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BLAST

BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit. The BLAST+ applications have a number of performance and feature improvements over the legacy BLAST applications. For details, please see the BLAST+ user manual.

Interactive Usage

After connecting to Iceberg (see Establishing a SSH connection), start an interactive session with the qrshx or qrsh command.

The latest version of BLAST+ (currently 2.3.0) is made available with the command

module load apps/binapps/ncbi-blast

Alternatively, you can load a specific version with

module load apps/binapps/ncbi-blast/2.3.0

This command makes the BLAST+ executables available to your session by adding the install directory to your PATH variable. It also sets the BLASTDB database environment variable.

You can now run commands directly. e.g.

blastn -help

Databases

The following databases have been installed following a user request

  • nr.*tar.gz Non-redundant protein sequences from GenPept, Swissprot, PIR, PDF, PDB, and NCBI RefSeq
  • nt.*tar.gz Partially non-redundant nucleotide sequences from all traditional divisions of GenBank, EMBL, and DDBJ excluding GSS,STS, PAT, EST, HTG, and WGS.

A full list of databases available on the NCBI FTP site is at https://ftp.ncbi.nlm.nih.gov/blast/documents/blastdb.html

If you need any of these installing, please make a request on our github issues log.

Installation notes

This was an install from binaries

#get binaries and put in the correct location
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.3.0+-x64-linux.tar.gz
tar -xzf ./ncbi-blast-2.3.0+-x64-linux.tar.gz
mkdir -p /usr/local/packages6/apps/binapps/ncbi-blast/
mv ncbi-blast-2.3.0+ /usr/local/packages6/apps/binapps/ncbi-blast/


#Create database directory
mkdir -p /usr/local/packages6/apps/binapps/ncbi-blast/ncbi-blast-2.3.0+/db

#Install the nr database
cd /usr/local/packages6/apps/binapps/ncbi-blast/ncbi-blast-2.3.0+/db
for num in `seq 0 48`;
do
paddednum=`printf "%02d" $num`
`wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.$paddednum.tar.gz`
done

#Install the nt database
for num in `seq 0 36`;
do
paddednum=`printf "%02d" $num`
`wget ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.$paddednum.tar.gz`
done

for f in *.tar.gz; do tar -xvzf $f; done

Testing

No testing has been performed. If you can suggest a suitable test suite, please contact us.

Modulefile

  • The module file is on the system at /usr/local/modulefiles/apps/binapps/ncbi-blast/2.3.0

The contents of the module file is

#%Module1.0#####################################################################
##
## BLAST 2.3.0 modulefile
##

## Module file logging
source /usr/local/etc/module_logging.tcl
##

proc ModulesHelp { } {
        puts stderr "Makes BLAST 2.3.0 available"
}

set BLAST_DIR /usr/local/packages6/apps/binapps/ncbi-blast/ncbi-blast-2.3.0+

module-whatis   "Makes BLAST 2.3.0 available"

prepend-path PATH $BLAST_DIR/bin
prepend-path BLASTDB $BLAST_DIR/db