Harry (CC'd) emailed me about some teething trouble getting
nucleotide BLAST databases to appear in the drop down lists
I suspect this is partly due to the partial data table sample that
ships with Galaxy:
Can any of the Galaxy Data Manager expects advise please?
---------- Forwarded message ----------
From: Harry Wright <Harry.Wright(a)moredun.ac.uk>
Date: Tue, Jul 26, 2016 at 9:25 AM
Subject: RE: Galaxy Blast
To: Peter Cock <p.j.a.cock(a)googlemail.com>
Sorry for the delay in response. If you think it would be useful please post it.
I have downloaded what I thought was the newest versions of NCIB
blast+ 2.2.31 from the toolshed.
The tool_data_table_conf.xml.sample I altered was in galaxy_dir/config/.
If you need anything else please ask.
From: Peter Cock [mailto:email@example.com]
Sent: 22 July 2016 16:28
To: Harry Wright
Subject: Re: Galaxy Blast
Hmm. I'm a little puzzled. That file looks fine on our GitHub and on
the Tool Shed:
(browse tip files)
Can you tell me exactly which version of things you got from the Tool
Shed, and exactly which tool_data_table_conf.xml and
tool_data_table_conf.xml.sample you had to edit?
My guess is the problem is this partial example that ships with Galaxy:
(There is talk of moving datatypes like this back into the Galaxy
core, which would simply this)
May I forward this email to the public Galaxy developers mailing list please?
On Fri, Jul 22, 2016 at 3:59 PM, Harry Wright
I have just installed a new instance of Galaxy here at Moredun and
have been busy setting up tools for us to use. One of the tools that I
have set up is blast with the NCBI nr and nt databases sitting in the
backend as a Locally installed database. I downloaded both files and
formatted them into databases. I then add lines to the blastdb_p.loc
and blastdb.loc. When I restarted the server I found that I could
access nr through the interface, for blastx, but not nt, using blastn.
For nt I was getting the message “No option available” in the
Nucleotide BLAST database drop down when I selected “Locally installed BLAST database”.
After some searching I found reference to
config/tool_data_table_conf.xml.sample. When I look there I could only
find reference to blastdb_p and not blastdb.
I added the lines below to the file and changed the file name to
tool_data_table_conf.xml. I restarted galaxy to find that I could now
use nt in blastn.
<!-- Locations of nucleotide (mega)blast databases -->
<table name="blastdb" comment_char="#">
<columns>value, name, path</columns>
<file path="tool-data/blastdb.loc" />
I was wondering if there was something that I have missed or has this
section of the code been missed out of the tool_data_table_conf.xml
file in the installation download?
Dr. Harry Wright
Moredun Research Institute
Pentlands Science Park
Midlothian EH26 0PZ
Tel - 0131 4455111
Fax - 0131 4456235
The Moredun Research Institute is a limited company registered in Scotland.
Registered number: SC149440
The Moredun Research Institute is a charity registered in Scotland.
Registered number: SC022353
Registered office: Moredun Research Institute, Pentlands Science Park,
Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
The Moredun Research Institute is a limited company registered
in Scotland. Registered number: SC149440
The Moredun Research Institute is a charity registered in
Scotland. Registered number: SC022353
Registered office: Moredun Research Institue, Pentlands
Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK