Sure, PR is here: https://github.com/galaxyproject/galaxy/pull/301
On 1 June 2015 at 15:17, Bjoern Gruening bjoern.gruening@gmail.com wrote:
Hi Marius,
do you mind to create a PR against the dev brach of Galaxy? https://github.com/galaxyproject/galaxy
Thanks, Bjoern
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.eduBootstrapping 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
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