Dear list,
I still have problems to get my head around tool data. Lets consider diamond for example (lets ignore data managers for the moment). After installation it seems that there are two relevant xml files:
- `config/shed_tool_data_table_conf.xml` - `tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/tool_data_table_conf.xml`
and two loc files:
- `tool-data/diamond_database.loc` - `tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/diamond_database.loc`
In both xml files the latter loc file is referenced. And therefor the tool-data/diamond_database.loc file is seemingly ignored.
What is the rational to have a loc and xml file for each tool version? It seems that they are merged upon startup anyway.
What would be the best way to administrate a single tool loc file?
Cheers, Matthias
Personally I tend to work with $GALAXY/tool-data/*.loc (and ignore the tool shed installed copies in their cryptically named folders) but this reflects in part the fact that this used to be the only copy of the file, and that's just what I always did.
If you use a data manager, I don't know which copy it updates - but the merging design is meant to hide these details I suppose.
Peter
On Mon, Oct 1, 2018 at 5:56 PM Matthias Bernt m.bernt@ufz.de wrote:
Dear list,
I still have problems to get my head around tool data. Lets consider diamond for example (lets ignore data managers for the moment). After installation it seems that there are two relevant xml files:
- `config/shed_tool_data_table_conf.xml`
`tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/tool_data_table_conf.xml`
and two loc files:
- `tool-data/diamond_database.loc`
`tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/diamond_database.loc`
In both xml files the latter loc file is referenced. And therefor the tool-data/diamond_database.loc file is seemingly ignored.
What is the rational to have a loc and xml file for each tool version? It seems that they are merged upon startup anyway.
What would be the best way to administrate a single tool loc file?
Cheers, Matthias
--
Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann
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Hi Peter,
then the I need to update all the paths in:
`config/shed_tool_data_table_conf.xml`?
Because currently the $GALAXY/tool-data/*.loc files are ignored in my instance.
For me it looks like a bug (caused by a misconfiguration?) that there are all xml files refer to the same loc file.
Wouldn't this be more useful:
- config/shed_tool_data_table_conf.xml -> tool-data/diamond_database.loc
- tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/tool_data_table_conf.xml -> tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/diamond_database.loc
Best, Matthias
On 02.10.2018 11:22, Peter Cock wrote:
Personally I tend to work with $GALAXY/tool-data/*.loc (and ignore the tool shed installed copies in their cryptically named folders) but this reflects in part the fact that this used to be the only copy of the file, and that's just what I always did.
If you use a data manager, I don't know which copy it updates - but the merging design is meant to hide these details I suppose.
Peter
On Mon, Oct 1, 2018 at 5:56 PM Matthias Bernt m.bernt@ufz.de wrote:
Dear list,
I still have problems to get my head around tool data. Lets consider diamond for example (lets ignore data managers for the moment). After installation it seems that there are two relevant xml files:
- `config/shed_tool_data_table_conf.xml`
`tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/tool_data_table_conf.xml`
and two loc files:
- `tool-data/diamond_database.loc`
`tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/diamond_database.loc`
In both xml files the latter loc file is referenced. And therefor the tool-data/diamond_database.loc file is seemingly ignored.
What is the rational to have a loc and xml file for each tool version? It seems that they are merged upon startup anyway.
What would be the best way to administrate a single tool loc file?
Cheers, Matthias
--
Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann
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/
Hi Matthias,
I'm getting out of my depth here - but if tool-data/xxx.loc is being ignored, you may need to enable this by adding the XML data table entries from the relevant tool_data_table_conf.xml.sample file for tool xxx to $GALAXY/config/tool_data_table_conf.xml.
At least, that's what I had to do and documented recently here: https://github.com/abaizan/kodoja_galaxy/commit/2cd7579a15887ae4ffdc5ab3a346...
Again, this may be me sticking to old pre-tool shed habits - so I'd like to hear how other people manage their *.loc files, especially when doing hand editing to add entries.
Peter On Tue, Oct 2, 2018 at 10:29 AM Matthias Bernt m.bernt@ufz.de wrote:
Hi Peter,
then the I need to update all the paths in:
`config/shed_tool_data_table_conf.xml`?
Because currently the $GALAXY/tool-data/*.loc files are ignored in my instance.
For me it looks like a bug (caused by a misconfiguration?) that there are all xml files refer to the same loc file.
Wouldn't this be more useful:
config/shed_tool_data_table_conf.xml -> tool-data/diamond_database.loc
tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/tool_data_table_conf.xml -> tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/diamond_database.loc
Best, Matthias
On 02.10.2018 11:22, Peter Cock wrote:
Personally I tend to work with $GALAXY/tool-data/*.loc (and ignore the tool shed installed copies in their cryptically named folders) but this reflects in part the fact that this used to be the only copy of the file, and that's just what I always did.
If you use a data manager, I don't know which copy it updates - but the merging design is meant to hide these details I suppose.
Peter
On Mon, Oct 1, 2018 at 5:56 PM Matthias Bernt m.bernt@ufz.de wrote:
Dear list,
I still have problems to get my head around tool data. Lets consider diamond for example (lets ignore data managers for the moment). After installation it seems that there are two relevant xml files:
- `config/shed_tool_data_table_conf.xml`
`tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/tool_data_table_conf.xml`
and two loc files:
- `tool-data/diamond_database.loc`
`tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/diamond_database.loc`
In both xml files the latter loc file is referenced. And therefor the tool-data/diamond_database.loc file is seemingly ignored.
What is the rational to have a loc and xml file for each tool version? It seems that they are merged upon startup anyway.
What would be the best way to administrate a single tool loc file?
Cheers, Matthias
--
Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann
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/
--
Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann
Hi all,
Again, this may be me sticking to old pre-tool shed habits - so I'd like
to hear how other people manage their *.loc files, especially when doing hand editing to add entries.
I **try** to stick to just editing the *.loc file in tool-data for those tools that do not have a data manager. This way I can also track them in my local git branch. But I do agree that it can be complicated to figure out which files to edit for which tool (bwa/bwamem...) and add the correct entry and in the right format. The data managers make it on the one hand easier, but harder to tell if I was adding entries by hand or through a data manager - especially when not being consistent..
Part of this could be mitigated if the admin web interface would allow for editing these "Tool Data Table Entries" and not just view them -> https://github.com/galaxyproject/galaxy/issues/6819
Cheers, Jelle
galaxy-dev@lists.galaxyproject.org
-
Jelle Scholtalbers -
Matthias Bernt -
Peter Cock