location of .loc-files/data tables -- bug or feature?

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location of .loc-files/data tables -- bug or feature?

Christian Hundsrucker-2
Hello, Galaxy developers!

I do a bit of tweaking to a local galaxy instance. Thus, I just realized that subdirectories are not supported for the location of .loc-files/data tables.
E.g. tool-data/somesub/my.loc is not recognized even if this location is correctly linked in the tool_data_table_conf.xml (<file path="tool-data/somesub/my.loc" />).
Via the Galaxy-Admin interface and 'Server', 'View data tables registry' the .loc file is marked as a "Missing index file" - in the example the displayed location would be  "tool-data/my.loc" (without the 'somesub' subdirectory). As soon as I store 'my.loc' directly in the tool-data directory galaxy runs smoothly again, even (!) if I keep the subdirectory in the file path in tool_data_table_conf.xml.

Is galaxy meant to behave like this? If so, a word about it in the documentation would be really helpful!

Best,
Christian

version:
changeset:   8796:961ae35ba612
branch:      stable
tag:         tip
parent:      8794:1c7174911392
user:        Nate Coraor <[hidden email]>
date:        Fri Feb 08 11:23:04 2013 -0500

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Re: location of .loc-files/data tables -- bug or feature?

Dannon Baker-2
Hey Christian,

This is a bug that surfaced in revision 8333 which should be fixed in 9326:d07c62f0067a, which is available in the most recent galaxy-dist (stable branch).  If you'd rather not update right away, we'll have another full-fledged dist release out soon.

-Dannon


On Tue, May 21, 2013 at 5:48 AM, Christian Hundsrucker <[hidden email]> wrote:
Hello, Galaxy developers!

I do a bit of tweaking to a local galaxy instance. Thus, I just realized that subdirectories are not supported for the location of .loc-files/data tables.
E.g. tool-data/somesub/my.loc is not recognized even if this location is correctly linked in the tool_data_table_conf.xml (<file path="tool-data/somesub/my.loc" />).
Via the Galaxy-Admin interface and 'Server', 'View data tables registry' the .loc file is marked as a "Missing index file" - in the example the displayed location would be  "tool-data/my.loc" (without the 'somesub' subdirectory). As soon as I store 'my.loc' directly in the tool-data directory galaxy runs smoothly again, even (!) if I keep the subdirectory in the file path in tool_data_table_conf.xml.

Is galaxy meant to behave like this? If so, a word about it in the documentation would be really helpful!

Best,
Christian

version:
changeset:   8796:961ae35ba612
branch:      stable
tag:         tip
parent:      8794:1c7174911392
user:        Nate Coraor <[hidden email]>
date:        Fri Feb 08 11:23:04 2013 -0500

___________________________________________________________
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:
 http://lists.bx.psu.edu/

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.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: location of .loc-files/data tables -- bug or feature?

Christian Hundsrucker-2
Hey Dannon,

thnx for the info and the quick reply!

On 21.05.2013 18:09, Dannon Baker wrote:
Hey Christian,

This is a bug that surfaced in revision 8333 which should be fixed in 9326:d07c62f0067a, which is available in the most recent galaxy-dist (stable branch).  If you'd rather not update right away, we'll have another full-fledged dist release out soon.

-Dannon


On Tue, May 21, 2013 at 5:48 AM, Christian Hundsrucker <[hidden email]> wrote:
Hello, Galaxy developers!

I do a bit of tweaking to a local galaxy instance. Thus, I just realized that subdirectories are not supported for the location of .loc-files/data tables.
E.g. tool-data/somesub/my.loc is not recognized even if this location is correctly linked in the tool_data_table_conf.xml (<file path="tool-data/somesub/my.loc" />).
Via the Galaxy-Admin interface and 'Server', 'View data tables registry' the .loc file is marked as a "Missing index file" - in the example the displayed location would be  "tool-data/my.loc" (without the 'somesub' subdirectory). As soon as I store 'my.loc' directly in the tool-data directory galaxy runs smoothly again, even (!) if I keep the subdirectory in the file path in tool_data_table_conf.xml.

Is galaxy meant to behave like this? If so, a word about it in the documentation would be really helpful!

Best,
Christian

version:
changeset:   8796:961ae35ba612
branch:      stable
tag:         tip
parent:      8794:1c7174911392
user:        Nate Coraor <[hidden email]>
date:        Fri Feb 08 11:23:04 2013 -0500

___________________________________________________________
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:
 http://lists.bx.psu.edu/

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.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

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.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/