib/rbbt/sources/ensembl_ftp.rb

@@ -23,6 +23,7 @@ module Ensembl
         release = Ensembl.releases[build]
         name = Organism.scientific_name(organism)
         ftp = Net::FTP.new(Ensembl::FTP::SERVER)
+        ftp.passive = true
         ftp.login
         ftp.chdir(File.join('pub', release, 'mysql'))
         file = ftp.list(name.downcase.gsub(" ",'_') + "_core_*").collect{|l| l.split(" ").last}.last

data/share/install/Organism/organism_helpers.rb

@@ -448,6 +448,7 @@ rule /^chromosome_.*/ do |t|
   release = Ensembl.releases[archive]
 
   ftp = Net::FTP.new("ftp.ensembl.org")
+  ftp.passive = true
   ftp.login
   ftp.chdir("pub/#{ release }/fasta/")
   ftp.chdir($scientific_name.downcase.sub(" ",'_'))

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 2.0.1
+  version: 2.0.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-01-07 00:00:00.000000000 Z
+date: 2013-01-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util