From p.j.a.cock@googlemail.com Tue Jul 26 06:08:38 2016 From: Peter Cock To: galaxy-dev@lists.galaxyproject.org Subject: [galaxy-dev] Fwd: Galaxy Blast Date: Tue, 26 Jul 2016 11:08:36 +0100 Message-ID: In-Reply-To: <9C4A7AE7BB16F0449D138A473B7192B40816FD73D6@exbeac02.moredun.net> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============8868905560572851946==" --===============8868905560572851946== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable 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 Date: Tue, Jul 26, 2016 at 9:25 AM Subject: RE: Galaxy Blast To: Peter Cock 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(a)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 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 =E2=80=9CNo option available=E2=80=9D in t= he > Nucleotide BLAST database drop down when I selected =E2=80=9CLocally instal= led BLAST database=E2=80=9D. > > > > 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. > > > > > > > > value, name, path > > > >
> > > > 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 --===============8868905560572851946==--