On Thu, Mar 20, 2014 at 5:46 AM, Nilaksha Neththikumara
<nilakshafree...@gmail.com> wrote:
> Thanks a lot for the information. :) I'm new to the field so get confused at
> times. I started downloading the NCBI databases locally, but I have two
> questions.
>
> 1) There is no proper updating process for the locally installed NCBI
> databases. (according to my knowledge) So it seems I have to re download
> the database totally if I need to get them updated. And those databases
> are almost always being updating. (.sigh)

The NCBI provide a perl script update_blastdb.pl to automate this,
usually run via cron on a regular basis (e.g. once a week). But
yes, basically when the NCBI makes an update, the new files
are just downloaded again.

Often your institute's Linux administrators would have setup a
central shared copy of the NCBI BLAST databases to avoid
duplication between researchers all making their own copies.

See ftp://ftp.ncbi.nlm.nih.gov/blast/db/README

If you want to have a single always (nearly) up to date copy
of the NCBI BLAST databases, then your Galaxy blastdb.loc
and blastdb_p.loc files just need to point there.

However, for full reproducibility the Galaxy approach would
be to have multiple (data stamped) copies of the database,
each with a separate entry in the *.loc file. This is more work
to setup and maintain, and needs more disk space - but it
does ensure you can rerun old BLAST searches and get
the same results.

> 2) After installing databases, is there a particular way to  let galaxy know
> where are my databases located? So that they can be included in the drop
> down menu of the blast+ wrappers for me to select :)
>
> Thanks a lot in advance
>
> Nilaksha Neththikumara.

Yes, you need to add each databases to relevant *.loc file
(nucleotide or protein), see the README file - either on
the ToolShed or here:

https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus/README.rst

Exactly where the *.loc files are on disk will depend on
how you installed the BLAST+ wrappers.

Peter
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