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
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.cock@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...
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 ___________________________________________________________ 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/
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 <dan@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.cock@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...
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 ___________________________________________________________ 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/
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.cock@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 <dan@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.cock@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...
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 ___________________________________________________________ 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/
participants (2)
-
Daniel Blankenberg -
Peter Cock