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Warning

Iceberg reaches end-of-life on 30th November 2020. If you are running jobs on Iceberg then you need to take urgent action to ensure that your jobs/scripts will run on ShARC or Bessemer. If you have never used ShARC or Bessemer then now is the time to test your scripts. Not all software on Iceberg is available on ShARC/Bessemer.

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