Re: [galaxy-dev] Error bootstrapping a toolshed
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_shedhttp://toolshed.g2.bx.psu.edu
Bootstrapping from tool shed athttp://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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Re: [galaxy-dev] validator type=empty_field is not working within repeat tags
Hi, I was trying to enforce not to allow empty string as an input to text field. It is working outside the repeat tags but not working within repeat tags. 1) Working fine param name=input type=text label=Enter Name validator type=empty_field/ /param 2) Not Working within repeat tags. repeat name=test title=Test param name=input type=text label=Enter Name validator type=empty_field/ /param /repeat Thanks Anmol On Fri, May 29, 2015 at 2:00 PM, Dave Clements cleme...@galaxyproject.org wrote: Hi Anmol, The best place to post this question is the Galaxy Dev List galaxy-dev@lists.galaxyproject.org. You can also search to see if anyone has asked a similar question at https://galaxyproject.org/search/web/ Thanks, Dave C On Fri, May 29, 2015 at 6:56 AM, anmol...@gmail.com wrote: Hi, I was trying to enforce not to allow empty string as an input to text field. It is working outside the repeat tags but not working within repeat tags. 1) Working fine param name=input type=text label=Enter Name validator type=empty_field/ /param 2) Not Working within repeat tags. repeat name=test title=Test param name=input type=text label=Enter Name validator type=empty_field/ /param /repeat Thanks Anmol _ Sent from http://dev.list.galaxyproject.org -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error bootstrapping a toolshed
Sure, PR is here:
https://github.com/galaxyproject/galaxy/pull/301
On 1 June 2015 at 15:17, Bjoern Gruening bjoern.gruen...@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.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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in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___
Please keep all replies on the list by using reply all
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] unable to install from toolshed. bounced e-mail
Alexey, In order to help track down the issue, I'd like to gather a bit more information on your setup: Which release of Galaxy are you running locally? Which toolshed are you attempting to install from? Additionally, there may be some more informative messages in the paster.log in the root of your galaxy installation. - Dave Bouvier http://galaxyproject.org http://usegalaxy.org On 06/01/2015 10:20 AM, Leontovich, Alexey A., Ph.D. wrote: 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.ale...@mayo.edu *Mayo Clinic* | 200 First Street SW | Rochester, MN 55905 | mayoclinic.org http://www.mayoclinic.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Error bootstrapping a toolshed
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
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
[galaxy-dev] minor visual bug found when using Firefox
In the workflow editor, if you add an Input dataset collection, the Collection Type: shows list. No dropdown arrow appears using Firefox. A dropdown arrow appears when you mouse over using Chrome. In Firefox, if you mouse over where the dropdown box should be, you can still click to choose list of datasets... For the longest time, I thought this was broken until a co-worker showed me it works with Chrome. I'd make a Trello card for this but I can't access Trello from behind the company firewall ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
