Install Blast+ and Blast legacy

DB

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

root@rachaelx:~# cp /usr/share/ncbi-blast-2.2.27+/bin/update_blastdb.pl /db/

Script help

root@rachaelx:~# cd /db
root@rachaelx:/db# ./update_blastdb.pl -help

List database names

root@rachaelx:~# cd /db
root@rachaelx:/db# ./update_blastdb.pl --showall

Download/update database

root@rachaelx:~# cd /db
root@rachaelx:/db# ./update_blastdb.pl --decompress --verbose swissprot

Blast+

Download and install

root@rachaelx:~# wget /forsomeserver/ncbi-blast-2.2.27+-x64-linux.tar.gz
root@rachaelx:~# tar xzf ncbi-blast-2.2.27+-x64-linux.tar.gz
root@rachaelx:~# mv ncbi-blast-2.2.27+ /usr/share/
root@rachaelx:~# chown -R root:root /usr/share/ncbi-blast-2.2.27+
root@rachaelx:~# chmod -R 755 /usr/share/ncbi-blast-2.2.27+

User script to activate Blast+

export PATH=/usr/share/ncbi-blast-2.2.27+/bin:$PATH
export BLASTDB=/db

Test installation

user@rachaelx:~$ blastp -db swissprot -query testseq.fasta

Blast legacy

Download and install

root@rachaelx:~# wget /forsomeserver/blast-2.2.26-x64-linux.tar.gz
root@rachaelx:~# tar xzf blast-2.2.26-x64-linux.tar.gz
root@rachaelx:~# mv /root/blast-2.2.26 /usr/share/
root@rachaelx:~# chown -R root:root /usr/share/blast-2.2.26
root@rachaelx:~# chmod -R 755 /usr/share/blast-2.2.26

User script to activate Blast legacy

export PATH=/usr/share/blast-2.2.26/bin:$PATH
export BLASTMAT=/usr/share/blast-2.2.26/data
export BLASTDB=/db

Test installation

user@rachaelx:~$ blastall -p blastp -i testseq.fasta -d swissprot

Schedule DB update

Copy update script in directory /db.

condupdatedb.sh

#!/bin/bash
        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 $DIRS
        do
                filelock=$user"/dblock"
                if [ -e $filelock ] && [ -f $filelock ]
                then
                        echo $filelock" -> NO update" >> "update.log"
                        exit
                fi
        done
        echo "SI Update" >> "update.log"
        ./update_blastdb.pl --decompress swissprot 16SMicrobial refseq_protein >> "update.log"
        echo "DONE" >> "update.log"
        exit

Schedule cron job

crontab -e

50 12 * * * /db/condupdatedb.sh > /dev/null 2>&1

NB
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.