Warning
Iceberg was decommissioned on 30th November 2020. Users of Iceberg need to switch to using ShARC and/or Bessemer instead.
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.
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
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.
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
No testing has been performed. If you can suggest a suitable test suite, please contact us.
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