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Installation Guide for Linux
There is no need to shut down other applications in order to install the software, however it may be advisable to enhance the speed of your installation. Your machine should be connected to the internet to enable the full installation of all applications.

The Java SDK is a pre-requisite for successful installation of your BioBind software. We recommend the Blackdown port for linux. Alternatively the SUN microsystems version may be used.

The software is loaded into a /usr/local/emboss directory. If you have little disc space under /usr/local then make /usr/local/emboss a symbolic link pointing to a suitable area of disc prior to installation.

Login as Root

Insert the CD into the drive and type

cd /mnt/cdrom

at the prompt. The mountpoint may be different depending on the hardware and Linux distribution.

Type

./install

to initiate installation. Alternatively, simply type

/mnt/cdrom/install

Your BioBind software will automatically search for the Java installation in the most obvious places. Should it fail to find it, you will be prompted for the exact path of the Java location on your machine.

Licence
The BioBind Ltd Licence is a legal document that must be accepted in order to continue with the installation of your BioBind software. Declining the licence will result in termination of the installation.
Licence Key
Your BioBind software will only function using a valid 32 character licence key. If the key fails to validate, check that all numbers are zero and not the letter O. Should you have entered an invalid key, an error message will appear. If you have checked the above and your key still fails to function, please contact us.
Proxy Settings
On most systems, web pages are retrieved directly from the internet. Most home users will not access the internet using proxies and should leave the fields blank. However, some sites have a central server and the site policy insists that web pages are accessed through the server. Such a server is known as a proxy and can cache frequently queried web pages to improve search efficiency. The server is accessed by specifying a name and a port. A port is a doorway into the computer. The most common port for web access is 8080.

In most cases the proxy will look something like wwwcache.institute.ac.uk:8080 for institutes or wwwcache.company.co.uk:8080 for companies.

Proxy information is available from the web browser. A variety of commonly used web browsers is listed below together with instructions for retrieving proxy data. Access this information and type it into the BioBind Proxy Settings window.

    Internet Explorer

    Open the Tools menu and access Internet Options. Select the Connections tab and then the LAN settings button. If you require a proxy, the Advanced button under the Proxy Server section will be accessible. Click this button and type into the BioBind Proxy Request Field the Proxy address to use information followed by a colon (:) and then the Port number for both the HTTP field and the FTP field.

    Netscape

    Open the Edit menu and select Preferences. Click on the arrow next to Advanced and highlight Proxies. Copy the information in the HTTP Proxy field followed by the information in the Port field. Do the same for the FTP field.

    Mozilla

    Open the Edit menu and select Preferences. Click on the plus sign next to Advanced and highlight Proxies. Copy the information in the HTTP Proxy field followed by the information in the Port field. Do the same for the FTP field.

    Opera

    Open the Tools menu and select the Preferences option. Choose the Network option from this sub menu and then Proxy Servers. Copy the relevant information from the HTTP and FTP fields.

    Konqueror

    Open the Settings menu and select the Configure Konqueror option. Choose the Proxy icon from the scroll list on the left hand side of the window. On the Proxy tab on the right hand side ensure that the Use Proxy option is checked. (If it isn't checked and you are otherwise connected to the Internet, then you do not need a proxy for your machine) Follow one of the Setup buttons. Copy the relevant information from the HTTP, FTP and Port fields.
Select RPMs
There are 8 RPM modules which include the entire EMBOSS package, the PHYLIP, ESIM4, DOMAINATRIX and primer3 applications together with the PRINTS and Rebase databases and aaindex. These are free from any restrictions and are all selected by default. Sizes shown are for the i386 version. RPMs for x86_64 are slightly larger.

  • EMBOSS - Sequence analysis package. Approx. 13.6 MB
  • PHYLIP - EMBASSY phylogeny package. Approx. 312.2 KB
  • ESIM4 - cDNA/Genomic alignment application. Approx. 47 KB
  • DOMAINATRIX - EMBASSY 3D structure package. Approx. 165 KB
  • Primer3 - EMBASSY primer design application. Approx. 233 KB
  • PRINTS - Protein motif database. Required for pscan. Approx. 22.8 MB
  • Rebase - Restriction enzyme database. Required for all restriction applications. Approx. 304.2 KB
  • aaindex - Amino acid biophysical properites index. Approx. 159.1 KB

BioBind Installation
All selected RPMs will now be installed on your machine. Should all 8 RPMs be selected, installation should take approximately 1 minute.

Select Downloads
BioBind does not distribute some EMBASSY packages or data which have potentially restrictive licencing conditions. If use of this data is allowed at your site then leave the selection boxes checked, otherwise de-select them. Please see our EMBASSY page for further details.

BioBind Downloads
Your software will automatically retrieve this information from the appropriate web site and install it. Total installation time for all additional modules is approximately 5 minutes using 512Kbps downstream speed.

Installation Complete
This message will tell you that your installation is complete. If you are installing a new version, and the final message states that "Nothing needed to be installed" you still have files left from an old installation which must be deleted.

Logout from the machine and log back in with your correct username. This will automatically set the paths to both Java and EMBOSS.

Accessing EMBOSS
Type the name of an EMBOSS program at the prompt to access this software. Applications can be incorporated into scripts using the path prefix /usr/local/emboss/bin.

Accessing Jemboss
Access the Jemboss graphical user interface by typing jemboss at the prompt.
Uninstalling your BioBind software
Should you upgrade to a new version of the software, you must first remove the old installation.

Log on as Root and re-insert your BioBind Software CD (either the original one or a new one). If your mountpoint is /mnt/cdrom type

/mnt/cdrom/scripts/uninstall

and the old software will be removed. If your mountpoint is different, replace /mnt/cdrom with the relevant path.

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