Inserted the 'sys' method into more places

Used the 'sys' method in several places where shell commands
are run.

Signed-off-by: Lawrence John Maynard <enjoyyourcopepods@gmx.com>

bin/sequenceserver

@@ -2,6 +2,7 @@
 require 'readline'
 require 'English'
 require 'slop'
+require 'sequenceserver'
 
 ENV['RACK_ENV'] ||= 'production'
 
@@ -17,7 +18,7 @@ def download_from_url(url)
   cmd = "curl -ip4 -C - #{url} -o #{archive} && " \
         'mkdir -p ~/.sequenceserver && '          \
         "tar xvf #{archive} -C ~/.sequenceserver"
-  system cmd
+  sys(cmd)
 end
 
 begin
@@ -153,8 +154,6 @@ BANNER
         exit
       end
 
-      require 'sequenceserver'
-
       begin
         SequenceServer.init clean_opts[to_h]
 

lib/sequenceserver.rb

@@ -273,9 +273,9 @@ def server_url
     def open_in_browser(server_url)
       return if using_ssh? || verbose?
       if RUBY_PLATFORM =~ /linux/ && xdg?
-        system "xdg-open #{server_url}"
+        sys("xdg-open #{server_url}")
       elsif RUBY_PLATFORM =~ /darwin/
-        system "open #{server_url}"
+        sys("open #{server_url}")
       end
     end
 
@@ -289,7 +289,7 @@ def xdg?
 
     # Return `true` if the given command exists and is executable.
     def command?(command)
-      system("which #{command} > /dev/null 2>&1")
+      sys("which #{command}")
     end
   end
 end

lib/sequenceserver/database.rb

@@ -168,12 +168,11 @@ def make_blast_database(file, type)
         _make_blast_database(file, type, title, taxid)
       end
 
-      def _make_blast_database(file, type, title, taxid, quiet = false)
+      def _make_blast_database(file, type, title, taxid)
         cmd = 'makeblastdb -parse_seqids -hash_index ' \
               "-in #{file} -dbtype #{type.to_s.slice(0, 4)} -title '#{title}'" \
               " -taxid #{taxid}"
-        cmd << ' &> /dev/null' if quiet
-        system cmd
+        sys(cmd)
       end
 
       # Show file path and guessed sequence type to the user and obtain a y/n