ejson.loads( urllib2.urlopen( req ).read() )
File
"/home/odoppelt/localStuff_VM/tools/galaxy-dist/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs4.egg/simplejson/__init__.py",
line 384, in loads
File
"/home/odoppelt/localStuff_VM/tools/galaxy-dist/eggs/simplejson-2.1.1-py2.7-linux-x8
ransmitted on the server side.
could somebody help me with that ?
Happy new Year !!! and Have a nice day,
--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur
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ts but it does, everything is transmitted to galaxy
do it should work.
Tell me if you need more information. I'll look further on monday but
i'm kind of stuck.
Thank you for your help,
Cheers,
--
Olivia Doppelt-Azeroual, PhD
CIB - Institut Pasteur
On Fri, Jan 3, 2014 at 5:36 AM, Ol
user bioblend.
--
Olivia
Le 04/01/14 22:10, Olivia Doppelt a écrit :
Le 03/01/14 15:44, John Chilton a écrit :
I am not sure I understand the problem. Can you clarify a few points:
Is bioblend letting users associate roles with data libraries that
they shouldn't be able to and the op
ioblend doesn't have a roles client for the
second.
I have created a Trello card for this feature: https://trello.com/c/qsQHnFlG.
Let me know if you have any additional questions or if this is unclear
in any way.
-John
On Sun, Jan 5, 2014 at 3:35 AM, Olivia Doppelt
wrote:
Hello again,
I jus
ntax for integer:
"odoppelt__at__pasteur.fr"
LINE 3: WHERE role.id = E'odoppelt__at__pasteur.fr'
^
'SELECT role.id AS role_id, role.create_time AS role_create_time,
role.update_time AS role_update_time, role.name AS role_name,
role.description AS role_des
:
I am stumped, I am not sure how this would happen. How did you apply
the patch against the -dist stable code? Can you send me the full
contents of the patched ..api/library_contents.py file?
-John
On Tue, Jan 7, 2014 at 9:48 AM, Olivia Doppelt
wrote:
Dear John,
Unfortunatly, I have
)
I get an error message which is very long and attached to this email.
Please help me on that it is the final step of several ones using bioblend.
Have a nice day,
--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur
Traceback (most recent call last):
File "script_testBio
when I try to access my
local galaxy url library permissions, the route isn't valid
(http://localhost:8080/api/libraries/f2db41e1fa331b3e/permissions)
Could you please help me with that ?
Best regards,
--
Olivia Doppelt-Azeroual, PhD
CIB - Institut Past
Hello to All,
I would like to reiterate this problem because it is causing major
problems in tha managment of our Galaxy instance
Are there some clues on how to solve this issue ?
Best regards,
--
Olivia Doppelt-Azeroual, PhD
Pasteur Institute, Paris
Le 23/04/13 22:38, Fabien Mareuil a
nnon Baker a écrit :
Olivia,
There's a fix for this available in galaxy-central, but I'm surprised
you're seeing it in -dist as I thought the problem was introduced
after the dist freeze. Can you provide the output of 'hg tip'?
-Dannon
On Mon, Apr
heers,
Olivia Doppelt-Azeroual
Pasteur Institute, CIB, PARIS
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and other Galaxy lists, please use the inter
y ?
Best regards,
--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur
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and other Galaxy lists, please
performing
the requested operation.
WSGI Server
___
I'm currently trying to understand this error. Please tell me if you
know anything about this error.
Have a nice day,
--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB -
er requires a history"
AssertionError: DataToolParameter requires a history
127.0.0.1 - - [24/Feb/2014:15:15:15 +0200] "POST
/api/tools?key=cd065330048989af4ae266cf94685e6b HTTP/1.1" 500 - "-"
"python-requests/2.0.1 CPython/2.7.5+ Linux/3.11.0-15-generic"
ot;data": {
"inputs": [
{
"input": "History does not include a dataset of the
required format / build"
}
]
},
"type": "error"
}
}
On the galaxy
ctionary.
For instance, the API driven test framework runs by calling this API
and does almost this exact dumps.
https://bitbucket.org/galaxy/galaxy-central/src/f573461f3667e8f120dc05bbd11a019d5fae1960/test/base/interactor.py?at=default#cl-251
Hope this helps.
-John
On Mon, Feb 24, 2014 at 8
ah command line.
Is there an example of a run_tool utilisation ? somewhere ?
Thanks in advance for your help.
Have a nice day,
--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur
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Does someone has an explanation for that ?
Thanks in advance,
--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur
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in your mail client. To manage your su
which asks me to specify
information about an 8th step (which does not exist)
Is there a test case available to use this script ?
Please keep me informed on that.
Have a nice day,
--
Olivia Doppelt-Azeroual, PhD
Tel: 92 15
CIB - Institut Pasteur
{
"a_galaxy_workflow": "tru
ow ever created on a brand
new galaxy instance, your step ids will not be 0 and 1.
-Dannon
On Wed, Apr 23, 2014 at 12:30 PM, Olivia Doppelt-Azeroual
mailto:olivia.dopp...@pasteur.fr>> wrote:
Dear developpers,
I'm trying to launch a small workflow using the api script
t;type": "tool"
}
},
"tags": [],
"url": "/api/workflows/f2db41e1fa331b3e"
}
----
as you can see, the parameter called prefix, is not there.
Thank you for your help
--
Olivia
Le 25/04/14 19:49, Dannon Baker a écrit :
Olivia,
I
correctly in the command line. options are there but no values are there.
Could you give me a use case, so I can mime it to my project ?
Thanks in advance,
--
Olivia Doppelt-Azeroual
CIB, Institut Pasteur, Paris
Le 27/02/14 14:46, John Chilton a écrit :
I think you are right, and I am right,
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