bio-ucsc-api 0.6.3 → 0.6.4
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- checksums.yaml +4 -4
- data/Gemfile +6 -9
- data/Gemfile.lock +27 -34
- data/README.md +4 -3
- data/VERSION +1 -1
- data/bio-ucsc-api.gemspec +49 -49
- data/lib/bio-ucsc.rb +2 -4
- data/lib/bio-ucsc/ailmel1.rb +4 -4
- data/lib/bio-ucsc/anocar2.rb +4 -4
- data/lib/bio-ucsc/anogam1.rb +4 -4
- data/lib/bio-ucsc/apimel2.rb +4 -4
- data/lib/bio-ucsc/aplcal1.rb +4 -4
- data/lib/bio-ucsc/bostau4.rb +4 -4
- data/lib/bio-ucsc/braflo1.rb +4 -4
- data/lib/bio-ucsc/caejap1.rb +4 -4
- data/lib/bio-ucsc/caepb2.rb +4 -4
- data/lib/bio-ucsc/caerem3.rb +4 -4
- data/lib/bio-ucsc/caljac3.rb +4 -4
- data/lib/bio-ucsc/canfam2.rb +4 -4
- data/lib/bio-ucsc/cavpor3.rb +4 -4
- data/lib/bio-ucsc/cb3.rb +4 -4
- data/lib/bio-ucsc/ce6.rb +4 -4
- data/lib/bio-ucsc/ci2.rb +4 -4
- data/lib/bio-ucsc/danrer7.rb +4 -4
- data/lib/bio-ucsc/dm3.rb +4 -4
- data/lib/bio-ucsc/dp3.rb +4 -4
- data/lib/bio-ucsc/droana2.rb +4 -4
- data/lib/bio-ucsc/droere1.rb +4 -4
- data/lib/bio-ucsc/drogri1.rb +4 -4
- data/lib/bio-ucsc/dromoj2.rb +4 -4
- data/lib/bio-ucsc/droper1.rb +4 -4
- data/lib/bio-ucsc/drosec1.rb +4 -4
- data/lib/bio-ucsc/drosim1.rb +4 -4
- data/lib/bio-ucsc/drovir2.rb +4 -4
- data/lib/bio-ucsc/droyak2.rb +4 -4
- data/lib/bio-ucsc/equcab2.rb +4 -4
- data/lib/bio-ucsc/felcat4.rb +4 -4
- data/lib/bio-ucsc/fr2.rb +4 -4
- data/lib/bio-ucsc/galgal4.rb +4 -4
- data/lib/bio-ucsc/gasacu1.rb +4 -4
- data/lib/bio-ucsc/go.rb +4 -4
- data/lib/bio-ucsc/hg18.rb +4 -4
- data/lib/bio-ucsc/hg19.rb +4 -4
- data/lib/bio-ucsc/hg38.rb +3 -3
- data/lib/bio-ucsc/hgfixed.rb +4 -4
- data/lib/bio-ucsc/loxafr3.rb +4 -4
- data/lib/bio-ucsc/mm10.rb +3 -3
- data/lib/bio-ucsc/mm9.rb +4 -4
- data/lib/bio-ucsc/mondom5.rb +4 -4
- data/lib/bio-ucsc/ornana1.rb +4 -4
- data/lib/bio-ucsc/orycun2.rb +4 -4
- data/lib/bio-ucsc/orylat2.rb +4 -4
- data/lib/bio-ucsc/oviari1.rb +4 -4
- data/lib/bio-ucsc/pantro3.rb +4 -4
- data/lib/bio-ucsc/petmar1.rb +4 -4
- data/lib/bio-ucsc/ponabe2.rb +4 -4
- data/lib/bio-ucsc/pripac1.rb +4 -4
- data/lib/bio-ucsc/proteome.rb +4 -4
- data/lib/bio-ucsc/rhemac2.rb +4 -4
- data/lib/bio-ucsc/rn4.rb +4 -4
- data/lib/bio-ucsc/rn5.rb +4 -4
- data/lib/bio-ucsc/saccer2.rb +4 -4
- data/lib/bio-ucsc/strpur2.rb +4 -4
- data/lib/bio-ucsc/susscr2.rb +4 -4
- data/lib/bio-ucsc/taegut1.rb +4 -4
- data/lib/bio-ucsc/tetnig2.rb +4 -4
- data/lib/bio-ucsc/uniprot.rb +4 -4
- data/lib/bio-ucsc/visigene.rb +4 -4
- data/lib/bio-ucsc/xentro2.rb +4 -4
- metadata +16 -16
data/lib/bio-ucsc/rn4.rb
CHANGED
@@ -1,9 +1,9 @@
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1
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#
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2
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# = AUTOMATIC Table Definition of the Rat Nov. 2004 (Baylor 3.4/rn4) assembly
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-
# Copyright:: Copyright (C) 2011
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3
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+
# Copyright:: Copyright (C) 2011-2017
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4
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# MISHIMA, Hiroyuki
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
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-
# License:: The
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6
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+
# License:: The MIT licence
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#
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require "#{::File.dirname(__FILE__)}/table_class_detector"
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@@ -33,7 +33,7 @@ chrX)
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include SafeAttributes
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self.inheritance_column = 'dummy_not_to_use'
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-
@@db_adapter ||= '
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+
@@db_adapter ||= 'mysql2'
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
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@@db_username ||= 'genome'
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@@db_password ||= ''
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@@ -44,7 +44,7 @@ chrX)
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self.abstract_class = true
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def self.default
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-
@@db_adapter = '
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+
@@db_adapter = 'mysql2'
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@@db_host = 'genome-mysql.cse.ucsc.edu'
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@@db_username = 'genome'
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@@db_password = ''
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data/lib/bio-ucsc/rn5.rb
CHANGED
@@ -1,9 +1,9 @@
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1
1
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#
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2
2
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# = AUTOMATIC Table Definition of the Rat Rn5 assembly
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-
# Copyright:: Copyright (C) 2011
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+
# Copyright:: Copyright (C) 2011-2017
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4
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# MISHIMA, Hiroyuki
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
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-
# License:: The
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+
# License:: The MIT licence
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#
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require "#{::File.dirname(__FILE__)}/table_class_detector"
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@@ -33,7 +33,7 @@ chrX)
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include SafeAttributes
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self.inheritance_column = 'dummy_not_to_use'
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-
@@db_adapter ||= '
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+
@@db_adapter ||= 'mysql2'
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
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@@db_username ||= 'genome'
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@@db_password ||= ''
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@@ -44,7 +44,7 @@ chrX)
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self.abstract_class = true
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def self.default
|
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-
@@db_adapter = '
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+
@@db_adapter = 'mysql2'
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@@db_host = 'genome-mysql.cse.ucsc.edu'
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@@db_username = 'genome'
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@@db_password = ''
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data/lib/bio-ucsc/saccer2.rb
CHANGED
@@ -1,9 +1,9 @@
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#
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# = AUTOMATIC Table Definition of the S. cerevisiae June 2008 (SGD/sacCer2) assembly
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-
# Copyright:: Copyright (C) 2011
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+
# Copyright:: Copyright (C) 2011-2017
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# MISHIMA, Hiroyuki
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
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-
# License:: The
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+
# License:: The MIT licence
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#
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require "#{::File.dirname(__FILE__)}/table_class_detector"
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@@ -32,7 +32,7 @@ chrXI chrXII chrXIII chrXIV chrXV chrXVI chrM 2micron)
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include SafeAttributes
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self.inheritance_column = 'dummy_not_to_use'
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-
@@db_adapter ||= '
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+
@@db_adapter ||= 'mysql2'
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
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@@db_username ||= 'genome'
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@@db_password ||= ''
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@@ -43,7 +43,7 @@ chrXI chrXII chrXIII chrXIV chrXV chrXVI chrM 2micron)
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self.abstract_class = true
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def self.default
|
46
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-
@@db_adapter = '
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+
@@db_adapter = 'mysql2'
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@@db_host = 'genome-mysql.cse.ucsc.edu'
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@@db_username = 'genome'
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@@db_password = ''
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data/lib/bio-ucsc/strpur2.rb
CHANGED
@@ -1,9 +1,9 @@
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1
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#
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2
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# = AUTOMATIC Table Definition of the S. purpuratus Sep. 2006 (Baylor 2.1/strPur2) assembly
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-
# Copyright:: Copyright (C) 2011
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+
# Copyright:: Copyright (C) 2011-2017
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# MISHIMA, Hiroyuki
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
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-
# License:: The
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+
# License:: The MIT licence
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#
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require "#{::File.dirname(__FILE__)}/table_class_detector"
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@@ -31,7 +31,7 @@ module Bio
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include SafeAttributes
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self.inheritance_column = 'dummy_not_to_use'
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|
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-
@@db_adapter ||= '
|
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+
@@db_adapter ||= 'mysql2'
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
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@@db_username ||= 'genome'
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@@db_password ||= ''
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@@ -42,7 +42,7 @@ module Bio
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self.abstract_class = true
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def self.default
|
45
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-
@@db_adapter = '
|
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+
@@db_adapter = 'mysql2'
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@@db_host = 'genome-mysql.cse.ucsc.edu'
|
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@@db_username = 'genome'
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@@db_password = ''
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data/lib/bio-ucsc/susscr2.rb
CHANGED
@@ -1,9 +1,9 @@
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1
1
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#
|
2
2
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# = AUTOMATIC Table Definition of the Dog May 2005 (Broad/canFam2) assembly
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-
# Copyright:: Copyright (C) 2011
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3
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+
# Copyright:: Copyright (C) 2011-2017
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# MISHIMA, Hiroyuki
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
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-
# License:: The
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6
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+
# License:: The MIT licence
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#
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8
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require "#{::File.dirname(__FILE__)}/table_class_detector"
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@@ -32,7 +32,7 @@ Chr10 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 ChrX)
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include SafeAttributes
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self.inheritance_column = 'dummy_not_to_use'
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|
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-
@@db_adapter ||= '
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+
@@db_adapter ||= 'mysql2'
|
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
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@@db_username ||= 'genome'
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@@db_password ||= ''
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@@ -43,7 +43,7 @@ Chr10 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 ChrX)
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self.abstract_class = true
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def self.default
|
46
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-
@@db_adapter = '
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+
@@db_adapter = 'mysql2'
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@@db_host = 'genome-mysql.cse.ucsc.edu'
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@@db_username = 'genome'
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@@db_password = ''
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data/lib/bio-ucsc/taegut1.rb
CHANGED
@@ -1,9 +1,9 @@
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1
1
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#
|
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# = AUTOMATIC Table Definition of the Zebra finch Jul. 2008 (WUGSC 3.2.4/taeGut1) assembly
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-
# Copyright:: Copyright (C)
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+
# Copyright:: Copyright (C) 2011-2017
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# MISHIMA, Hiroyuki
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
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-
# License:: The
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+
# License:: The MIT licence
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#
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require "#{::File.dirname(__FILE__)}/table_class_detector"
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@@ -34,7 +34,7 @@ chr21 chr22 chr23 chr24 chr25 chr26 chr27 chr28 chrZ chrM)
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include SafeAttributes
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self.inheritance_column = 'dummy_not_to_use'
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-
@@db_adapter ||= '
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+
@@db_adapter ||= 'mysql2'
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
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@@db_username ||= 'genome'
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@@db_password ||= ''
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@@ -45,7 +45,7 @@ chr21 chr22 chr23 chr24 chr25 chr26 chr27 chr28 chrZ chrM)
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self.abstract_class = true
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def self.default
|
48
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-
@@db_adapter = '
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+
@@db_adapter = 'mysql2'
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@@db_host = 'genome-mysql.cse.ucsc.edu'
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@@db_username = 'genome'
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@@db_password = ''
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data/lib/bio-ucsc/tetnig2.rb
CHANGED
@@ -1,9 +1,9 @@
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#
|
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# = AUTOMATIC Table Definition of the Tetraodon Mar. 2007 (Genoscope 8.0/tetNig2) assembly
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# Copyright:: Copyright (C) 2011
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+
# Copyright:: Copyright (C) 2011-2017
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# MISHIMA, Hiroyuki
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
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-
# License:: The
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+
# License:: The MIT licence
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#
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require "#{::File.dirname(__FILE__)}/table_class_detector"
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@@ -33,7 +33,7 @@ Chr20 Chr21 ChrM ChrUn_random)
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include SafeAttributes
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self.inheritance_column = 'dummy_not_to_use'
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-
@@db_adapter ||= '
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+
@@db_adapter ||= 'mysql2'
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
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@@db_username ||= 'genome'
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@@db_password ||= ''
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@@ -44,7 +44,7 @@ Chr20 Chr21 ChrM ChrUn_random)
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self.abstract_class = true
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def self.default
|
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-
@@db_adapter = '
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+
@@db_adapter = 'mysql2'
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@@db_host = 'genome-mysql.cse.ucsc.edu'
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@@db_username = 'genome'
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@@db_password = ''
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data/lib/bio-ucsc/uniprot.rb
CHANGED
@@ -1,9 +1,9 @@
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#
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# = AUTOMATIC Table Definition of Uniprot
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# Copyright:: Copyright (C) 2011
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+
# Copyright:: Copyright (C) 2011-2017
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# MISHIMA, Hiroyuki
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
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6
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-
# License:: The
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6
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+
# License:: The MIT licence
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#
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require "#{::File.dirname(__FILE__)}/table_class_detector"
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@@ -29,7 +29,7 @@ module Bio
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include SafeAttributes
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self.inheritance_column = 'dummy_not_to_use'
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-
@@db_adapter ||= '
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+
@@db_adapter ||= 'mysql2'
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
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@@db_username ||= 'genome'
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@@db_password ||= ''
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@@ -40,7 +40,7 @@ module Bio
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self.abstract_class = true
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def self.default
|
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-
@@db_adapter = '
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+
@@db_adapter = 'mysql2'
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@@db_host = 'genome-mysql.cse.ucsc.edu'
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@@db_username = 'genome'
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@@db_password = ''
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data/lib/bio-ucsc/visigene.rb
CHANGED
@@ -1,9 +1,9 @@
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1
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#
|
2
2
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# = AUTOMATIC Table Definition of VisiGene
|
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-
# Copyright:: Copyright (C) 2011
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+
# Copyright:: Copyright (C) 2011-2017
|
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4
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# MISHIMA, Hiroyuki
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5
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# <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
6
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-
# License:: The
|
6
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+
# License:: The MIT licence
|
7
7
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#
|
8
8
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9
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require "#{::File.dirname(__FILE__)}/table_class_detector"
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@@ -29,7 +29,7 @@ module Bio
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include SafeAttributes
|
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self.inheritance_column = 'dummy_not_to_use'
|
31
31
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|
32
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-
@@db_adapter ||= '
|
32
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+
@@db_adapter ||= 'mysql2'
|
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@@db_host ||= 'genome-mysql.cse.ucsc.edu'
|
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@@db_username ||= 'genome'
|
35
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@@db_password ||= ''
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@@ -40,7 +40,7 @@ module Bio
|
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self.abstract_class = true
|
41
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|
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def self.default
|
43
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-
@@db_adapter = '
|
43
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+
@@db_adapter = 'mysql2'
|
44
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@@db_host = 'genome-mysql.cse.ucsc.edu'
|
45
45
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@@db_username = 'genome'
|
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@@db_password = ''
|
data/lib/bio-ucsc/xentro2.rb
CHANGED
@@ -1,9 +1,9 @@
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|
1
1
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#
|
2
2
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# = AUTOMATIC Table Definition of the X. tropicalis Aug. 2005 (JGI 4.1/xenTro2) assembly
|
3
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-
# Copyright:: Copyright (C) 2011
|
3
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+
# Copyright:: Copyright (C) 2011-2017
|
4
4
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# MISHIMA, Hiroyuki
|
5
5
|
# <missy at be.to / hmishima at nagasaki-u.ac.jp>
|
6
|
-
# License:: The
|
6
|
+
# License:: The MIT licence
|
7
7
|
#
|
8
8
|
|
9
9
|
require "#{::File.dirname(__FILE__)}/table_class_detector"
|
@@ -31,7 +31,7 @@ module Bio
|
|
31
31
|
include SafeAttributes
|
32
32
|
self.inheritance_column = 'dummy_not_to_use'
|
33
33
|
|
34
|
-
@@db_adapter ||= '
|
34
|
+
@@db_adapter ||= 'mysql2'
|
35
35
|
@@db_host ||= 'genome-mysql.cse.ucsc.edu'
|
36
36
|
@@db_username ||= 'genome'
|
37
37
|
@@db_password ||= ''
|
@@ -42,7 +42,7 @@ module Bio
|
|
42
42
|
self.abstract_class = true
|
43
43
|
|
44
44
|
def self.default
|
45
|
-
@@db_adapter = '
|
45
|
+
@@db_adapter = 'mysql2'
|
46
46
|
@@db_host = 'genome-mysql.cse.ucsc.edu'
|
47
47
|
@@db_username = 'genome'
|
48
48
|
@@db_password = ''
|
metadata
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: bio-ucsc-api
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.6.
|
4
|
+
version: 0.6.4
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Hiroyuki Mishima
|
@@ -9,7 +9,7 @@ authors:
|
|
9
9
|
autorequire:
|
10
10
|
bindir: bin
|
11
11
|
cert_chain: []
|
12
|
-
date: 2017-
|
12
|
+
date: 2017-09-12 00:00:00.000000000 Z
|
13
13
|
dependencies:
|
14
14
|
- !ruby/object:Gem::Dependency
|
15
15
|
name: activerecord
|
@@ -17,42 +17,42 @@ dependencies:
|
|
17
17
|
requirements:
|
18
18
|
- - "~>"
|
19
19
|
- !ruby/object:Gem::Version
|
20
|
-
version: 4.
|
20
|
+
version: 4.2.9
|
21
21
|
type: :runtime
|
22
22
|
prerelease: false
|
23
23
|
version_requirements: !ruby/object:Gem::Requirement
|
24
24
|
requirements:
|
25
25
|
- - "~>"
|
26
26
|
- !ruby/object:Gem::Version
|
27
|
-
version: 4.
|
27
|
+
version: 4.2.9
|
28
28
|
- !ruby/object:Gem::Dependency
|
29
29
|
name: activesupport
|
30
30
|
requirement: !ruby/object:Gem::Requirement
|
31
31
|
requirements:
|
32
32
|
- - "~>"
|
33
33
|
- !ruby/object:Gem::Version
|
34
|
-
version: 4.
|
34
|
+
version: 4.2.9
|
35
35
|
type: :runtime
|
36
36
|
prerelease: false
|
37
37
|
version_requirements: !ruby/object:Gem::Requirement
|
38
38
|
requirements:
|
39
39
|
- - "~>"
|
40
40
|
- !ruby/object:Gem::Version
|
41
|
-
version: 4.
|
41
|
+
version: 4.2.9
|
42
42
|
- !ruby/object:Gem::Dependency
|
43
|
-
name:
|
43
|
+
name: mysql2
|
44
44
|
requirement: !ruby/object:Gem::Requirement
|
45
45
|
requirements:
|
46
46
|
- - "~>"
|
47
47
|
- !ruby/object:Gem::Version
|
48
|
-
version:
|
48
|
+
version: 0.4.9
|
49
49
|
type: :runtime
|
50
50
|
prerelease: false
|
51
51
|
version_requirements: !ruby/object:Gem::Requirement
|
52
52
|
requirements:
|
53
53
|
- - "~>"
|
54
54
|
- !ruby/object:Gem::Version
|
55
|
-
version:
|
55
|
+
version: 0.4.9
|
56
56
|
- !ruby/object:Gem::Dependency
|
57
57
|
name: safe_attributes
|
58
58
|
requirement: !ruby/object:Gem::Requirement
|
@@ -73,14 +73,14 @@ dependencies:
|
|
73
73
|
requirements:
|
74
74
|
- - "~>"
|
75
75
|
- !ruby/object:Gem::Version
|
76
|
-
version: 1.0.
|
76
|
+
version: 1.0.4
|
77
77
|
type: :runtime
|
78
78
|
prerelease: false
|
79
79
|
version_requirements: !ruby/object:Gem::Requirement
|
80
80
|
requirements:
|
81
81
|
- - "~>"
|
82
82
|
- !ruby/object:Gem::Version
|
83
|
-
version: 1.0.
|
83
|
+
version: 1.0.4
|
84
84
|
- !ruby/object:Gem::Dependency
|
85
85
|
name: bio-genomic-interval
|
86
86
|
requirement: !ruby/object:Gem::Requirement
|
@@ -101,14 +101,14 @@ dependencies:
|
|
101
101
|
requirements:
|
102
102
|
- - ">="
|
103
103
|
- !ruby/object:Gem::Version
|
104
|
-
version:
|
104
|
+
version: 12.1.0
|
105
105
|
type: :development
|
106
106
|
prerelease: false
|
107
107
|
version_requirements: !ruby/object:Gem::Requirement
|
108
108
|
requirements:
|
109
109
|
- - ">="
|
110
110
|
- !ruby/object:Gem::Version
|
111
|
-
version:
|
111
|
+
version: 12.1.0
|
112
112
|
- !ruby/object:Gem::Dependency
|
113
113
|
name: rspec
|
114
114
|
requirement: !ruby/object:Gem::Requirement
|
@@ -129,14 +129,14 @@ dependencies:
|
|
129
129
|
requirements:
|
130
130
|
- - ">="
|
131
131
|
- !ruby/object:Gem::Version
|
132
|
-
version: 1.
|
132
|
+
version: 1.15.4
|
133
133
|
type: :development
|
134
134
|
prerelease: false
|
135
135
|
version_requirements: !ruby/object:Gem::Requirement
|
136
136
|
requirements:
|
137
137
|
- - ">="
|
138
138
|
- !ruby/object:Gem::Version
|
139
|
-
version: 1.
|
139
|
+
version: 1.15.4
|
140
140
|
- !ruby/object:Gem::Dependency
|
141
141
|
name: jeweler
|
142
142
|
requirement: !ruby/object:Gem::Requirement
|
@@ -624,7 +624,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
624
624
|
version: '0'
|
625
625
|
requirements: []
|
626
626
|
rubyforge_project:
|
627
|
-
rubygems_version: 2.
|
627
|
+
rubygems_version: 2.6.11
|
628
628
|
signing_key:
|
629
629
|
specification_version: 4
|
630
630
|
summary: 'The Ruby UCSC API: accessing the UCSC Genome Database using Ruby'
|