ESTIMA Installation Instructions by Z13tl82


									                          ESTIMA Installation Instructions

ESTIMA is currently tested and installed on SGI IRIX v6.5 and Solaris 8 and 9 SUN
machines. The scripts are platform independent and should run on any system that has
Perl (with DBD/DBI, zlib, libpng, GD, Bioperl modules), Java and C compilers, any web
server (currently installed on Apache 1.3.27) and Oracle database.

System Prerequisites
Warning: All of the following need to be installed by a system/database administrator:

1. Compiling and Archiving Utilities These are typically distributed as a package for
the specific platform, and the list is meant as an example.
             GCC
             Autoconf
             Automake
             make
             gzip
             LD
             AR
             AS

2. Perl 5.6 or higher. The following Perl modules are required to be installed. The
source code for most of these modules is available from, unless noted
otherwise. To install all of these modules conveniently, we would suggest installing
Bundle::CPAN first.
    BioPerl
    Freetype
    GCC
    HTML
    Text
    Libexpat
    XML
    LWP
    IO
    zlib (
    Libpng (
    Gd (
    DBD 1.15
    DBI 1.43

3. JDK for TraceViewer

4. Apache web server (
5. Oracle 8i or 9i

External Bioinformatics Software

BLASTALL – Suite of programs from NCBI to search DNA or protein sequences
against sequence databases (flatfiles).
        Available from
Phred – A base calling program that takes trace files (chromatograms) as input. Contacts
for obtaining the programs and for questions, bug reports:
     Brent Ewing,
TraceViewer -- To view Trace Files on the web. TraceViewer is available from Baylor
College of Medicine
[]. It needs
Phred for base calling.

ESTIMA Installation

1. Download the ESTIMA distribution from the web site by following the link ‘Download Software’
at the bottom of the page.

Uncompress and untar it as follows:
     gunzip –c ESTIMA_Upload.tar.gz | tar xf -

You will see four directories:
            for_cgi-bin – needs to go into wherever your cgi-bin directory is
            for_htdocs – needs to go into wherever your htdocs directory is
            schema_scripts – This directory has two SQL scripts for creating the
               ‘genome’ schema, and for creating the specific PROJECT schema. Every
               instance of a project will have its own PROJECT schema.
            sample_data_fload_scripts —This directory contains two subdirectories,
               GENOME, PROJECT. GENOME folder contains data loading SQL query
               scripts for the GENOME schema tables that were created using the
               genome_schema.sql. PROJECT folder contains data loading scripts for the
               PROJECT schema tables created using project_schema.sql.

2. Instructions to the Database Administrator
        ESTIMA is designed to operate in conjunction with any ODBC compliant
database. To that end, exact instructions creating ESTIMA databases are not possible.
None the less, it is relatively straight forward. ESTIMA requires a database schema
called GENOME and then one additional schema for each project that your installation of
ESTIMA will support. Since it is impossible for us to know what you will name your
projects, in this document this additional schemas will collectively be called PROJECT.

       First, create a schema (and if needed a table space and whatever else your DB
engine require) named GENOME. Execute the genome_schema.sql script in your
favorite SQL editor. This script will create all of the tables needed in the GENOME

        Next, create your first PROJECT schema. If you are installing our demonstration
data, create a schema named DEMO. Once this is done, run the PROJECT_schema.sql
script (again in your favorite SQL editor) to create all of the tables needed for the DEMO

        In the sample_data_load_scripts folder there are two subfolders, each containing a
series of SQL files. Each file contains a series of INSERT statements that can be used to
populate all of the tables just created.

    If your project is to require a password, you will need to create a record in the

3. Instructions to the Webmaster
        Although we have made an effort to keep ESTIMA simple, there are still several
steps required in order to get the system up and running. First, move all the files in the
FOR_CGI-BIN folder to a location suitable for CGI scripts. We like to keep them all in a
folder called ‘estima’ in cgi-bin. Thus the URL for the scripts would be
http://hostURL/cgi-bin/estima/whatever_script, as explained below in detail. Next, move
the image files that we have provided for the ‘DEMO’ example project from
FOR_HTDOCS folder to somewhere that the web server can see them (these are the
graphical elements that are displayed on the top banner).
        The HTML used to generate the look of the page is contained in
in the print_header routine. This can be edited to give your site it’s own look. Please
follow the detailed instructions given below.

4. Configuration
       Go into directory ‘for_cgi-bin’
       Open file for editing.
           Set all of the system variables as indicated in the file
                  o ORACLE_HOME---Path to your Oracle installation
                  o home --Your cgi-bin URL for the ESTIMA scripts (website)
                  o temp_dir -- Some of the scripts need some scratch space which is
                      visible to the web. Make sure this is a valid directory.
                  o blastall – Path to blastall executable
                  o background – URL to some pretty picture for webpage
                      background. The image ‘bases.gif’ has been provided by us and is
                      in the ‘for_htdocs/images/estima_h/ folder.
                  o contact_email – Contact person email
                  o contact – Name of contact person
                  o SEQDBlink – URL to estima_seqQuery script
                  o Contiglink – URL to estima_contigviewer script
                  o blast_db_location – Central location of BLAST databases that
                      would be available to users from the web for running BLAST
          o myDIR -- This holds the path to where output file is written. It
            needs to be a valid directory visible to the web server.
          o myURL – URL that points to the above ‘myDIR’ directory.
          o go_local – Same as temp_dir path to scratch space visible to the
          o go_hostname – Your host URL only e,g,
          o go_home – Same as path for output file in ‘myDIR’
          o go_title – Title for your annotation window.
          o seqquery_script – URL to estima_seqQuerry script
          o trace_viewer – URL to TraceViewer along with cgi parameters
          o launcher_phred – Path to Phred executable for base calling
          o launcher_temp – Some temporary directory not visible to the web
          o launcher_trace_data – Path to trace data visible to web
          o seqQueryURL – cgi-bin URL to estima_seqQuery script
          o cv_home – Scratch space visible to web, same as temp_dir
          o webhome – URL path to cv_home

Open for editing
   This file contains all of the project specific configuration variables. It
      reads the estima_SEQDBConfig.xml file.
   So set the location of estima_SEQDBConfig.xml in $file variable
   Go to connectdb subroutine . Set the following:
          o ORACLE_HOME path to Oracle application
          o LD_LIBRARY_PATH variables for Oracle library and system
              library paths (/usr/local/lib ??)
          o Set DBI connection info for every project instance. We have given
              examples for ‘demo’ project and ‘some_other_project’. Replace
              these with your project names, and database connection info.
          o Enter the connection info for the ‘genome’ schema.
   Go to the print_header subroutine.
          o For every project, enter the path to project-specific images. We
              have     provided      some       generic, dummy       images   in
              for_htdocs/images/estima_h/ folder. Please make your own, or
              have a project supervisor, provide their own.
          o map name="home_map" – Substitute your intitution’s URL, and
              path to estima_start webpage. Pass a specific project name (demo
              in example), to seqSet variable.
          o Go through rest of the HTML for ‘demo’ project. Carefully
              substitute paths to various images to change the look and feel.
          o Do exactly the same for some_other_project (if you choose to).
   If you have a third project etc, repeat the code in elsif {seqSet block in
      both connectdb and print_header subroutines.

Open estima_SEQDBConfig.xml for editing
              This file contains XML for an example project ‘demo’. Rename and
               change carefully all of the info for your own project.
              If you have a second project, take the code between and including
               <SEQDB:ESTSet> and </SEQDB:ESTSet> tags. Repeat it as many times
               as the number of unique EST projects.

Thanks to Keith Frazier (email:, System administrator for invaluable
help with System installations.
If you need help, contact Dr.Lei Liu, email:

Charu Gupta Kumar and Rich LeDuc

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