Re: [galaxy-dev] Galaxy Blast

[Peter Cock]

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  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  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  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 
>>> 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.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
>>>  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 

Re: [galaxy-dev] Galaxy Blast

[Peter Cock]

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  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  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 
>> 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.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
>>  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.
>>>
>>>
>>>
>>> 
>>>
>>>
>>>
>>>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 

Re: [galaxy-dev] Galaxy Blast

[Daniel Blankenberg]

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  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 
> 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.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
>  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.
>> 
>> 
>> 
>> 
>> 
>>
>> 
>>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