blast 2.2.25.RC3

data/LICENSE.txt

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+Copyright © 2012 Anurag Priyam
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

data/Rakefile

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+require 'fileutils'
+
+module BLAST
+  class Package
+    def initialize(url)
+      self.url = url
+    end
+
+    def name
+      name = archive[/.*\+/]
+    end
+
+    def install
+      download and extract and generate_wrappers and remove
+    end
+
+    private
+
+    attr_accessor :url
+
+    def archive
+      File.basename(@url)
+    end
+
+    def download
+      puts "Downloading #{url}."
+      system "wget -c #{url}"
+    end
+
+    def extract
+      puts "Extracting #{archive}."
+      system "tar xvf #{archive}"
+    end
+
+    def generate_wrappers
+      puts "Generating wrappers."
+
+      # Each entry in gem's bin/ is a script template that is supposed to exec
+      # corresponding BLAST+ binaries.  Now that BLAST+ is available, we fill
+      # in the templates with the path to the corresponding binaries.
+      Dir[File.join('bin', '*')].each do |bin|
+        script = File.read(bin) % File.expand_path(File.join(name, bin))
+        File.open(bin, 'w') do |f|
+          f.write(script)
+        end
+      end
+    end
+
+    def remove
+      puts "Removing #{archive}."
+      FileUtils.rm archive
+    end
+  end
+end
+
+task :default do
+  puts "RUBY_PLATFORM #{RUBY_PLATFORM}"
+  package = case RUBY_PLATFORM
+            when /i686-linux/   # 32 bit Linux
+              "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.25+-ia32-linux.tar.gz"
+            when /x86_64-linux/ # 64 bit Linux
+              "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.25+-x64-linux.tar.gz"
+            when /darwin/       # Mac
+              "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.25+-universal-macosx.tar.gz"
+            else
+              puts <<ERR
+
+------------------------------------------------------------------------
+  FAILED!! to install NCBI BLAST+.
+
+  We currently support Linux and Mac only (both 32 and 64 bit). If you
+  believe you are running a supported platform, please open a support
+  ticket titled "#{RUBY_PLATFORM}" at:
+
+  https://github.com/yeban/blast/issues
+------------------------------------------------------------------------
+
+ERR
+              exit 1
+            end
+
+  package = BLAST::Package.new(package)
+  package.install
+end

data/bin/blast_formatter

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/blastdb_aliastool

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/blastdbcheck

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/blastdbcmd

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/blastn

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/blastp

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/blastx

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/convert2blastmask

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/dustmasker

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/legacy_blast.pl

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/makeblastdb

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/makembindex

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/psiblast

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/rpsblast

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/rpstblastn

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/segmasker

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/tblastn

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/tblastx

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/update_blastdb.pl

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

data/bin/windowmasker

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+#!/usr/bin/env ruby
+
+exec "%s", *ARGV
+

metadata

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+--- !ruby/object:Gem::Specification
+name: blast
+version: !ruby/object:Gem::Version
+  version: 2.2.25.RC3
+  prerelease: 7
+platform: ruby
+authors:
+- Anurag Priyam
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-06-21 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: &22928240 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: *22928240
+description: ! 'This gem will automatically download and install pre-compiled NCBI
+  BLAST+
+
+  binaries that is most appropriate for your local system.  The version of
+
+  BLAST+ installed is the same as that of the gem.
+
+'
+email: anurag08priyam@gmail.com
+executables:
+- blastp
+- psiblast
+- blastx
+- segmasker
+- rpstblastn
+- windowmasker
+- tblastn
+- makembindex
+- blastdbcmd
+- convert2blastmask
+- tblastx
+- dustmasker
+- blastdbcheck
+- makeblastdb
+- blastdb_aliastool
+- blast_formatter
+- update_blastdb.pl
+- legacy_blast.pl
+- rpsblast
+- blastn
+extensions:
+- Rakefile
+extra_rdoc_files: []
+files:
+- Rakefile
+- LICENSE.txt
+- !binary |-
+  YmluL2JsYXN0cA==
+- !binary |-
+  YmluL3BzaWJsYXN0
+- !binary |-
+  YmluL2JsYXN0eA==
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+- !binary |-
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+- !binary |-
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+- !binary |-
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+- !binary |-
+  YmluL2JsYXN0bg==
+homepage: https://github.com/yeban/blast
+licenses:
+- MIT
+post_install_message: ! "\n------------------------------------------------------------------------\n
+  \ All NCBI BLAST+ commands should be accessible from the command line.\n\n    $
+  blastp -h\n    [...]\n\n  Visit https://github.com/yeban/blast to report issues,
+  and/or track\n  development.\n------------------------------------------------------------------------\n\n"
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>'
+    - !ruby/object:Gem::Version
+      version: 1.3.1
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.11
+signing_key: 
+specification_version: 3
+summary: Install NCBI BLAST+.
+test_files: []