[Bio-Linux] help regarding BLAST running

[Tony Travis]

On 04/02/13 11:41, Tim Booth wrote:
> Hi Simon and Vijay,
>
> I disagree with Simon - NR is a translated database so it is a peptide
> DB and blastx is therefore appropriate for a nucleotide query.
>
> Also, there is no reason to revert to the legacy "blastall" version of
> BLAST, even though it is still available on Bio-Linux 7.
>
> The only problem I can see is that your file name contains spaces.  This
> is a bad idea as the shell has no way of knowing that the spaces are
> part of the file name and assumes they are new parameters to the
> command.  In this case you can put the file name in "quotes" but a
> better idea is to ensure that your file names never contain spaces.
>
> Does that fix it?

Hi, Tim.

There is another potential problem because bio-linux-blast installs a 
profile.d fragment that sets the environment variable BLASTDB:

> ajt at beluga:~$ cat /etc/profile.d/blast_environment.sh
> #Added by package bio-linux-blast
> export  BLASTDB=/home/db/blastdb

In Vijay's command-line he used:

> blastx -db blastdb/nr.02 -query sra_data contig list - nucleotide_ sequences.fasta -evalue 0.1 > vijay.blastx

So, he would be looking for:

   /home/db/blastdb/blastdb/nr.02

Unless he has created a directory called blastdb in the folder where he 
runs "blastall -p blastx" containing a 'formatted' BLAST database.

It is also important to note that "bio-linux-blast" does NOT populate 
/home/db/blastdb with "nr", so Vijay will need to create the BLAST 
database using "formatdb" or copy the files from another machine.

One other thing to note is that you need to set the Gnome Terminal to 
run as a login shell to source the correct files from /etc/profile.d and 
~/.profile. The Gnome Terminal does not run as a login shell by default, 
because it is a sub-shell that only sources ~/.bashrc, and it doesn't 
inherit a shell login environment that a command-line sub-shell would. 
This is a known problem with Gnome Terminal "bash" sessions.

> Gnome Terminal / Edit / Profile Preferences / Title and Command / Command [x] Run command as a login shell

HTH,

   Tony.