Installation of the HEART-2DPAGE Software

Contents

• Introduction
• License terms
• Requirements
• Installation
  • Installation of the C programs
  • Installation of the CGI scripts
    • Setting up the Perl Environment
    • Making the CGI scripts World Wide Web-accessible
    • Configuration of most of the CGI scripts
    • Configuration of Imagemap
• Documentation
• Known problems

Introduction

License terms

Permission to copy and distribute HEART-2DPAGE in its entirety, for non-commercial purposes, is hereby granted without fee, provided that this license information and copyright notice appear in all copies.

If you redistribute HEART-2DPAGE, the *entire* contents of this distribution must be distributed.

The software may be modified for your own purposes, but modified versions may not be distributed without prior consent of the author.

This software is provided 'as-is', without any express or implied warranty. In no event will the author be held liable for any damages arising from the use of this software .

Requirements

The HEART-2DPAGE software uses the gd library for manipulating gif images. gd library is copyright 1994, Quest Protein Database Center, Cold Spring Harbor Labs and is written by Thomas Boutell. The library (version 1.1.1) is included in this package.

Installation

This package is a compressed (gzip) tar archive. To unpack into the current directory use:

gtar -zxf HEART-2DPAGE.tar.gz

or:

gzip -dc HEART-2DPAGE.tar.gz | tar -xf -

The archive includes:

• the HEART-2DPAGE software in the directory DB-software-sources/.
  It contains:
  • all perl written CGI scripts in perl-scripts/
  • the cgi script findlink in findlink/
  • programs to manipulate GIF images in c-source/
  • imagemap in imagemap/
  • gd library in gd/
  • shell scripts in sh-scripts/

• the HEART-2DPAGE documents in the directory 2dprot/.
  It contains:
  • HTML documents
  • map files for clickable images
  • spot information in spots/
  • some gel images in images/
  • all CGI scripts needed by HEART-2DPAGE in script/

Not included:

• Mapedit: a program to generate map files for clickable images. You can get Mapedit from www.boutell.com/mapedit.

Installation of the C programs

BUILD compile all C programs in their corresponding directoy including gd library, imagemap, findlink and utilities for manipulating gif images (gifcrossxy, gifshadow, gifzoom ...). In addition the executable programs imagemap, findlink, gifcrossxy and gifshadow are copied into the cgi directory 2dprot/script because they are used as cgi scripts.

For systems running SunOs 4.* the script BUILD.sunos4 should be used. Arising linker warnings like "warning: table of contents for archive is out of date, ..." can be ignored.

Installation of the CGI scripts

The HEART-2DPAGE makes use of executable server scripts (CGI scripts) to produce documents on the fly. This section describes how to configure these scripts. The configuration is somewhat difficult because different scripts exist and some things have be done:

Setting up the Perl Environment

Most of the CGI scripts are written in perl. These scripts require the perl interpreter to be at /usr/local/bin/perl.

If your perl interpreter stays at another place you can do one of the following:

1. make a link (probably you have to login as root to do this):

   ln -s /your/directory/perl /usr/local/bin/perl .

   Assuming your perl interpreter is at /usr/bin/perl then use:

   ln -s /usr/bin/perl /usr/local/bin/perl

2. change the first line of each of the following perl scripts in the directory 2dprot/script:
   • Parse
   • ReadConf
   • get-2d-entry
   • markquadrant
   • nph-startgifcrossxy
   • nph-startgifcrossxy.lg
   • picture
   • picture.lg
   • startimagemap.lg
   • startimagemap.sml
   • zoom

   Use an editor to change the first line from '#!/usr/local/bin/perl' to '#!/your/directory/perl'.

   Assuming your perl interpreter is at /usr/bin/perl then change the first line from

   #!/usr/local/bin/perl to #!/usr/bin/perl

Making the CGI scripts World Wide Web-accessible

To make the CGI scripts accessible by the World Wide Web you can:
1. copy the CGI scripts from 2dprot/script into the WWW server's cgi-bin directory

2. reconfigure your WWW server by adding a new translation rule to the WWW server's configuration file.
   For instance this could be done for the CERN WWW Server by: 'Exec /cgi-bin/dhzb/* /directory/you/unpacked/this/package/2dprot/script/*'.

For details consult the documentation of your WWW server.

Configuration of most of the CGI scripts

The CGI scripts get-2d-entry, markquadrant, nph-startgifcrossxy, nph-startgifcrossxy.lg, picture, picture.lg, startimagemap.lg, startimagemap.sml and zoom are written in perl. They are configured by the configuration file 'Heart-CGI.conf'.

The configuration file 'Heart-CGI.conf' consists of lines with the format: entry = value. Comments can be inserted. A comment starts with a hash sign # and ends at the end of line.

Example:

# # Configuration file for the HEART-2DPAGE # # Directories where the server finds the CGI-scripts and images # CGIDir = /home/pleiss/heart-2dpage/2dprot/script ImageDir = /home/pleiss/heart-2dpage/2dprot/images # Directory to save temporary data # TempDir = /tmp You have to setup your own configuration file. Copy your 'Heart-CGI.conf' into the directory the CGI scripts are started by the WWW server.

You can use 2dprot/script/Heart-CGI.conf as basis; adapt it to your own needs.

The configuration file must contain values for each of the following entries:

CGIDir dir

This entry sets the (real) directory the cgi scripts are located. dir is an absolute path of the directory on the server the cgi scripts can be found. This entry is used by cgi scripts to start other scripts. For example:

CGIDir = /home/pleiss/2dprot/script

ImageDir dir

This entry sets the (real) directory the images are located. dir is an absolute path of the directory on the server the images can be found. This entry is used by cgi scripts to access images on the fly. For example:

ImageDir = /home/pleiss/2dprot/images

TempDir dir

This entry sets the (real) directory the scripts can store temporary data. dir is an absolute path of the directory on the server the data can be stored. For example:

TempDir = /tmp

BinDir dir

This entry sets the (real) directory the scripts can find the unix commands 'rm' and 'cp'. dir is an absolute path of the directory on the server the scripts look for 'rm' and 'cp'. For example:

BinDir = /usr/bin

HomeURL url

This entry sets the URL of the (virtual) home directory of the HEART-2DPAGE. url is an URL pointing to the directory the HEART-2DPAGE starts.

For example:

HomeURL = http://www.chemie.fu-berlin.de/user/pleiss

Because of browser capabilities this one works too:

HomeURL = /user/pleiss

The HomeURL entry is used by cgi scripts to generate hypertext links within HTML documents. These links can then point to other HEART-2DPAGE pages.

HomepageURL url

This entry sets the URL of the home page of the HEART-2DPAGE. url is an URL pointing to the home page of the HEART-2DPAGE. For example:

For example:

HomepageURL = http://www.chemie.fu-berlin.de/user/pleiss/dhzb.html

Because of browser capabilities this one works too:

HomeURL = /user/pleiss/dhzb.html

ImageURL url

This entry sets the URL of the (virtual) directory the images are in. url is an URL pointing to the directory the images for the HEART-2DPAGE can be found.

For example:

ImageURL = http://www.chemie.fu-berlin.de/user/pleiss/images

Because of browser capabilities this one works too:

ImageURL = /user/pleiss/images

CGIURL url

This entry sets the URL for the (virtual) directory the cgi scripts can be executed. url is an URL pointing to the directory the server can find and execute the cgi scripts.

For example:

CGIURL = http://www.chemie.fu-berlin.de/cgi-bin/dhzb

Because of browser capabilities this one works too:

ImageURL = /cgi-bin/dhzb

A sample 'Heart-CGI.conf'.

Configuration of Imagemap

To use clickable images you have to create an imagemap configuration file. The name and path of the configuration file is selected within the C source code of imagemap. To change name and path of the configuration you have to edit the source code DB-software-sources/imagemap/imagemap.c at line 60. Then you have to recompile imagemap.c.
Change line 60: #define CONF_FILE "/usr/local/etc/httpd/conf/imagemap.conf" To: #define CONF_FILE "<path_to_your_conffile>/imagemap.conf" For details about imagemap and map files read the Imagemap documentation .

To create map files for clickable images use the program Mapedit. You can get it from www.boutell.com/mapedit.

Documentation

• HEART-2DPAGE (only in german)

• Mapedit

• gd library

Known problems

• The usage of other gel images is hard to achieve because most of the cgi scripts depend on given images and on given image sizes.
• Documentation and comments in programs are in german
• The shell scripts in DB-software-sources/sh-scripts/ require the images to manipulate and the executed programs (gifzoom, gifaxes, ..) to be in the same directory

If you have problems, feel free to write an email to Stefan Sander.