Hello all,
Harry (CC'd) emailed me about some teething trouble getting nucleotide BLAST databases to appear in the drop down lists (see below).
I suspect this is partly due to the partial data table sample that ships with Galaxy:
https://github.com/galaxyproject/galaxy/blob/dev/config/tool_data_table_conf...
Can any of the Galaxy Data Manager expects advise please?
Thanks,
Peter
---------- Forwarded message ---------- From: Harry Wright Harry.Wright@moredun.ac.uk Date: Tue, Jul 26, 2016 at 9:25 AM Subject: RE: Galaxy Blast To: Peter Cock p.j.a.cock@googlemail.com
Hi Peter,
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.
Thanks Harry
-----Original Message----- From: Peter Cock [mailto:p.j.a.cock@googlemail.com] Sent: 22 July 2016 16:28 To: Harry Wright Subject: Re: Galaxy Blast
Hi Harry,
Hmm. I'm a little puzzled. That file looks fine on our GitHub and on the Tool Shed:
https://github.com/peterjc/galaxy_blast/blob/master/tool-data/tool_data_tabl...
http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus (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:
https://github.com/galaxyproject/galaxy/blob/dev/config/tool_data_table_conf...
(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?
Thanks,
Peter
On Fri, Jul 22, 2016 at 3:59 PM, Harry Wright Harry.Wright@moredun.ac.uk wrote:
Dear Peter,
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" /> </table>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?
Regards
Harry
Dr. Harry Wright
Moredun Research Institute
Pentlands Science Park
Bush Loan
Penicuik
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