Install Blast+

  • DB

Make directory /db and mount it as separated partition.
Copy update script from Blast+ bin directory.

# cp /usr/share/ncbi-blast-2.6.0+/bin/ /db/

# apt-get install liblist-moreutils-perl

List database names

# cd /db
# ./ --showall

Download/update database

# cd /db
# ./ --decompress --verbose swissprot
  • Blast+

Download and install

# wget
# tar xzf ncbi-blast-2.6.0+-x64-linux.tar.gz
# mv ncbi-blast-2.6.0+ /usr/share/
# chown -R root:root /usr/share/ncbi-blast-2.6.0+
# changemod -R 755 /usr/share/ncbi-blast-2.6.0+

User script to activate Blast+

export PATH=/usr/share/ncbi-blast-2.6.0+/bin:$PATH
export BLASTDB=/db

Test installation

$ blastp -db swissprot -query testseq.fasta
  • Schedule DB update

Copy update script in directory /db.
        cd /db
        date > "update.log"
	#verify lock db
        echo "verifica lock" >> "update.log"
        DIRS=$(find "/home/" -mindepth 1 -maxdepth 1 -type d)
        for user in $DIRS
                if [ -e $filelock ] && [ -f $filelock ]
                        echo $filelock" -> NO update" >> "update.log"
        echo "SI Update" >> "update.log"
        ./ --decompress swissprot 16SMicrobial refseq_protein >> "update.log"
        echo "DONE" >> "update.log"

Schedule cron job

crontab -e

50 12 * * * /db/ > /dev/null 2>&1

Before blast execution, user must create a file named “dblock” in his home directory to avoid update while blast is running. At the end of the process the file must be removed.

rxr/blast.txt · Last modified: 2017/01/11 15:28 by giancarlo

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Giancarlo Birello (g.birello _@_ and Anna Perin (a.perin _@_
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