Local DISOPRED setup

NOTE:
I am reproducing all the steps that I needed to get a working copy of DISOPRED on my machine. If you are a commercial user, you should pay attention to DISOPRED’s license files and get permission for its use before proceeding.

Before we get to the actual DISOPRED setup, we need to install required software/libraries:

I am working on an Ubuntu 12.04 machine.

1. Install ncbi-tools (they contain all possible blast software)

   sudo apt-get install ncbi-tools*

2. Fetch database downloader (was not part of my ncbi tools distribution)

   wget www.ncbi.nlm.nih.gov/BLAST/docs/update_blastdb.pl
   chmod +x update_blastdb.pl

3. Download required database (nr). I’ve decided to create a folder in my home folder called blastdb.

   mkdir ~/blastdb/nr 
   cd ~/blastdb/nr
   
   # fetch database
   update_blastdb.pl --verbose nr
   
   # extract all the files (lazy TextMate block edit instead of loops..)
   tar -xzvf nr.00.tar.gz &>nr.00.tar.log
   tar -xzvf nr.01.tar.gz &>nr.01.tar.log
   tar -xzvf nr.02.tar.gz &>nr.02.tar.log
   tar -xzvf nr.03.tar.gz &>nr.03.tar.log
   tar -xzvf nr.04.tar.gz &>nr.04.tar.log
   tar -xzvf nr.05.tar.gz &>nr.05.tar.log
   tar -xzvf nr.06.tar.gz &>nr.06.tar.log
   tar -xzvf nr.07.tar.gz &>nr.07.tar.log
   tar -xzvf nr.08.tar.gz &>nr.08.tar.log
   tar -xzvf nr.09.tar.gz &>nr.09.tar.log
   tar -xzvf nr.10.tar.gz &>nr.10.tar.log
   tar -xzvf nr.11.tar.gz &>nr.11.tar.log
   tar -xzvf nr.12.tar.gz &>nr.12.tar.log
   tar -xzvf nr.13.tar.gz &>nr.13.tar.log
   
   # remove archives
   rm *.tar.gz

4. Obtain matrices for blastpgp

   mkdir ~/blastdb/data
   cd ~/blastdb/data
   wget -r ftp://ftp.ncbi.nih.gov/blast/matrices/
   # move the files back to the database folder
   mv ftp.ncbi.nih.gov/blast/matrices/* .

5. Configure blast to know where to look for all the directories

   vim ~/.ncbirc 

   And put in required parameters:

   ; Start the section for BLAST configuration
   [BLAST]
   ; Specifies the path where BLAST databases are installed
   BLASTDB=/home/petr/blastdb/nr
   BLASTMAT=/home/petr/blastdb/data
   ; Specifies the data sources to use for automatic resolution
   ; for sequence identifiers
   DATA_LOADERS=blastdb
   [NCBI]
   data=/home/petr/blastdb/data

So far so good, let’s get to the actual disopred setup! (replace with current/latest version if needed)

wget http://bioinfadmin.cs.ucl.ac.uk/downloads/DISOPRED/OLD/disopred2.43.tar.gz
tar xvf disopred2.43.tar.gz
cd disopred/src
rm disopred seq2mtx
make
make install

Last part is to point the rundisopred script to the correct ncbi_tools installation directory, for me it was following:

cd ..
vim rundisopred

# change
set ncbidir = /usr/local/bin
# to 
set ncbidir = /usr/bin

And now it’s the time to test it all!

./rundisopred small_example.fasta