Introduction to the Standalone WWW Blast server


Index

Introduction

This standalone BLAST server was designed similar to regular NCBI BLAST server and command-line NCBI BLAST program "blastall". It incorporates most features, which exist in NCBI BLAST program and should be relatively easy to use. The main points here, that this server DOES NOT support any request queuing and load balancing. As soon as user hit "Search" button, BLAST will start immediately if entered information is valid. So, this server is not intended to handle large load, which may exist in public service. Standalone server assumes, that user has its own BLAST database, that should be searched and want to have simple WWW interface to this search. It is STRONLY recommended that user has experience to install and run standalone NCBI BLAST programs.

After files uncompressed server is ready to be used immediately. Any customizations to the program are welcomed and may be done by experienced programmers using source code, which also provided. Recompilation of the server executables require, that programmer has compiled NCBI toolkit libraries available. This toolkit may be downloaded from NCBI FTP web site: ftp://ncbi.nlm.nih.gov

Installation of the Standalone WWW server

After downloading file wwwblast.Your_platform.tar.gz to your computer place it into document directory of HTTPD server and uncompress it by

    gzip -d wwwblast.Your_platform.tar.gz
    tar -xvpf wwwblast.Your_platform.tar

Please note that parameter "p" in tar options is significant - it will preserve file access options stored in the distribution. Temporary directory for BLAST overview images (TmpGifs) should have 777 permission and logfile (wwwblast.log) should have 666.

After you uncompressed distribution file "blast" directory will be created. You can access sample BLAST HTML input form using URL http://your_hostname/blast/blast.html. This distribution comes with 2 BLAST databases: "test_aa_db" - sample protein database and "test_na_db" - sample nucleotide database. These databases configured to be searchable immediately with corresponding BLAST program.

Description of files in the distribution

blast.cgi

- BLAST search start-up C-shell file

blast.html

- sample BLAST search input HTML form

blast.rc

- Default configuration file for the WWW BLAST server

blast.REAL

- Main BLAST server executable

blast_form.map

- Auxiliary map file for the front BLAST image

nph-viewgif.cgi

- CGI program used to view and delete overview images

readme.html

- this documentation

wwwblast.log

- default logfile

Configuration of BLAST databases

To set up databases for the standalone WWW BLAST server it is necessary to follow these steps:

  1. Copy file with concatenated FASTA entries, that will be used as a database into directory "./db"
  2. Run "formatdb" program to format this database there.
  3. Add name of the database into server configuration file
  4. Add name of the database into WWW BLAST search form

Description of tags for main BLAST input page

This standalone server has the same tag convention as regular NCBI BLAST server. Sample BLAST search form may be changed to accommodate particular needs of the user in the custom search. Here is the list of these tags and their meaning. If some tag is missing from the search input page this will take default value. Exceptions are tags PROGRAM, DATALIB and SEQUENCE (or SEQFILE), that should always be set.

Server configuration file and logfile

Default configuration file is "blast.rc" and logfile "wwwblast.log". Setting tag WWW_BLAST_TYPE to specific value may change these names. This is useful if few different search input pages use the same CGI search engine, but significantly different by content and priorities. Here is sample configuration file comes with this distribution:

# Number of CPUs to use for a single request
#
NumCpuToUse     4
#
# Here is list of combination program/database, 
# that allowed by BLAST service. Format:    ...
#
blastn test_na_db
blastp test_aa_db
blastx test_aa_db
tblastn test_na_db
tblastx test_na_db

This file will set how many CPUs of computer will be used in the BLAST search and what databases may be used with what programs. Logfile currently store only limited information but also may be updated by programmers to store more values in it. Please note, that usually HTTPD servers run by accounts, that do not have write access to disk, so to write logfile - its permission should be set to 666.


Sergei Shavirin

Last modified: Fri Mar 17 13:51:15 EST 2000