Hello Philipp

I'm assuming this is the 'ceas' tool from the toolshed which is owned by 'pjbriggs' (that is me)?


If it is then from what you describe I'm not sure whether this is a problem with the specific tool or a more general issue with Galaxy's tool installation.

My own experiences of trying to debug tool dependency installation issues have been quite haphazard, and although I've seen this particular error (i.e the "database had no record") a few times with various tools, I've never been able to understand what has caused it.

First it may be worth trying the "Repair repository" option from the "Repository Actions" menu. If that doesn't help then I've also had some success in the past using the "Manage tool dependencies" option (which allows individual dependencies to be uninstalled and then re-installed). This might work if just one dependency is giving an error.

Beyond that I've found it necessary to start drilling into the Galaxy log files. Aside from the log of the actual Galaxy process (verbose but sometimes useful, I don't know how easy this is to find on your Docker instance - I don't have any experience of working with them), often the tool dependencies also create their own INSTALLATION.log files which are worth looking for/at.

The following recipe should allow you to access these from within Galaxy (this is for v15.10):

- Go to "Admin" -> "Manage installed tools"
- Click on the name of the tool of interest (e.g. 'ceas')
- Click on the name of an errored dependency under the "Missing tool dependencies" section - In the list of dependencies, click on the name of the errored dependency again

This should take you to a page which includes a "folder browser" underneath the heading "Contents", where you can browse the contents of the installed tool dependency folder. Hopefully this will include a file called INSTALLATION.log, and if you click on it then the contents should be displayed and you can look to see if there are any error messages to indicate what went wrong.

Sometimes there is no INSTALLATION.log file however, in which case the main log file of the Galaxy process is probably the next place to look (if possible).

Sorry I don't have any more definitive answers - please let me know if any of the above helps.

Best wishes

Peter

On 17/01/16 18:36, Rathert, Philipp, Dr. wrote:
Dear All,


We are running a local docker-galaxy-stable instance on a Mac OS X
system. and observe a strange error:


CEAS
Description:
Revision:f411ce97a351

is not installing correctly.

After installing mysql-python in the container directly basically every
package is installed:

Installed tool dependencies/ - click the name to browse the dependency
installation directory/
Name    Version Type    Installation status
R
<http://129.69.102.42/admin_toolshed/browse_tool_dependency?id=52d6bdfafedbb5e5>
3.1.2   package Installed
ucsc_fetchChromSizes
<http://129.69.102.42/admin_toolshed/browse_tool_dependency?id=ae9879a80bd0a7bc>
1.0     package Installed
python_mysqldb
<http://129.69.102.42/admin_toolshed/browse_tool_dependency?id=03552bdee8c8190f>
1.2.5   package Installed
bx_python
<http://129.69.102.42/admin_toolshed/browse_tool_dependency?id=f6509e58756240f2>
0.7.1   package Installed


Missing tool dependencies/ - click the name to install the missing
dependency/
Name    Version Type    Installation status
cistrome_ceas
<http://129.69.102.42/admin_toolshed/manage_repository_tool_dependencies?tool_dependency_ids=71b3098c1ce064d4>
1.0.2.d8c0751   package Error



cistrome_ceas
<http://129.69.102.42/admin_toolshed/manage_repository_tool_dependencies?repository_id=be0a27b9edd0db03&operation=browse&tool_dependency_ids=71b3098c1ce064d4>
1.0.2.d8c0751   package Error
The installation directory for this tool dependency had contents but the 
database had no record. The installation log may show this tool dependency to 
be correctly installed, but due to the missing database record it is now being 
set to Error.



A reinstall results in the same error on different dependencies and it
looks like a random event.


Does anybody have an idea what could solve the issue?


I hope I provided enough information. In your answer please keep in mind
I am a newcomer to all this and a wet lab scientist.


Thank you for your help.


Cheers,


philipp



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--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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