PGI Guide to BLAST

This guide is intended to help build the Basic Local Alignment Search Tool (BLAST) package for 64 bit Linux using PGI 2012 compilers.

Version Information

This guide was created for BLAST compiled using the PGI 2012 compilers.

Application Notes

Information about BLAST can be found on the NIH website.

"The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. "

Obtaining the Source Code

The BLAST source code is available from the NIH ftp site.

Prerequisites

None

Building BLAST

  1. Untar the BLAST package: 

      tar -xvzf ncbi.tar.gz

  2. Edit the file ncbi/platform/linux64.ncbi.mk as follows: 

      NCBI_CC = pgcc -D_GNU_SOURCE
  NCBI_CFLAGS1 = -c
  NCBI_LDFLAGS1 = -fast -O3
  NCBI_OPTFLAG = -fast -O3
  NCBI_BIN_MASTER = /usr/local/ncbi/bin
  NCBI_BIN_COPY = /usr/local/ncbi/bin
  NCBI_INCDIR = /usr/local/ncbi/include
  NCBI_LIBDIR = /usr/local/ncbi/lib
  NCBI_ALTLIB = /usr/local/ncbi/altlib

  3. Edit the ncbi/make/makedis.csh file to enable building on a 64-bit Linux platform such as Ubuntu by adding an additional stanza to the case GNU/Linux: logic: 

      case "x86_64":
    set platform=linux64
    breaksw

  4. Build the code: 

      ./ncbi/make/makedis.csh

  5. The executables will end up in the directory ./ncbi/build

    6. Known Issues and Limitations

    None besides those noted above

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