Hi, I'm trying to add blast (or megablast actually) to galaxy. To allow it to use databases, I need to tell it what there are available. That is done with file 'blastdb.loc' In page http://g2.trac.bx.psu.edu/wiki/XmlQuickReference There is little information, but where exactly should that file be? It doesn't seem to read it from tools (where the xmls are) directory or the main directory of galaxy at least. Thanks, -- Henrikki Almusa
Henrikki Almusa wrote:
Hi,
I'm trying to add blast (or megablast actually) to galaxy. To allow it to use databases, I need to tell it what there are available. That is done with file 'blastdb.loc' In page
http://g2.trac.bx.psu.edu/wiki/XmlQuickReference
There is little information, but where exactly should that file be? It doesn't seem to read it from tools (where the xmls are) directory or the main directory of galaxy at least.
I discovered that this file should be in tool-data actually :). It might be nice to comment on the XmlQuickReference page. Regards, -- Henrikki Almusa
Hi Henrikki, Thank you for bring it up. I have added a note in the page for future reference. Best, Wen-Yu Galaxy team On Nov 7, 2008, at 4:59 AM, Henrikki Almusa wrote:
Henrikki Almusa wrote:
Hi,
I'm trying to add blast (or megablast actually) to galaxy. To allow it to use databases, I need to tell it what there are available. That is done with file 'blastdb.loc' In page
http://g2.trac.bx.psu.edu/wiki/XmlQuickReference
There is little information, but where exactly should that file be? It doesn't seem to read it from tools (where the xmls are) directory or the main directory of galaxy at least.
I discovered that this file should be in tool-data actually :). It might be nice to comment on the XmlQuickReference page.
Regards, -- Henrikki Almusa _______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
Dear all, I am very new into Galaxy. I was doing analysis on the ucsc based service and i had problems making a workflow from my history. I did install galaxy on my computer (Mac OS 10.5.5, running python 2.5.1) thinking it may be easier to track the problem. I get this error message on the web "Server ErrorAn error occurred. See the error logs for more information. (Turn debug on to display exception reports here)" and the one at the bottom with the local installation. I get the same error if I try to make the workflow from scratch. I hope you can help me. Best, Inti Pedroso URL: http://127.0.0.1:8080/workflow/build_from_current_history File '/ Applications/Galaxy_dist/eggs/py2.5-noplatform/WebError-0.8a-py2.5.egg/ weberror/evalexception/middleware.py', line 364 in respond File '/ Applications/Galaxy_dist/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/ paste/debug/prints.py', line 98 in __call__ File '/Applications/ Galaxy_dist/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/ wsgilib.py', line 539 in intercept_output File '/Applications/ Galaxy_dist/eggs/py2.5-noplatform/Beaker-0.5-py2.5.egg/beaker/ session.py', line 103 in __call__ File '/Applications/Galaxy_dist/eggs/ py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/recursive.py', line 80 in __call__ File '/Applications/Galaxy_dist/eggs/py2.5-noplatform/ Paste-1.5.1-py2.5.egg/paste/httpexceptions.py', line 632 in __call__ File '/Applications/Galaxy_dist/lib/galaxy/web/framework/base.py', line 126 in __call__ body = method( trans, **kwargs ) File '/ Applications/Galaxy_dist/lib/galaxy/web/controllers/workflow.py', line 382 in build_from_current_history step = model.WorkflowStep() File '/ Applications/Galaxy_dist/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1- py2.5.egg/sqlalchemy/orm/attributes.py', line 1215 in init File '/ Applications/Galaxy_dist/lib/galaxy/model/__init__.py', line 576 in __init__ self.input_connections = None File '/Applications/Galaxy_dist/ eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/orm/ attributes.py', line 36 in __set__ File '/Applications/Galaxy_dist/ eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/orm/ attributes.py', line 586 in set File '/Applications/Galaxy_dist/eggs/ py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/orm/ attributes.py', line 602 in _set_iterable File '/Applications/ Galaxy_dist/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/ sqlalchemy/orm/attributes.py', line 586 in <lambda> File '/ Applications/Galaxy_dist/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1- py2.5.egg/sqlalchemy/orm/collections.py', line 522 in adapt_like_to_iterable TypeError: Incompatible collection type: None is not list-like -- Social, Genetic and Developmental Psychiatry PhD programme, NIHR BRC for Mental Health; MRC SGDP Research Centre (PO82), Institute of Psychiatry, Kings College London. SE5 8AF, London, UK. Inti.PedrosoRovira@iop.kcl.ac.uk phone: +44 020 7848 0798 -- Social, Genetic and Developmental Psychiatry PhD programme, NIHR BRC for Mental Health; MRC SGDP Research Centre (PO82), Institute of Psychiatry, Kings College London. SE5 8AF, London, UK. Inti.PedrosoRovira@iop.kcl.ac.uk phone: +44 020 7848 0798
Hello Inti, Thanks for pointing this out, this problem should be fixed in the latest build. Please let us know if you encounter similar problems after updating your instance. Greg Von Kuster Galaxy Development Team Inti Pedroso wrote:
Dear all, I am very new into Galaxy. I was doing analysis on the ucsc based service and i had problems making a workflow from my history. I did install galaxy on my computer (Mac OS 10.5.5, running python 2.5.1) thinking it may be easier to track the problem. I get this error message on the web "Server ErrorAn error occurred. See the error logs for more information. (Turn debug on to display exception reports here)" and the one at the bottom with the local installation. I get the same error if I try to make the workflow from scratch.
I hope you can help me.
Best,
Inti Pedroso
URL: http://127.0.0.1:8080/workflow/build_from_current_history File '/ Applications/Galaxy_dist/eggs/py2.5-noplatform/WebError-0.8a-py2.5.egg/ weberror/evalexception/middleware.py', line 364 in respond File '/ Applications/Galaxy_dist/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/ paste/debug/prints.py', line 98 in __call__ File '/Applications/ Galaxy_dist/eggs/py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/ wsgilib.py', line 539 in intercept_output File '/Applications/ Galaxy_dist/eggs/py2.5-noplatform/Beaker-0.5-py2.5.egg/beaker/ session.py', line 103 in __call__ File '/Applications/Galaxy_dist/eggs/ py2.5-noplatform/Paste-1.5.1-py2.5.egg/paste/recursive.py', line 80 in __call__ File '/Applications/Galaxy_dist/eggs/py2.5-noplatform/ Paste-1.5.1-py2.5.egg/paste/httpexceptions.py', line 632 in __call__ File '/Applications/Galaxy_dist/lib/galaxy/web/framework/base.py', line 126 in __call__ body = method( trans, **kwargs ) File '/ Applications/Galaxy_dist/lib/galaxy/web/controllers/workflow.py', line 382 in build_from_current_history step = model.WorkflowStep() File '/ Applications/Galaxy_dist/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1- py2.5.egg/sqlalchemy/orm/attributes.py', line 1215 in init File '/ Applications/Galaxy_dist/lib/galaxy/model/__init__.py', line 576 in __init__ self.input_connections = None File '/Applications/Galaxy_dist/ eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/orm/ attributes.py', line 36 in __set__ File '/Applications/Galaxy_dist/ eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/orm/ attributes.py', line 586 in set File '/Applications/Galaxy_dist/eggs/ py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/orm/ attributes.py', line 602 in _set_iterable File '/Applications/ Galaxy_dist/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1-py2.5.egg/ sqlalchemy/orm/attributes.py', line 586 in <lambda> File '/ Applications/Galaxy_dist/eggs/py2.5-noplatform/SQLAlchemy-0.4.7p1- py2.5.egg/sqlalchemy/orm/collections.py', line 522 in adapt_like_to_iterable TypeError: Incompatible collection type: None is not list-like
-- Social, Genetic and Developmental Psychiatry PhD programme, NIHR BRC for Mental Health; MRC SGDP Research Centre (PO82), Institute of Psychiatry, Kings College London. SE5 8AF, London, UK. Inti.PedrosoRovira@iop.kcl.ac.uk phone: +44 020 7848 0798
-- Social, Genetic and Developmental Psychiatry PhD programme, NIHR BRC for Mental Health; MRC SGDP Research Centre (PO82), Institute of Psychiatry, Kings College London. SE5 8AF, London, UK. Inti.PedrosoRovira@iop.kcl.ac.uk phone: +44 020 7848 0798
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participants (4)
-
Greg Von Kuster -
Henrikki Almusa -
Inti Pedroso -
WENYU CHUNG