bacterial-annotator 0.8.4 → 0.8.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 33f9bdce9a193dadcc78a42d6e60a4b2b6d517d41c9a4020f5fe69a10c99c826
+  metadata.gz: da5221d8f00eb6042cc1b7ea5f99101dc9acb7120c7e2c8f85833e3a1d52045f
+  data.tar.gz: 2836e79ce4062db2cd8ae795cbdcfeba81a8dfcaa6c44bf4610d1a4da20e4786
 SHA512:
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+  metadata.gz: 93f660143c5c67ed505c9cdd9ba6d41e70bc788e6578c0fb440de4519b60ca9b79297f2c149f6489a10b205ea3767e1f3649cc369dd7f1c4122843562200f179
+  data.tar.gz: 88e3aa0ed0a1f15cb27fe9ad61a216ba2bbd2cd0654c61f4105273eb041cfbfb07ae89e5f9e079178cdc81946b8c7bb73f38eefecc7bbd523858338bfafa4996

data/bin/bacterial-annotator

@@ -38,6 +38,8 @@ bacterial-annotator [annotate | compare] [OPTIONS]
 
 # Choose either to annotate a genome or compare several genome annotations
 
+  install   Install the third parties dependencies
+
   identify  [OPTIONS]
             .. see identify -h for OPTIONS
 
@@ -281,15 +283,9 @@ def parseOptions_identify
 end
 
 
+def install_dep
 
-
-########
-# MAIN #
-########
-
-if ARGV.size >= 1
-
-  ROOT = File.dirname(__FILE__)
+  # requirement ruby, ruby-dev, unzip
 
   # Check for 3rd party dependencies : Prodigal, Blat, MAFFT, ...
   system("ba_prodigal")
@@ -303,6 +299,18 @@ if ARGV.size >= 1
   system("ba_mash")
   system("ba_trnascan")
 
+end
+
+
+
+########
+# MAIN #
+########
+
+if ARGV.size >= 1
+
+  ROOT = File.dirname(__FILE__)
+
   options = {}
 
   if ARGV[0] == "annotate"
@@ -310,6 +318,8 @@ if ARGV.size >= 1
     ARGV.shift
     options = parseOptions_annotate
 
+    install_dep
+
     if ! File.exist? ("#{ROOT}/blat.linux")
       puts "Exiting program because blat is missing"
       abort
@@ -351,6 +361,8 @@ if ARGV.size >= 1
     print_version
     abort
 
+  elsif ARGV[0] == "install"
+    install_dep
   else
     usage
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bacterial-annotator
 version: !ruby/object:Gem::Version
-  version: 0.8.4
+  version: 0.8.5
 platform: ruby
 authors:
 - Maxime Deraspe
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-05-24 00:00:00.000000000 Z
+date: 2018-07-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bio
@@ -126,7 +126,7 @@ 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: Bacterial Annotator