Cross referencing this open issue which looks like the same thing: https://github.com/peterjc/galaxy_blast/issues/80
We're probably going to return the BLAST datatypes to the Galaxy core, which will resolve this in a different way: https://lists.galaxyproject.org/pipermail/galaxy-dev/2016-August/024696.html https://github.com/galaxyproject/galaxy/pull/2696 Peter On Wed, Jul 27, 2016 at 9:34 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > Thank Dan, that's what I thought. > > So databases can added to any of the multiple blastdb.loc > files which Galaxy ought to be combining. I'm not sure what > went wrong for Harry (and therefore how to avoid it for > others in future). :( > > (Separately I have raised the issue of returning the BLAST > datatypes to the Galaxy core on the IUC mailing list) > > Peter > > On Tue, Jul 26, 2016 at 10:28 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote: >> Hi Peter and Harry, >> >> When a tool is installed from the toolshed, the tool data table loc files >> are installed to the configured location and are then referenced in >> shed_tool_data_table_conf.xml. You should be able to modify the .loc files >> as referenced in this file, or, as you did, add a new entry to the >> tool_data_table_conf.xml file. Each instance of the tool data table (one >> will exist per tool shed repository revision that has been installed) will >> be merged together into a single entity that can then be accessed by the >> tools. You can also find the paths to the .loc files for each tool data >> table under the admin interface. Data Managers will write to the specific >> .loc file that was created during their installation. >> >> Please let me know if I can provide additional clarification. >> >> >> >> Thanks for using Galaxy, >> >> Dan >> >> >>> On Jul 26, 2016, at 6:08 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: >>> >>> 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/ >> ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. 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