Installing BLAST

BLAST is needed either when running Pathway Tools in WWW server mode, where the server.html query page allows the option of performing a BLAST search for some sequence within the genome of a given organism (see the description of the command-line argument -no-blast to disable this functionality). Or the other use for BLAST is to run the Pathway Hole Filler (PHF). The Pathway Hole Filler assumes that a local installation of the BLAST program capable of XML output (newer than BLAST version 2.1.2) is available and correctly configured.

Download

The Pathway Tools distribution does not include a copy of the BLAST software, but it can be downloaded from NCBI (see http://www.ncbi.nih.gov/blast/). There is a WWW download page at http://www.ncbi.nih.gov/blast/download.shtml. Please make sure to download the legacy version of BLAST, not the newer BLAST+, as Pathway Tools does not work with the new version yet. The NCBI BLAST executables and instructions for installation can also be acquired at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST and ftp://ftp.ncbi.nlm.nih.gov/blast/documents/blast.html, respectively.

The examples in the remainder of this page assumes you have installed BLAST in /var/blast/

Additional Setup

Add the path of the directory containing the executable programs blastall and formatdb to the PATH environment variable of the user launching Pathway Tools. This is required for all operating systems, including Linux, Windows, Unix, and Mac OS X. For a UNIX example, in csh syntax:

setenv PATH /var/blast:${PATH}

In addition, on a computer with a Unix-like operating system, a file named .ncbirc must exist in the home directory of the user who launches Pathway Tools, and must contain these two lines of text:

[ncbi]
Data=`pwd`/../data

It is also possible to use an absolute directory name, like this:

[ncbi]
Data=/var/blast/data

For users running Pathway Tools on a computer with a MSWindows operating system, a file named ncbi.ini must be placed in the MSWindows search path, such as into the C:\Windows directory. An example of the content of the file:

[ncbi]
Data=C:\Program Files\Blast\data

For a user's particular BLAST setup, the location of the BLAST data directory might be different. Be sure to double-check its exact location.

Once BLAST has been installed, the BLAST sequence databases for each organism must be created before web users can access them. From the Tools menu, select Prepare Blast Reference Data -> Both.

After the .ncbirc file has been created, any Pathway Tools web server or other Pathway Tools sessions that might already be running must be restarted in order to incorporate changes to .ncbirc.