Install BLAST in ubuntu
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19 months ago
lexa_2294 • 0

How to install BLAST in ubuntu? How to use the command terminal to install it?

bioinformatics • 2.6k views
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Best option would be to use conda. Take a look at bioconda documentation. Once you have conda installed it can be as simple as

conda create -n blast blast
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by far the easiest option is conda! Install it on your linux system if you haven't already:

https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html

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You may also consider to use a Docker image for BLAST, like the ones available at the pegi3s Bioinformatics Docker Images Project: https://hub.docker.com/r/pegi3s/blast

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19 months ago
Carambakaracho ★ 2.8k

In case you have sufficient privileges and don't fancy the latest release, the by far easiest option is the Ubuntu/Debian package manager apt.

sudo apt install ncbi-blast+
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19 months ago
anicet.ebou ▴ 170

This answer should help you.

1.Retrieve blast executables (if not already done) in the terminal:

1.1 Download the executables with the command:

wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.10.0+-x64-linux.tar.gz

1.2 Decompress the archive and rename it:

tar zxvf ncbi-blast-2.10.0+-x64-linux.tar.gz
mv ncbi-blast-2.10.0+ blast
rm ncbi-blast-2.10.0+-x64-linux.tar.gz

1.3 Add a folder for blast databases

cd blast
mkdir db
cd...

1.4 you become administrator (you enter your password):

sudo su

1.5 You place the executables in /usr/share to make them usable by everyone:

mv blast /usr/share.
chmod a+w+r /usr/share/blast/db
export PATH="$PATH:/usr/share/blast/bin"
export BLASTDB="/usr/share/blast/db/"
exit

You will need to put the two export lines in files likes ~/.bash_profile or ~/.bashrc for executables o be available across all sessions.

2.Retrieves the databases (if needed for example with SwissProt DB, needs admin rights)

cd /usr/share/blast/db
cp ../bin/update_blastdb.pl .
perl update_blastdb.pl swissprot
tar zxvf swissprot.tar.gz
rm swissprot.tar.gz

Done :)

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