added pre-built database

ChangeLog

@@ -3,6 +3,7 @@ ChangeLog of HGTector
 == Version 0.2.2 (8/23/2017) ==
 
 New features:
+- Provided a pre-built standard database.
 - Added an installation script "installer.sh".
 - Adopted new NCBI standard, i.e., using accession instead of GI as sequence identifier.
 - Modified the mechanism of databaser.py. Now it downloads both DNA and protein sequences.

HGTector.pl

@@ -74,12 +74,16 @@
         }
         print "\n";
 
-        print "Now I will assist you to generate a reference database.\n";
-        print "Unless you plan to use HGTector in remote mode, a local reference database is recommended for consistant and controllable analyses.\n";
+        print "Now I will assist you to prepare a reference database.\n";
+        print "Unless you plan to always use HGTector in remote mode, a local reference database is recommended for consistant and controllable analyses.\n";
+        print "The database will have three components: a protein sequence database, a taxonomy database, and a protein-to-taxonomy dictionary.\n";
+        print "Using proper databases is important for optimal results. Please consider reading about the details of choice of databases in the GUI.\n";
+        print "\n";
+
+        print "A pre-built database is available (see README.md for download link). Alternatively, I will build an up-to-date one for you now.\n";
         print "Proceed (YES/no)? ";
         $s = <STDIN>; chomp $s;
         if (not $s or $s =~ /^yes$/i or $s =~ /^y$/i) {
-            print "HGTector requires three databases: a protein sequence database, a taxonomy database, and a protein-to-taxonomy dictionary. Using proper databases is important for optimal results. Please read about the details of choice of databases in the GUI.\n";
             print "\nPlease specify a location to store the databases (default: db/ in the program directory): ";
             $s = <STDIN>; chomp $s; $s =~ s/\/$//;
             $db = $s if $s;
@@ -110,7 +114,7 @@
             }
             my $i = system "python $scripts/databaser.py -format=$format -range=$range -represent=$represent -subsample=$subsample -out=$out";
             chdir $cwd;
-            print "\nThere appear to be some problems in database building.\n" unless -s "$db/$out.faa";
+            print "\nThere appears to be some problems in database building.\n" unless -s "$db/$out.faa";
             print "\nNow that databases are created. Your may link HGTector to them in future analyses, by setting the following parameters in config.txt:\n";
             if ($format eq "blast") {
                 print "protdb=$db/blast/$out\n";

README.md

@@ -1,28 +1,22 @@
 HGTector
-==========
-
-**Note: Instead of downloading the release, please git clone the master branch, which contains an important update in match with the new NCBI FTP site structure.**
-
-**Alternatively, please download a pre-constructed database from [here](https://u21438014.dl.dropboxusercontent.com/u/21438014/HGTector/stdb_20170128.tar.xz).**
+========
 
 A computational pipeline for genome-wide detection of putative horizontal gene transfer (HGT) events based on sequence homology search hit distribution statistics
 
-Latest release: [0.2.1](https://github.com/DittmarLab/HGTector/archive/0.2.2.zip)
-
-Last update: 2017-1-28
-
 Authors: Qiyun Zhu (<[email protected]>), Katharina Dittmar (<[email protected]>)
 
 Affiliation: Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, USA
 
 License: [BSD 2-clause](http://opensource.org/licenses/BSD-2-Clause).
 
-An article detailing the method and its performance on simulated and real genomic datasets can be found [here](http://www.biomedcentral.com/1471-2164/15/717):
+Download the latest release: [0.2.2](https://github.com/DittmarLab/HGTector/archive/0.2.2.zip), updated on 2017-8-23; and a standard [database](https://u21438014.dl.dropboxusercontent.com/u/21438014/HGTector/stdb_20170630.tar), updated on 2017-6-30.
+
+An article detailing the method and its performance on simulated and real genomic datasets can be found [here](https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-717):
 
 Zhu Q, Kosoy M, Dittmar K. HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers. *BMC Genomics*. 2014. 15:717.
 
 Please visit our lab's [website](http://katharina-dittmar.squarespace.com/) for details.
 
 Usage: Simply execute **perl HGTector.pl**, or, open **GUI.html** in a web browser to see a step-by-step wizard.
 
-Download [HGTector 0.2.1](https://github.com/DittmarLab/HGTector/archive/0.2.1.zip).
+Download [HGTector 0.2.2](https://github.com/DittmarLab/HGTector/archive/0.2.2.zip).