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
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