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Installing BLAST

Installing BLAST (Blast+ or Legacy Blast)

BLAST is used 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. You only need to install BLAST+ OR legacy blast (ie blastall).

Download

The Pathway Tools distribution does not include a copy of the BLAST software, but it can be downloaded from NCBI (see NCBI Blast). There is a WWW download page at http://www.ncbi.nih.gov/blast/download.shtml. The NCBI BLAST+ executables and instructions for installation can also be acquired at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ and http://www.ncbi.nlm.nih.gov/books/NBK1762/, respectively.

MSWindows Users: For Pathway Tools v15.5+, it's recommended to download the 64-bit version of BLAST+.

The examples in the remainder of this page assumes you have installed BLAST in /var/blast/ (for Unix platforms).

Additional Setup

Add the path of the directory containing the executable programs blastp 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

MS Windows Users:
For users running Pathway Tools on a computer with a MSWindows operating system, the installer will only add the Blast+ path for ONLY the user who installed BLAST+. If multiple there are multiple users who use BLAST+ on the computer, you MUST add the BLAST+ bin directory to the SYSTEM PATH variable. Also, the ncbi.ini file is no longer required on Windows.

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.

Legacy Blast:

  1. Download:

    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.

  2. 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.

    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.