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.xml.sample Can any of the Galaxy Data Manager expects advise please? Thanks, Peter ---------- Forwarded message ---------- From: Harry Wright <harry.wri...@moredun.ac.uk> Date: Tue, Jul 26, 2016 at 9:25 AM Subject: RE: Galaxy Blast To: Peter Cock <p.j.a.c...@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.c...@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_table_conf.xml.sample 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.xml.sample (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.wri...@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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
