WebAGCoL Package  
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This document describes how to install the WebAGCoL Package.

CONTENTS OF WebAGCoL PACKAGE
  • WebFPC: A web based java program to view the contigs of FPC database.
  • WebChrom: A web based display to browse the chromosome for markers and contigs.
  • WebBSS: A web interface to BSS. BSS organizes sequence searches against target sequences which are located on an FPC map. The target sequences can be BAC-end sequences (BES) or sequenced clones.
  • WebFcmp: A web tool for fingerprint comparison.
  • Install: Script to Install the WebAGCoL package and a skeleton configuration file.
  • demo: A set of demo files that can be installed for demostration.


WebAGCoL PACKAGE PREREQUISITES  [ Back ]

The following software packages must be installed on your system:


INSTALLING WebAGCoL PACKAGE  [ Back ]

Download the WebAGCoL Package from following link
-- http://agcol.arizona.edu/software/webagcol/download/

Untar the downloaded file with following command:
-- tar -zxvf webagcol_install.tar.gz

Change the webagcol_install directory
-- cd webagcol_install

Follow these steps to install the demo:
1. Go to the demo directory (cd demo),
2. Read the config.demo file for further instructions -- you need to change the file paths in config.demo,
3. Run the install script
-- perl ../Install/setup.pl config.demo
4. View the results from your web page (as explained in config.demo).

To install WebAGCoL for your FPC:
1. Go to the Install directory. This directory has the setup.pl script that will install the WebAGCoL package on your local system. It also has a skeleton configuration file that you customize to your site.
2. Make a copy of config.template (i.e. cp config.template config).
3. Edit the config file. The file has instructions, and the following section has details.
4. Install the WebAGCoL package by running the following command
-- perl setup.pl config

This will install all the contents of the WebAGCoL Package based on the details provided in the config file.



WebAGCoL PACKAGE CONFIG FILE DESCRIPTION  [ Back ]

Config file is used by the setup.pl script to get the detail on installing the WebAGCoL Package.

The configuration file is divided into two sections:

  • General Section: This section specifies the options for installing common files used by the package. The following options are recognized by the setup.pl script:

    • HTML_DIR_PATH: The location of the directory accessible from the web server that will contain all the HTML files for the package.
    • HTML_DIR_URL: The URL corresponding to HTML_DIR_PATH which can be accessed from the web
    • CGI-BIN_DIR_PATH: The location where all the cgi files for the package are installed
    • CGI-BIN_URL: The URL corresponding to CGI-BIN_DIRECTORY_PATH
    • FPC_EXECUTABLE_PATH: The path where the FPC executable is installed on your local machine. This can be left blank if WebBSS and WebFcmp will not be installed (as specified below).

  • Project Section: This section of the config file is for defining one or more FPC projects. The following options are recognized by the setup.pl script:
    • MAP_NAME: The name of the FPC project for which the WebAGCoL tools will be installed.
    • SETUP: WebFPC must be installed, but the other three packages are optional. Specify which packages you want installed by entering the following values seperated by commas.
      -- WebFPC
      -- WebChro
      -- WebBSS
      -- WebFcmp
      For example, "WebFPC, WebChro" only installs WebFPC and WebChrom. The options below are for the tools specified in parenthesis, and additional information is provided in the tool's Site Manual.
    • FPC_FILE: (All) The full path of the FPC file (*.fpc) for the FPC project
    • REFERENCES_DIR: (WebFPC, WebChrom) The path to the references directory which has the files used by WebFPC and WebChrom for adding external references.
    • TYPE_COLORS: (WebFPC) These are the Marker type colors shown in the WebFPC display.
      The FPC marker type is specified followed by its color in parenthesis. More then one type(color) can be specified by delimiting them by a comma.
    • SHOTGUN_COLORS: (WebFPC) These are the Shotgun type colors shown in WebFPC display.
      The FPC shotgun type is specified followed by its color in parenthesis. More then one type(color) can be specified by delimiting them by a comma.
    • CHROMOSOME_FILE: (WebChrom) The path to the location of chromosome file used by WebChrom. The chromosome file contains the locations of the centromere for chromosomes and the sizes (in Mb) of the chromosomes.
    • FPC_COR_FILE: (WebFcmp) The full path of the FPC cor file (*.cor) for the FPC project.
    • LIBRARY_NAME: (WebFcmp) Defines the clone prefix of the libraries in the FPC project seperated by comma (e.g. a,b,c). It may also be left blank if there is only one library.
    • BES_FILE_PATH: (WebBSS) The full path to the directory of the BAC End Sequences. This is left blank if here are only genomics sequences.
    • GENOME_FILE_PATH: (WebBSS) The full path to the directory of Genome sequences. This is left blank if if there are only BES sequences. Note, if WebBSS is installed, either BES_FILE_PATH or GENOME_FILE_PATH or both must be defined.
    • WEBBSS_SEQ_FILE: (WebBSS) Path to the location of sequence file. This is an sequence file used as an example sequence for the WebBSS page.
Note: You can define as may projects as you want in one config file with each new project starting with a MAP_NAME.



HOW TO HANDLE UPDATES  [ Back ]

After the setup.pl script is run on the demo files (or your project files), the following directories will be created:
WebAGCoL/
Demo/ HelpDir/ ScriptDir/ WebFPC_jar
And under the Demo directory will be the files:
Data/ WebBSS/ WebChrom/ WebFPC/ WebFcmp/ config/ index.html references/ update.sh

The files in directories Data, config and references can be changed and the update.sh script needs to be run to update the WebAGCoL site with the new information/data. For example, if the demo.fpc file is changed, we could move the updated one into Data and run update.sh and the site would get updated. (If you have installed the demo, try changing the config/type_colors file, e.g. change yellow to blue, and run the update.sh and note the changed color in WebFPC).

To be more specific, the setup.pl script writes the 'update.sh' script in the project directory in location
-- <HTML_DIR_PATH>/WebAGCoL/<project name>/

If your FPC file has been updated and you want the WebAGCoL site updated with the new release, copy the updated FPC files (*.fpc, *.cor) to the following location
-- <HTML_DIR_PATH>/WebAGCoL/<project name>/Data

Then run the update script from the project directory.


WebFPC PREREQUISITES [ Back ]

Install Java 1.4.0_03
-- http://java.sun.com/products/archive/j2se/1.4.0_03/index.html



HOW WebFPC WORKS [ Back ]

The setup.pl script writes the necessary files for the project.

The following files are written to <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME>/WebFPC directory

  • index.html html file that displays the initial page for WebFPC.

    • The following files are written to <CGI-BIN_DIR_PATH>/WebAGCoL/WebFPC directory

  • WebFPC_Direct_v2.1.cgi a cgi scripts to link into the FPC Java display.

    • The following files are written to <CGI-BIN_DIR_PATH>/WebAGCoL/WebFPC_jar directory

  • agcol.jar, crimson.jar, gnu-regexp-1.1.4.jar and webfpc.jar are used by WebFPC Java display. WebFPC is written as a Java applet, and its class files are compressed into 'jar' files. index.html an HTML file references these jar files, and loads the applet into the web browser at the size specified in the HTML file.

    The setup.pl script uses splitter.pl ( in ScriptDir directory ) to generate the data files used by WebFPC. These files are written to <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME>/WebFPC/DATA directory. The applet retrieves files from the host server containing information on the contigs as they are needed, and uses the data in the files to display contig information in the applet window. For each contig, a separate gzipped XML file is created. The applet retrieves the information from this location for the contig that needs to be displayed. The Java implementation of the SAX parser is used by WebFPC to retrieve the contig's XML file while simultaneously parsing it.

    Web References: The splitter.pl script looks in the <REFERENCES_DIR> for files that contain information on linking clones and/or markers to remote sites. A separate file must be created for each remote site to link to. The information retrieved from these files is written into the contig XML files. For the format of these files, see the File formats section.



    LINKING TO WebFPC FROM A REMOTE SITE [ Back ]

    WebFPC allows external applications to initiate the contig display. To do so, the CGI script "WebFPC_Direct_v2.1.cgi" is called with the project name, and either a clone name or marker name or contig number. Note, all parameters are currently case sensitive.

    Parameter Rule Value
    name Required The name of the FPC project.
    contig Either The index number of the contig. Note: Value must be an integer, i.e. do not prefix with 'ctg'.
    clone Or The name of the clone that is to be selected.
    marker Or The name of the marker that is to be selected.

    Examples

    For example, AGCoL'S URL is
    http://agcol.arizona.edu/cgi-bin/WebAGCoL/WebFPC/WebFPC_Direct_v2.1.cgi

    To display contig 14 in the rice project, append the following to the above url: ?name=Demo&contig=1.

    If you wish to display the contig containing clone a0025J10, append ?name=Demo&&clone=a0003L03 .

    If you wish to display the contig containing marker A07, append ?name=Demo&&marker=A07. If the marker is contained in more than one contig, the list of contigs will be displayed

    Project Parameter

    The 'name' parameter must be in the config file as MAP_NAME. See Installing WebAGCoL for more information.



    FILE FORMATS & CONFIG [ Back ]

    The following config variables are used: FPC_FILE, REFERENCE_DIR, SHOTGUN_COLORS, TYPE_COLORS.

    All files in this section are put into the <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME> directory by the setup.pl script, and can later be changed by the user (the update.sh needs to be rerun after a change). This directory will be referred to as the MAP directory in the following discussion.

    Reference file

    One or more reference files are in the a directory specified by REFERENCE_DIR. The update.sh will create a sub-directory /references of the MAP directory, and move the reference files into it. Thereafter, you can update the directory yourself, and run update.sh so that WebFPC will have the new/modified links. The format for the input files:

    <Site Name>
    ["Clone List:"<clone url prefix> [<clone url postfix>]
    (<clone name in fpc file> [<clone name on site>])+|"all"
    "end"]
    ["Marker List:"<marker url prefix> [<marker url postfix>]
    (<marker name in fpc file> [<marker name on site>])+|"all"
    "end"]

    Example File:

    Clone List:http://www.ncbi.nlm.nih.gov:80/entrex/query.fcgi?cmd=Search&term=&dopt=GenBank 
aDC1A0 DCPaDC1A0
aDC1B3 DCPaDC1B3
end
    
Marker List:http://www.ncbi.nlm.nih.gov:80/entrex/query.fcgi?cmd=Search&db=Probe&term=
all
end

    Explanation of Example:

    The site name is the name by which the site will be referred to by WebFPC.

    The URL may have two parts: one that goes before the clone or marker identifier, and one that goes after it. The second one is optional. The two parts are separated by white space. An example of the clone URL, aDC1A0, would be http://www.ncbi.nlm.nih.gov:80/entrex/query.fcgi?cmd=Search&db=Nucleotide&term=DCPaDC1A0&dopt=GenBank . Notice that the clone is referred to as aDC1A0 in WebFPC, but DCPaDC1A0 is used to look it up on the web site.

    If all clones in FPC are also on the remote site, and they use the same names, the word 'all' can be entered.

    The marker list works the same as the clone list.

    Shotgun colors

    An optional file, called 'shotgun_colors', is created in the /config sub-directory of the MAP directory by the upate.pl script. It is used to highlight clones with a sequencing status. The format is: 

    <SHOTGUN TYPE> <COLOR>
    An example, highlighting all clones with a SENT, FINISHED, or SHOTGUN status yellow, is given below: 
    SENT blue
FINISHED yellow
SHOTGUN yellow
    Valid colors that can be used are blue, dark_gray, gray, light_gray, magenta, orange, pink, red and yellow.

    Type colors

    An optional file, called 'type_colors', is created by the /config sub-directory of the MAP directory by the update.sh script. It is used to highlight markers of a particular type. The format is: 

    <MARKER TYPE> <COLOR>
    An example, highlighting STS and eMRK clones yellow, is given below: 
    STS yellow
eMRK yellow
    The list of valid colors is the same as for the Shotgun colors.

    Help URL   Back to top

    A file containing the URL of the WebFPC User's Manual is placed in config directory by the setup.pl script. It is called 'help_url', and should not need to be modified, unless the documentation is moved.



    • WebChrom PREREQUISITES     [ Back ]

    For WebChrom, the following software packages must be installed on your web server:


    HOW WebChrom WORKS         [ Back ]

    The setup.pl script uses two scripts webchrom.pl and wcSearch.pl ( in ScriptDir directory ) to generate the files for the WebChrom and WebChrom Search tools.

    The webchrom.pl script reads the FPC file, the chromosome file and references file(see File Formats) and generates the files in <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME>/WebChrom directory.

  • index.html html file that displays the initial page of chromosomes.
  • For each chromosome or linkage group, webchrom.pl generates the *.html files and *.png files.
  • A JavaScript/Jscript file named zmenu.js is also generated, containing code allowing the popup menus to work for each HTML file.

    • The wcSearch.pl script reads the FPC file, the chromosome file and references file(see File Formats) and generates the files in <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME>/WebChrom directory.

  • wcSearch.html html file that displays the initial for WebChrom search.
  • A sub-directory called DATA which contains "storables" for the Search tool.
  • A 'tmp' directory is created to which the Search tool writes temporary images generated for searches. (Note: These temperory image files are removed from the system by the script after 24 hours) The wcSearch.pl generates the following files in <CGI-BIN_DIR>/WebAGCoL/WebChrom directory:
  • wcSearch.cgi a cgi script which generates the results for WebChrom Search.


    •



    FILE FORMATS & CONFIG     [ Back ]

     

    The following config variables are used: FPC_FILE, CHROMOSOME_FILE, REFERENCE_DIR.

    All files in this section are put into the <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME>/config directory by the setup.pl script, and can later be changed by the user (Note: the update.sh needs to be rerun after a change). This directory will be referred to as the MAP directory in the following discussion.

    Chromosome File

    The chromosome file is specified by the CHROMOSOME_FILE variable, and is copied to the 'config' sub-directory of the MAP directory. This file contains the locations of the centromere for chromosomes and the sizes (in Mb) of the chromosomes. The file has two parts divided with the following specification:

    <Chr or Lg> CENTROMERE_POS <3 digits.1 digit> [<3 digits.1 digit>]

    and

    <Chr or Lg> LENGTH <3 digits.1 digit>

    For example: 

    
1  CENTROMERE_POS 73.5 73.5
2  CENTROMERE_POS  50 54.6

1  LENGTH 43.3
2  LENGTH 39.9
    defines two chromosomes, both with centromeres. The centromere section is optional. The start and end coordinates of the centromere can be the same. The length is also optional; if absent, webchrom.pl will calculate a length based on the length of the contigs located on the chromosome.

    Reference Files

    The reference files are shared by both WebFPC and WebChrom, though WebChrom only uses the markers. See references for more information.



    WebBSS PREREQUISITES [ Back ]

  • Standalone FPC program -- http://agcol.arizona.edu/software/fpc/
  • NCBI Standalone BLAST -- ftp://ftp.ncbi.nlm.nih.gov/blast/executables/
  • Data::Page -- http://cpan.org/modules/by-module/Data/
  • Storable -- http://cpan.org/modules/by-module/Storable/



    • HOW WebBSS WORKS     [ Back ]

    The setup.pl script writes the necessary files for the project.

    Following files are written to <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME>/WebBSS directory

  • index.html html file that displays the initial form page for WebBSS for sequence input.

    • Following files are written to <CGI-BIN_DIR_PATH>/WebAGCoL/WebBSS directory

  • webbss.cgi a cgi scripts that runs the FPC in batch mode and displays the BSS results to the browser.
  • Tableizer.pm a perl module to convert a dataset into a cached, pageable, sortable HTML table.

    • Following files are written to <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME>/Data directory:

  • BSS.fpc a truncated version of FPC file used by WebBSS. The BSS.fpc file is generated by trunc_fpc.pl script (in ScriptDir directory)
  • BSS_results directory where the BSS search results are stored.
  • BSS.pag file ( a BES to clone mapping file ) in BES directory which is used by FPC version 8.2 or higher.

    When a sequence in FASTA format are submitted from index.html with BSS parameters, WebBSS runs BSS searches via FPC's batch mode function and outputs the results to a temporary 'BSS_results' directory and then displays the results in browser. For more details on BSS refer to the BSS tutorial.

     


    FILE FORMATS & CONFIG    [ Back ]

    The following config variables are used: FPC_FILE, BES_FILE_PATH, GENOME_FILE_PATH, WEBBSS_SEQ_FILE.

    All files in this section are put into the <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME>/Data directory by the setup.pl script, and can later be changed by the user (Note: the update.sh needs to be rerun after a change). This directory will be referred to as the MAP directory in the following discussion.

    BES Files:

    You specify a directory of BES files in the BES_FILE_PATH variable of the configuration file. The BES files should be in FASTA format and files should have ".bes" extension.
    To associate a BES with a clone name, the clone name in FPC must a substring of the BES name. For example, clone a0001a01 in FPC has the BES OSJNBa0001a01.f and OSJNBa0001a01.r. The setup.pl will make a soft link to the directory in <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME>/Data directory.

    BSS.pag File (Used by FPC version 8.2 or higher):

    This file is created by create_besmap.pl script and is stored in the BES's folder (i.e. BES_FILE_PATH). This file stores the mapping information of BES's to clones from FPC. Run update.sh script to update WebAGCoL package with the new BES's data.

    Sequence Files:

    The sequence clones must be in FPC as simulated digest (SD) clones. This can be done for agarose gels using the FSD program. (For HICF, contact us). The clone is entered into FPC with its GenBank name followed by "sd".

    You specify a directory of sequence files in the GENOME_FILE_PATH of the configuration file. The sequence files must be named by their GenBank accession number, though they can have a suffix, e.g. AC00000.seq. The BSS will match this to the FPC clone AC0000sd1. The setup.pl will make a soft link to the directory in <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME>/Data directory.

    Sample Files:

    You specify a file name for the example file in the WEBBSS_SEQ_FILE variable of the configuration file. You will want to use a file that you know will have a hit to either one or more BES's or Genome sequence. This is the file that is used when the "Load Example Sequence" is selected on the WebBSS page.





    • WebFcmp PREREQUISITES [ Back ]

  • Standalone FPC program -- http://agcol.arizona.edu/software/fpc/


    •



    HOW WebFcmp WORKS     [ Back ]

     

    The setup.pl script writes the necessary files for the project.

    Following files are written to <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME>/WebFcmp directory:

  • index.html html file that displays the initial form page for WebFcmp for clone names input.

    • Following files are written to <CGI-BIN_DIR_PATH>/WebAGCoL/WebFcmp directory:

  • fcmp_plate.cgi a cgi scripts that reads the clonenames.txt file and displays the plate information in browser for users to select the clone names.
  • fcmp.cgi a cgi scripts that runs the FPC in batch mode and displays the comparison results to the browser for the clone names provided by the user.
  • tmp directory where the comparison results are stored.

    Following files are written to <HTML_DIR_PATH>/WebAGCoL/<MAP_NAME>/Data directory:

  • clonenames.txt file which contains clone names and indexes from the FPC files (*.fpc,*.cor). The clonenames.txt file is generated by clonenames.pl script (in ScriptDir directory)

    When a set of clones are submitted from index.html, the CGI script fcmp.cgi executes FPC in batch mode, and outputs the results into a temporary 'tmp' directory and then displays the results in browser.

     



    FILE FORMATS & CONFIG     [ Back ]

     

    The following config variables are used: FPC_FILE, FPC_COR_FILE, LIBRARY_NAME

    There are often multiple libraries in a FPC file, so there is a drop-down menu on the WebFcmp that allows the user to select the library to assist in getting the clone name. For example, our rice FPC is made of OSJNBa and OSJNBb. In FPC, we leave off the OSJNB and just prefix each clone with a or b. The LIBRARY_NAME variable in config file lets you specify the prefixes, e.g. we use prefixes a and b for rice. These values will be shown in the Library drop-down menu.
    Note: If the Library naming schemes are different then you need to modify the clonenames.pl in ScriptDir directory and fcmp_plate.cgi in /WebAGCoL/WebFcmp directory to parse the plate names.

    There is no input file for this tool.

    • Email Comments To: www@agcol.arizona.edu