INSTALLATION NOTES for AceBrowser-MODS-x.x.x.tar.gz

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    This HOWTO file describes the configuration of a suite of Perl scripts which we hope will provide some useful improvements to your
    AceBrowser-3.1 installation.   Go here for a quick tour of these features. Installation and knowledge of AceDB 4_9i, AceBrowser-3.10,
    AcePerl 1.83, Perl 5.6.0, Apache 1.2 and CGI.pm 2.7 is assumed.

1) Install AcePerl + AceBrowser-3.1 as described here: http://stein.cshl.org/AcePerl/AceBrowser/
   And familiarize yourself with related files which have been installed in directories under your systems Perl
   installation as a result. (for example: /usr/local/lib/perl5/site_perl/5.6.0/Ace/Browser or someplace very much like this)
   In this directory you will see these files: AceSubs.pm, GeneSubs.pm, LocalSiteDefs.pm, SearchSubs.pm, SiteDefs.pm,TreeSubs.pm
   Simply knowing where these files are may come in handy later.

2) GO here and get the most current AceBrowser-Mods-x.x.x.tar.gz and then cd to your cgi-bin/AceBrowser-3.1 directory . The exact name
of this directory you would have chosen during the AceBrowser-3.1 installation (look at the variable called $CGI_PATH in LocalSiteDefs.pm
to see) Unzip the new tar.gz file with the following command:

% gzip -d -c AceBrowser-MODS-x.x.x.tar.gz |tar xvf -

   The following files and directories and files will appear:
acelib/
            Acedb.pm
            Aceobj.pm
alignm
custom/
            ace2fasta
            aqlInterface
            blastHTML
            bquery
            dispatch
            dnaDump
            fasta
            goBlast
            tDump
            table
            webace
feedback
other/
            MouseOver.pm
            Utilities.pm
            batchQuery.pm
            externalUrls
            grain.css
            markup.pl
            queries.arg.pl
            queries.pl
            quickAQL.html
            sampleDB.pm
pic
query
search
text
tree

3) copy the files
            other/Mouseover.pm
            other/Utilities.pm
            other/batchQuery.pm
    into the Ace/Browser/ directory (see #1 above)

4) copy the files
            other/queries.pl
            other/markup.pl
     into the wspec/ directory of your acedb database.

5) copy the files
            other/sampleDB.pm
            other/externalUrls
    into the AceBrowser-3.1 conf directory (look at the variable $SITE_DEFS in LocalSiteDefs.pm to find the location of the AceBrowser-3.1conf directory).
    You may use the sampleDB.pm file as a template for your own database configuration file. As mentioned at the start of this guide, we assume you have a
    working installation of AceBrowser-3.1. Under this condition it is advisable for you to compare sampleDB.pm with your already-working database.pm and
    make suitable changes to your database.pm . Note the variables in the section of the file described in #6 below. ... some (or all) of these paths will need to be changed
    based on your system.

6) The variables in the section below are from the sampleDB.pm. fileVariable description/purpose:
# ========= mods =========
$APACHE_PATH = "/usr/local/apache"; # user to configure this path
$EXTERNALURLS = "$SITE_DEFS/externalUrls"; # used by tree script for markup urls...customize individual externalUrls per database
$PICROOT = $HTML_PATH . "/images";
$FASTAKEYSET = 'true', # value examined by Utilities::queryURL()in search or query script
$BLASTURL = "http://" . $HOST . $ROOT . "/custom/goBlast",
$WSPEC = '/data1/ftp/pub/GrainGenes/graingenes.current/wspec/',# user to configure this path (dir must contain queries.pl for aqlInterface )
$MQUERY = 'q2', # this specifies which query to run in MouseOver.pm
$HELPSEQ = '/helpSeq.html'; # path to html help file for class Sequence (pic will check for Sequence or Map and put url on page accordingly)
$HELPMAP = '/helpMap.html'; # path to html help file for class Map (user can customize by adding conditions to pic script)
$NAME2 = 'GrainGenes'; # to get proper case in spelling of db name
$TEMPLATE = "/usr/local/apache" . $ROOT . "/custom/blastHTML/blastnsf.html";
#$TEMPLATE = $CGI_PATH . "/custom/blastHTML/blastnsf.html";
$CAP3 = 'cap3'; # must be Actual Name of executables...user to configure this path.
$PHRAP = 'phrap'; # " " "
$CLUSTAL = 'clustalw'; # " " "
$CAP3PATH = '/usr/local/bin/'; # path to executable ....user to configure this path
$PHRAP_PATH = '/usr/local/bin/'; # path to executable ....user to configure this path
$CLUSTALPATH = '/usr/local/bin/'; # path to executable ....user to configure this path
$ACE2FASTA = $APACHE_PATH . $ROOT . "/custom/ace2fasta"; # user to configure this path
$JAR = "http://" . $HOST . "/jalview/jalview-1.7.5b.jar"; # user to set url path to JALVIEW jar file

7) Also, some of the features described in this document require the
HTMLTMPL parser as well as the Jalview sequence alignment viewer (download the Jalview jarfile and place it in your document root directory).

Acknowledgments:
The scripts and modifications described in this document were made possible by a grant from the National Science Foundation.
Also, without the previous work by numerous people on such diverse tools and software as: Acebrowser, WebAce,AceDB,
Perl, AcePerl, CGI.pm, Emacs, Apache, Linux and Sun, none of this work would have been possible.

Special thanks to these folks for finding bugs and/or providing useful suggestions:
Dave Matthews
Vickie Carolla
Gerry Lazo
Morten Hulden

If you have any questions or experience installation problems, please email me!
Hugh Edwards, June 03 2003