Hello galaxy team,
This e-mail was bounced, so I am sending it again.
When I try to install tools (bismark, bisulfighter, bscall) to my local instance of Galaxy, I get an error message:
Internal Server Error
Galaxy was unable to successfully complete your request
An error occurred.
This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.
The error has been logged to our team.
The first time I tried to install was Friday, May 31, 2015.
I have installed many tools before, about 6 months ago and it worked just fine.
Could you please help with current installation problems?
Thank you.
Alexey Leontovich
Alexey Leontovich, Ph.D. | Assistant Professor of Medical Informatics | Biomedical Statistics and Informatics |Phone: 507-284-4850 | Fax: 507-538-0850 | leontovich.alexey(a)mayo.edu
Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | mayoclinic.org<http://www.mayoclinic.org>
Hello everyone,
I had some trouble bootstrapping a new toolshed with the 15_05 release
(worked fine in the past),
and I thought the solution might be interesting.
~/toolshed2/galaxy$ sh run_tool_shed.sh
-bootstrap_from_tool_shed http://toolshed.g2.bx.psu.edu
Bootstrapping from tool shed at http://toolshed.g2.bx.psu.edu.
Creating database... done.
Starting tool shed in order to populate users and categories... done.
Retrieving admin user's API key from http://127.0.0.1:9009... done.
Creating users... usage: create_users.py [-h] -a API -f FROM_TOOL_SHED
-t TO_TOOL_SHED
create_users.py: error: unrecognized arguments:
8f754ebd516ff576c3b30b6a3402a518 }
done.
Creating categories... usage: create_categories.py [-h] -a API -f
FROM_TOOL_SHED -t TO_TOOL_SHED
create_categories.py: error: unrecognized arguments:
8f754ebd516ff576c3b30b6a3402a518 }
done.
Bootstrap complete, shutting down temporary tool shed process. A log
has been saved to tool_shed_bootstrap.log
The solution is to exclude the curl braces coming from the API response. A
quick fix is to change the line
api_key=`curl -s --user $admin_user_email:$admin_user_password
$local_shed_url/api/authenticate/baseauth/ | sed
's/..*api_key[^0-9a-f][^0-9a-f]*\([0-9a-f]*\)..*/\1/'`
to
api_key=`curl -s --user $admin_user_email:$admin_user_password
$local_shed_url/api/authenticate/baseauth/ | sed
's/..*api_key[^0-9a-f][^0-9a-f]*\([0-9a-f]*\)..*/\1/'| sed
's/[{}]//g'`
in lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh .
Hope it’s useful,
Marius
Hello galaxy team,
When I try to install tools (bismark, bisulfighter, bscall) to my local instance of Galaxy, I get an error message:
Internal Server Error
Galaxy was unable to successfully complete your request
An error occurred.
This may be an intermittent problem due to load or other unpredictable factors, reloading the page may address the problem.
The error has been logged to our team.
The first time I tried to install was Friday, May 31, 2015.
I have installed many tools before, about 6 months ago and it worked just fine.
Could you please help with current installation problems?
Thank you.
Alexey Leontovich
Alexey Leontovich, Ph.D. | Assistant Professor of Medical Informatics | Biomedical Statistics and Informatics |Phone: 507-284-4850 | Fax: 507-538-0850 | leontovich.alexey(a)mayo.edu
Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | mayoclinic.org<http://www.mayoclinic.org>