June 2015 - galaxy-dev - lists.galaxyproject.org

unable to install from toolshed. bounced e-mail
by Leontovich, Alexey A., Ph.D. 01 Jun '15

01 Jun '15

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>

2 1

Error bootstrapping a toolshed
by Marius van den Beek 01 Jun '15

01 Jun '15

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

2 2

unable to install tools from the toolshed
by Leontovich, Alexey A., Ph.D. 01 Jun '15

01 Jun '15

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>

1 0