How galaxy workflow work ?
Hi , As we know galaxy tools work with the python,perl,and other tools script in galaxy-dist/tools,but are there any workflow scripts will be created when we edit or import it to run and where they saved? Are there some details about how galaxy workflow work? Thank you very much.
Galaxy workflows are stored in the database, but can be exported in JSON format (intended for importing into another Galaxy server). Peter On Wed, Dec 3, 2014 at 3:38 PM, Weiyan Shen <shenwiyn@gmail.com> wrote:
Hi , As we know galaxy tools work with the python,perl,and other tools script in galaxy-dist/tools,but are there any workflow scripts will be created when we edit or import it to run and where they saved? Are there some details about how galaxy workflow work? Thank you very much.
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Hi All, I faced a problem after I tested the Bio-Blend API. I cannot access the history anymore with the below error messages. Although, I tried installation from the scratch, but I got the same error message. Please let me know how to fix this problem. Thanks! (GALAXY User Interface) ======================================================= "xhr": { "readyState": 4, "responseText": "{\"err_msg\": \"Uncaught exception in exposed API method:\", \"err_code\": 0}", "responseJSON": { "err_msg": "Uncaught exception in exposed API method:", "err_code": 0 }, "status": 500, "statusText": "Internal Server Error", "responseHeaders": { "Date": "Wed, 03 Dec 2014 15:50:02 GMT\r", "cache-control": "max-age=0,no-cache,no-store\r", "Server": "PasteWSGIServer/0.5 Python/2.7.8\r", "Connection": "close\r", "content-type": "application/json\r" } ======================================================= I found the error message in the Galaxy instance shell interface. ======================================================= galaxy.web.framework.decorators ERROR 2014-12-03 10:50:02,279 Uncaught exception in exposed API method: Traceback (most recent call last): File "/home/bxp12/galaxy-dist/lib/galaxy/web/framework/decorators.py", line 244, in decorator rval = func( self, trans, *args, **kwargs) File "/home/bxp12/galaxy-ist/lib/galaxy/webapps/galaxy/api/history_contents.py", line 76, in index and ( history_id == trans.security.encode_id( trans.history.id ) ) ): AttributeError: 'NoneType' object has no attribute 'id' ======================================================= Best, Bongsoo
Somehow your user object is not being set. Are you sure you have initialized bioblend with the correct API key? Do other operations work with that key? -John On Wed, Dec 3, 2014 at 11:00 AM, Bongsoo Park <bxp12@psu.edu> wrote:
Hi All,
I faced a problem after I tested the Bio-Blend API. I cannot access the history anymore with the below error messages. Although, I tried installation from the scratch, but I got the same error message. Please let me know how to fix this problem. Thanks!
(GALAXY User Interface)
=======================================================
"xhr": {
"readyState": 4,
"responseText": "{\"err_msg\": \"Uncaught exception in exposed API method:\", \"err_code\": 0}",
"responseJSON": {
"err_msg": "Uncaught exception in exposed API method:",
"err_code": 0
},
"status": 500,
"statusText": "Internal Server Error",
"responseHeaders": {
"Date": "Wed, 03 Dec 2014 15:50:02 GMT\r",
"cache-control": "max-age=0,no-cache,no-store\r",
"Server": "PasteWSGIServer/0.5 Python/2.7.8\r",
"Connection": "close\r",
"content-type": "application/json\r"
}
=======================================================
I found the error message in the Galaxy instance shell interface.
=======================================================
galaxy.web.framework.decorators ERROR 2014-12-03 10:50:02,279 Uncaught exception in exposed API method:
Traceback (most recent call last):
File "/home/bxp12/galaxy-dist/lib/galaxy/web/framework/decorators.py", line 244, in decorator
rval = func( self, trans, *args, **kwargs)
File "/home/bxp12/galaxy-ist/lib/galaxy/webapps/galaxy/api/history_contents.py", line 76, in index
and ( history_id == trans.security.encode_id( trans.history.id ) ) ):
AttributeError: 'NoneType' object has no attribute 'id'
=======================================================
Best,
Bongsoo
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participants (4)
-
Bongsoo Park -
John Chilton -
Peter Cock -
Weiyan Shen