bacterial-annotator 0.8.0 → 0.8.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 1c90c64fd59297a06dd9b50def86f8ba9305b23e
-  data.tar.gz: '008eec9088d41505c8c9ffbbc097ce4cee5b5c3b'
+  metadata.gz: 3db94963e7c81c71fd28b372bcdc9cf6271b635b
+  data.tar.gz: 077d431814bf5a44e6c74fb000869c11e8b087ab
 SHA512:
-  metadata.gz: 7904dc06b85e1dca28bab9fbb5a84d2919da714990775df637ed27f504f25218eeffd264146fd1082e2a44e1188b2faf6e2a0ce923183eb88caf15595cf26500
-  data.tar.gz: 1c3a09f9952e5750faad5fa5c5c27492967dcebcb6f2fa5a8fd89ef79f5a074d2e6e4f4eeb299729304328777af8e752a1747409ee24150ce1f96354243a0f38
+  metadata.gz: fb06e7960a775911f0a701105f7f49b68862cdb98d6f9fd29d05a5940b476f88495ac721fb32f3b87cce557e44c08fe21c0f59140d6e81da692f729f5bb63c3d
+  data.tar.gz: ec3edcb9bcb68880b428d07a0cb33e13d8e12b7132dc244bfd3b2b59fca3d07b600d5a55c7e0b931c6d0aeb6b65e3e791e9d81e44cb57f2e4c2a793452be5ffe

data/bin/ba_trnascan

@@ -0,0 +1,57 @@
+#!/usr/bin/env ruby
+# -*- coding: utf-8 -*-
+# author:  	maxime déraspe
+# email:	maximilien1er@gmail.com
+# review:  	
+# date:    	18-05-22
+# version: 	0.01
+# licence:  	
+
+require 'open-uri'
+
+ROOT_path = File.dirname(__FILE__)
+# trnascan URL = "http://trna.ucsc.edu/software/trnascan-se-2.0.0.tar.gz"
+# infernal URL = "http://eddylab.org/infernal/infernal-1.1.2.tar.gz"
+
+# Install trnascan on the user system
+def installTrnascan
+  begin
+
+    # infernal as dependencies
+    resp = open("http://eddylab.org/infernal/infernal-1.1.2.tar.gz")
+    open("#{ROOT_path}/infernal-1.1.2.tar.gz", "wb") do |file|
+      file.write(resp.read)
+    end
+    Dir.chdir("#{ROOT_path}/")
+    `tar xvf infernal-1.1.2.tar.gz && rm infernal-1.1.2.tar.gz`
+    `cd infernal-1.1.2 && ./configure --prefix=#{ROOT_path}/infernal-1.1.2/build && make && make install`
+
+    # trnascan-se
+    resp = open("http://trna.ucsc.edu/software/trnascan-se-2.0.0.tar.gz")
+    open("#{ROOT_path}/trnascan-se-2.0.0.tar.gz", "wb") do |file|
+      file.write(resp.read)
+    end
+    Dir.chdir("#{ROOT_path}/")
+    `tar xvf trnascan-se-2.0.0.tar.gz; rm trnascan-se-2.0.0.tar.gz`
+    `cd tRNAscan-SE-2.0/ && ./configure --prefix=#{ROOT_path}/tRNAscan-SE-2.0/build && make && make install && cd build/bin && ln -s #{ROOT_path}/infernal-1.1.2/build/bin/ .`
+    `cp #{ROOT_path}/tRNAscan-SE-2.0/build/bin/tRNAscan-SE #{ROOT_path}/trnascan.linux`
+    File.chmod(0755, "#{ROOT_path}/trnascan.linux")
+  rescue
+    abort "Problem installing tRNAscan-SE, aborting"
+  end
+
+end
+
+
+# Install trnascan if not already install
+if ! File.exists? "#{ROOT_path}/trnascan.linux"
+
+  puts "Installing tRNAscan-SE tRNA finder.."
+  puts "See http://lowelab.ucsc.edu/tRNAscan-SE/"
+  puts "The Licence is BSD"
+  installTrnascan
+  puts "Trnascan successfully installed in #{ROOT_path}/trnascan.linux"
+  puts ""
+
+end
+

data/bin/bacterial-annotator

@@ -301,6 +301,7 @@ if ARGV.size >= 1
   system("ba_cdhit")
   system("ba_fasttree")
   system("ba_mash")
+  system("ba_trnascan")
 
   options = {}
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bacterial-annotator
 version: !ruby/object:Gem::Version
-  version: 0.8.0
+  version: 0.8.1
 platform: ruby
 authors:
 - Maxime Deraspe
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-04-18 00:00:00.000000000 Z
+date: 2018-05-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -84,6 +84,7 @@ executables:
 - ba_cdhit
 - ba_fasttree
 - ba_mash
+- ba_trnascan
 extensions: []
 extra_rdoc_files: []
 files:
@@ -96,6 +97,7 @@ files:
 - bin/ba_mash
 - bin/ba_prodigal
 - bin/ba_raxml
+- bin/ba_trnascan
 - bin/bacterial-annotator
 - lib/bacterial-annotator.rb
 - lib/bacterial-annotator/sequence-annotation.rb