genevalidatorapp 2.1.2 → 2.1.3

checksums.yaml

@@ -1,7 +1,7 @@
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data/.travis.yml

@@ -5,7 +5,17 @@ rvm:
   - "2.4.4"
   - "2.5.1"
 before_install:
-  - gem install genevalidator
-  - sh -c "$(curl -fsSL install-genevalidator.wurmlab.com)"
-cache: bundler
-script: rake test
+  # Install MAFFT
+  - mkdir dependencies
+  - mkdir dependencies/mafft
+  - curl -L --fail https://mafft.cbrc.jp/alignment/software/mafft-7.397-linux.tgz | tar -xzf - --strip-components=1 -C dependencies/mafft
+  - MAFFT_DIR="$PWD/dependencies/mafft/mafftdir"
+  - MAFFT_BINARIES="${MAFFT_DIR}/libexec"; export MAFFT_BINARIES;
+  # BLAST
+  - mkdir dependencies/blast
+  - curl -L --fail https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-x64-linux.tar.gz | tar -xzf - --strip-components=1 -C dependencies/blast
+  - BLAST_BIN="$PWD/dependencies/blast/bin"
+  - export PATH=${MAFFT_DIR}/bin:${BLAST_BIN}:$PATH
+  # add GV as a dependency
+  - echo  "gem 'genevalidator'" >> Gemfile
+script: bundle exec rake test

data/lib/genevalidatorapp/exceptions.rb

@@ -81,9 +81,19 @@ MSG
     end
   end
 
+  ## MAFFT NOT INSTALLED OR NOT COMPATIBLE ##
+
+  # Raised if GV could not locate MAFFT binaries on
+  # user's system.
+  class MAFFT_NOT_INSTALLED < StandardError
+    def to_s
+      'Could not locate MAFFT binaries.'
+    end
+  end
+
   ## BLAST NOT INSTALLED OR NOT COMPATIBLE ##
 
-  # Raised if SequenceServer could not locate NCBI BLAST+ installation on
+  # Raised if GV could not locate NCBI BLAST+ installation on
   # user's system.
   class BLAST_NOT_INSTALLED < StandardError
     def to_s
@@ -91,7 +101,7 @@ MSG
     end
   end
 
-  # Raised if SequenceServer could not successfully execute 'blastp -version'
+  # Raised if GV could not successfully execute 'blastp -version'
   # on user's system (see #141).
   class BLAST_NOT_EXECUTABLE < StandardError
     def to_s
@@ -99,8 +109,8 @@ MSG
     end
   end
 
-  # Raised if SequenceServer determined NCBI BLAST+ present on the user's
-  # system but not meeting SequenceServer's minimum version requirement.
+  # Raised if GV determined NCBI BLAST+ present on the user's
+  # system but not meeting GV's minimum version requirement.
   class BLAST_NOT_COMPATIBLE < StandardError
     def initialize(version)
       @version = version
@@ -111,7 +121,7 @@ MSG
     def to_s
       <<MSG
 Your BLAST+ version #{version} is outdated.
-SequenceServer needs NCBI BLAST+ version #{MINIMUM_BLAST_VERSION} or higher.
+GV needs NCBI BLAST+ version #{MINIMUM_BLAST_VERSION} or higher.
 MSG
     end
   end
@@ -167,7 +177,7 @@ Tried: #{cmd}
 Error:
 #{out.strip}
 
-Please could you report this to 'https://groups.google.com/forum/#!forum/sequenceserver'?
+Please could you report this to 'https://groups.google.com/forum/#!forum/GV'?
 MSG
     end
   end

data/lib/genevalidatorapp/version.rb

@@ -1,3 +1,3 @@
 module GeneValidatorApp
-  VERSION = '2.1.2'.freeze
+  VERSION = '2.1.3'.freeze
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: genevalidatorapp
 version: !ruby/object:Gem::Version
-  version: 2.1.2
+  version: 2.1.3
 platform: ruby
 authors:
 - Monica Dragan