full_lengther_next 1.0.3 → 1.0.5
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- checksums.yaml +4 -4
- data/bin/download_fln_dbs.rb +2 -2
- data/full_lengther_next.gemspec +1 -1
- data/lib/full_lengther_next/version.rb +1 -1
- metadata +3 -5
- data/bin/setup +0 -8
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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|
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1
1
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---
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2
2
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SHA256:
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
3
|
+
metadata.gz: ec9502db695b0828eaddec43a408cbe7713cc7e909fcde49d294e0390016ca22
|
|
4
|
+
data.tar.gz: 616bbdb100362df4645a1597c52cdf17807f75d64d2f81f4c624b63da8516e93
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: 0bd5dc77fbb523319068d6f8eff6238f925b1cf97883f5c5154fe9c75df6ab298deefc767b32ae7dc7f96c0bbad5f08cdf4c8ff93b9fa17fc66ab446509f4cad
|
|
7
|
+
data.tar.gz: ef2e04e7eb12252fa370ce65078d4e34996e8821164fc36db86b2d27d16532f90aa542f821fbf10fd29f425067de6dd5b4456750ec04d2afce9486398c42fe36
|
data/bin/download_fln_dbs.rb
CHANGED
|
@@ -10,7 +10,7 @@ require 'scbi_zcat'
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|
|
10
10
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require 'optparse'
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|
11
11
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require 'cdhit'
|
|
12
12
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require 'handle_db'
|
|
13
|
-
require 'bio_patch'
|
|
13
|
+
#require 'bio_patch'
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|
14
14
|
|
|
15
15
|
##############################################################################################
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|
16
16
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## METHODS
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@@ -376,7 +376,7 @@ Dir.mkdir(formatted_db_path) if !File.exists?(formatted_db_path)
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|
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376
376
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ENV['BLASTDB'] = formatted_db_path
|
|
377
377
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puts "Databases will be downloaded at: #{ENV['BLASTDB']}"
|
|
378
378
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puts "\nTo set the path for storing databases, execute next line in your terminal or add it to your .bash_profile:\n\n\texport BLASTDB=/my_path/\n\n"
|
|
379
|
-
puts "Patched? #{Bio::UniProtKB.patched?}"
|
|
379
|
+
#puts "Patched? #{Bio::UniProtKB.patched?}"
|
|
380
380
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download_ncrna(formatted_db_path, options[:no_download]) if !options[:no_ncrna]
|
|
381
381
|
|
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382
382
|
if !options[:no_download]
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data/full_lengther_next.gemspec
CHANGED
|
@@ -32,7 +32,7 @@ Gem::Specification.new do |spec|
|
|
|
32
32
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spec.add_runtime_dependency 'scbi_blast'
|
|
33
33
|
spec.add_runtime_dependency 'scbi_mapreduce'
|
|
34
34
|
spec.add_runtime_dependency 'scbi_zcat'
|
|
35
|
-
spec.add_runtime_dependency 'bio'
|
|
35
|
+
spec.add_runtime_dependency 'bio' "~> 2.0.4"
|
|
36
36
|
#spec.add_runtime_dependency 'bio-cd-hit-report' # Removed due to conflicts with bio-ruby2. This gem depends on bio ruby 1.4.3. cdhit options disabled
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|
37
37
|
spec.add_runtime_dependency 'report_html'
|
|
38
38
|
|
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: full_lengther_next
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 1.0.
|
|
4
|
+
version: 1.0.5
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Pedro Seoane
|
|
@@ -10,7 +10,7 @@ authors:
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|
|
10
10
|
autorequire:
|
|
11
11
|
bindir: bin
|
|
12
12
|
cert_chain: []
|
|
13
|
-
date:
|
|
13
|
+
date: 2023-05-10 00:00:00.000000000 Z
|
|
14
14
|
dependencies:
|
|
15
15
|
- !ruby/object:Gem::Dependency
|
|
16
16
|
name: xml-simple
|
|
@@ -83,7 +83,7 @@ dependencies:
|
|
|
83
83
|
- !ruby/object:Gem::Version
|
|
84
84
|
version: '0'
|
|
85
85
|
- !ruby/object:Gem::Dependency
|
|
86
|
-
name: bio
|
|
86
|
+
name: bio~> 2.0.4
|
|
87
87
|
requirement: !ruby/object:Gem::Requirement
|
|
88
88
|
requirements:
|
|
89
89
|
- - ">="
|
|
@@ -167,7 +167,6 @@ executables:
|
|
|
167
167
|
- full_lengther_next
|
|
168
168
|
- make_test_dataset.rb
|
|
169
169
|
- make_user_db.rb
|
|
170
|
-
- setup
|
|
171
170
|
extensions: []
|
|
172
171
|
extra_rdoc_files: []
|
|
173
172
|
files:
|
|
@@ -183,7 +182,6 @@ files:
|
|
|
183
182
|
- bin/full_lengther_next
|
|
184
183
|
- bin/make_test_dataset.rb
|
|
185
184
|
- bin/make_user_db.rb
|
|
186
|
-
- bin/setup
|
|
187
185
|
- full_lengther_next.gemspec
|
|
188
186
|
- lib/full_lengther_next.rb
|
|
189
187
|
- lib/full_lengther_next/artifacts.rb
|