genevalidatorapp 2.0.2 → 2.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 9b8ddf28dbafbfd70105a35216e39df09ec55265825916497886d5f3dc5dd100
+  metadata.gz: 335e59756610dbf42e458acae01444e5c4931db68cfa167348ea9b746fafa258
+  data.tar.gz: 6463d4162b3e4475faa71065085f98b9dc9fb47a301d24c40fedecea7e3d4638
 SHA512:
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+  metadata.gz: 4b99f80233d2ae778d279ea4af7cf2c9415ecc1710581eb3583e66b821e34196e7f5ed02095dea81f1836cac75cc651547922a2eb491e44e7d243268e793eda6
+  data.tar.gz: c17e9cd599202ff003872dd5c02ba55f23b1fa48b77a0f08feeb1110d99fa82279701593c5a63f1c17f1bb36394c3ecc2ca6ed7e22d33725dc819906ebdd3b9c

data/.travis.yml

@@ -1,16 +1,11 @@
 language: ruby
 rvm:
-  - "2.0.0"
-  - "2.1.3"
-  - '2.2.0'
+  - "2.2.10"
+  - "2.3.7"
+  - "2.4.4"
+  - "2.5.1"
 before_install:
-  - wget -c "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-x64-linux.tar.gz" && tar xvf ncbi-blast-2.2.30+-x64-linux.tar.gz && export PATH="./ncbi-blast-2.2.30+/bin:$PATH"
-  - wget -P ~ http://mafft.cbrc.jp/alignment/software/mafft-7.205-with-extensions-src.tgz
-  - tar -zxvf ~/mafft-7.205-with-extensions-src.tgz -C ~
-  - mkdir ~/mafft
-  - ruby -pi -e "gsub(/^PREFIX = \/usr\/local/, 'PREFIX = ~/mafft/')" ~/mafft-7.205-with-extensions/core/Makefile
-  - (cd ~/mafft-7.205-with-extensions/core/ && make clean && make && make install)
-  - export PATH=$PATH:~/mafft/bin
+  - gem install genevalidator
+  - sh -c "$(curl -fsSL install-genevalidator.wurmlab.com)"
 cache: bundler
-sudo: false
-script: bundle exec rake test
+script: rake test

data/genevalidatorapp.gemspec

@@ -22,7 +22,6 @@ Gem::Specification.new do |s|
 
   s.required_ruby_version = '>= 2.2.0'
 
-  s.add_development_dependency 'bundler', '~> 1.6'
   s.add_development_dependency 'capybara', '~> 2.4', '>= 2.4.4'
   s.add_development_dependency 'minitest', '~> 5.10'
   s.add_development_dependency 'rake', '~> 12.3'

data/lib/genevalidatorapp/config.rb

@@ -73,7 +73,8 @@ module GeneValidatorApp
     def defaults
       {
         :num_threads    => 1,
-        :port           => 4567,
+        :mafft_threads  => 1,
+        :port           => 5678,
         :host           => '0.0.0.0',
         :gv_public_dir  => File.join(Dir.home, '.genevalidatorapp/'),
         :max_characters => 'undefined'

data/lib/genevalidatorapp/genevalidator.rb

@@ -177,8 +177,10 @@ module GeneValidatorApp
           validations: @params[:validations],
           db: @db,
           num_threads: config[:num_threads],
+          mafft_threads: config[:mafft_threads],
+          min_blast_hits: 5,
           input_fasta_file: @input_file,
-          output_formats: %w[json html],
+          output_formats: %w[html csv json summary],
           output_dir: File.join(@run_dir, 'output')
         }
       end

data/lib/genevalidatorapp/version.rb

@@ -1,3 +1,3 @@
 module GeneValidatorApp
-  VERSION = '2.0.2'
+  VERSION = '2.1.0'
 end

data/views/index.slim

@@ -38,11 +38,11 @@ section#search
       .form-group.form-inline
         label.control-label  Advanced Parameters: Database
         br/
-        label.radio-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12
+        label.radio-inline.no_indent.col-xs-12
           <input type="radio" name="database" value="#{@default_db.title.chomp}" checked=""> #{@default_db.title.chomp}
         - unless @non_default_dbs.empty?
           - @non_default_dbs.each do |db|
-            label.radio-inline.no_indent.col-lg-3.col-md-5.col-sm-6.col-xs-12
+            label.radio-inline.no_indent.col-xs-12
               <input type="radio" name="database" value="#{db.title.chomp}"> #{db.title.chomp}
       .clearfix
     .form-group

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: genevalidatorapp
 version: !ruby/object:Gem::Version
-  version: 2.0.2
+  version: 2.1.0
 platform: ruby
 authors:
 - Monica Dragan
@@ -11,22 +11,8 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-06-28 00:00:00.000000000 Z
+date: 2018-08-14 00:00:00.000000000 Z
 dependencies:
-- !ruby/object:Gem::Dependency
-  name: bundler
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.6'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.6'
 - !ruby/object:Gem::Dependency
   name: capybara
   requirement: !ruby/object:Gem::Requirement
@@ -229,7 +215,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.7.6
+rubygems_version: 2.7.7
 signing_key: 
 specification_version: 4
 summary: A Web App wrapper for GeneValidator.