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BugFix for dynamic_options ParamValueFilter to run IUC SnpEff in a workflow
by Jim Johnson 19 Mar '14

19 Mar '14

The current code in: lib/galaxy/tools/parameters/dynamic_options.py only searches the top layer of the dict to find the dependency value. A fix is provide in pull request: #343: Need to traverse the other_value dict to find dependencies for ParamValueFilter in<https://bitbucket.org/galaxy/galaxy-central/pull-request/343/need-to-traver…> SnpEff tool_config <inputs> <param format="vcf,tabular,pileup,bed" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> ... <conditional name="snpDb"> <param name="genomeSrc" type="select" label="Genome source"> <option value="cached">Locally installed reference genome</option> <option value="history">Reference genome from your history</option> <option value="named">Named on demand</option> </param> <when value="cached"> <param name="genomeVersion" type="select" label="Genome">  <options from_data_table="snpeff_genomedb"> <filter type="unique_value" column="0" /> </options> </param> <param name="extra_annotations" type="select" display="checkboxes" multiple="true" label="Additional Annotations"> <help>These are available for only a few genomes</help> <options from_data_table="snpeff_annotations"> <filter type="param_value" ref="genomeVersion" key="genome" column="0" /> <filter type="unique_value" column="1" /> </options> </param> When running workflow: input.vcf -> SnpEff The values in ParamValueFilter filter_options function: |>>>| ||self*.*ref_name|| |'genomeVersion' ||>>>| ||other_values|| |{u'spliceSiteSize': '1', u'filterHomHet': 'no_filter', u'outputFormat': 'vcf', u'filterOut': None, u'inputFormat': 'vcf', u'filterIn': 'no_filter', u'udLength': '5000', u'generate_stats': True, u'noLog': True, u'chr': 'None', u'intervals': None, u'snpDb': {'extra_annotations': None, 'regulation': None, 'genomeVersion': 'GRCh37.71', 'genomeSrc': 'cached', '__current_case__': 0}, u'offset': '', u'input': <galaxy.tools.parameters.basic.DummyDataset object at 0x11451b8d0>, u'transcripts': None, u'annotations': ['-canon', '-lof', '-onlyReg']} || Since |||'genomeVersion' isn't in the keys of other_values, but rather in ||||||other_values['|||||||||snpDb'] this failed the assertion: |||||||||| assert self.ref_name in other_values, "Required dependency '%s' not found in incoming values" % self.ref_name Pull request |||||343: |||||<https://bitbucket.org/galaxy/galaxy-central/pull-request/343/need-to-traver…> |||||$ hg diff lib/galaxy/tools/parameters/dynamic_options.py diff -r 95517f976cca lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py Thu Feb 27 16:56:25 2014 -0500 +++ b/lib/galaxy/tools/parameters/dynamic_options.py Fri Feb 28 11:37:04 2014 -0600 @@ -177,8 +177,27 @@ return self.ref_name def filter_options( self, options, trans, other_values ): if trans is not None and trans.workflow_building_mode: return [] - assert self.ref_name in other_values, "Required dependency '%s' not found in incoming values" % self.ref_name - ref = other_values.get( self.ref_name, None ) + ## Depth first traversal to find the value for a dependency + def get_dep_value(param_name, dep_name, cur_val, layer): + dep_val = cur_val + if isinstance(layer, dict ): + if dep_name in layer: + dep_val = layer[dep_name] + if param_name in layer: + return dep_val + else: + for l in layer.itervalues(): + dep_val = get_dep_value(param_name, dep_name, dep_val, l) + if dep_val: + break + elif isinstance( layer, list): + for l in layer: + dep_val = get_dep_value(param_name, dep_name, dep_val, l) + if dep_val: + break + return None + ref = get_dep_value(self.dynamic_option.tool_param.name, self.ref_name, None, other_values) + assert not ref, "Required dependency '%s' not found in incoming values" % self.ref_name for ref_attribute in self.ref_attribute: if not hasattr( ref, ref_attribute ): return [] #ref does not have attribute, so we cannot filter, return empty list -- James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota

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Empty history pane
by Liisa Koski 18 Mar '14

18 Mar '14

Hello, Our site maintains a local Galaxy installation (Nov.4th distributuion). One of our usrers has lost the ability to view anything in his history pane. He is able to run tools and view the list of 'Saved Histories' in the middle pane but the History pane itself stays empty. When I impersonate him I can see his history pane. Very weird. Any insight would be much appreciated. Thanks, Liisa

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ToolSheds
by César Acevedo 18 Mar '14

18 Mar '14

Hi everyone, I am just wondering if there is some problems with: http://testtoolshed.g2.bx.psu.edu/ ? Getting "operation time out" from my galaxy stand-alone admin view when i try to search and browse tools, no response to ping neither. Thanks! CA

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inserting .js file for visualization with d3.js
by Chiron Lionel 18 Mar '14

18 Mar '14

Hi, I'm struggling to insert d3.js graphs in the results of tool created in galaxy but it is not clear how to do that.. I received some precious help for permitting to galaxy not to remove head and css parts.. but can't figure out how to enable galaxy to use the .js files I created for visualizing the data.. What is the best way to do that? .. where do have I do put the .js files and how to call them? Thanks in advance! Lionel

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http://toolshed.g2.bx.psu.edu/ is down?
by changyu 18 Mar '14

18 Mar '14

Is http://toolshed.g2.bx.psu.edu/ down?

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Reorder Sam files
by Alexander Kurze 17 Mar '14

17 Mar '14

Hi there, we are running a local instant of galaxy and when running Picard tools Reorder Sam files I get following error message: "An error occurred with this dataset: *## exit code=1; stdout= Error: Unable to access jarfile /ReorderSam.jar*" Now, I thought that when installing picard-tools via the toolshed the dependency should be added automatically. I am really not sure why it looks for ReorderSam.jar in the top directory /. Any clues? Best wishes, Alex -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341

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I can't impersonate an user
by Perez, Ricardo 17 Mar '14

17 Mar '14

Dear all, We are currently using the stable build of Galaxy and we are encountering the following problem: When we try to impersonate an user, the user drop down menu hangs in looking up the user. In consequence, we can not impersonate the user. This behaviour started when we upgraded to the Feb 10, 2014 version. Do we have to modify a configuration file to make this to work again? Thank you all, --Ricardo Perez

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InterMine data import tools missing?
by Joel Richardson 17 Mar '14

17 Mar '14

Hi, First let me apologize if this is not the right place to post this – I wasn't sure. It seems that the various InterMine tools under GetData (FlyMine, YeastMine, MouseMine, …) have gone missing from the main Galaxy site. Can they be restored? Thanks. Cheers, Joel -- Joel E. Richardson, Ph.D. Sr. Research Scientist Mouse Genome Informatics The Jackson Laboratory 600 Main Street Bar Harbor, Maine 04609 207-288-6435 joel.richardson(a)jax.org The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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FTP password and web interface password
by Yec'han Laizet 17 Mar '14

17 Mar '14

Hello, I set up a FTP server with SFTP support on my galaxy instance. I have a strange behavior when trying to connect by SFTP. Some users cannot authentify (access denied) whereas other can. As all users can login to the web interface with their credentials, I wanted to check if the length of the password could be the problem with SFTP. To do so, I went to the admin interface to reset the password of a user who could connect by SFTP. Then, this user can connect to the galaxy web interface with the new password but not by SFTP ; if we use the old password, it still works for SFTP authenfication as if both passwords are independent. Could you help me to solve the problem? Yec'han ================================================ Dr. Yec'han LAIZET Ingenieur Bioinformatique Tel: +33 (0)5 57 12 27 75 _________________________________ INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS ================================================

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upload error
by ruiwang.sz 15 Mar '14

15 Mar '14

Hi Guys, Our galaxy instance has been in use for a couple years but since Feb 2014 it started to show us some weird behavior. Recently the upload function suddenly stopped working properly. We are getting messages like the following. I'm not sure if this only happens to us. If someone has seen this before, please give me some hints. P.S., I searched online and many says that this is because the browser does not wait till all the data from the server is received and closes the socket. However it happens both in firefox and chrome. I'm wondering if it is because galaxy has any change recently but when I do 'hg update stable' it reported that it is up to date. Thanks! Rui Error messages: Exception happened during processing of request from ('127.0.0.1'---------------------------------------- Exception happened during processing of request from (, 52259'127.0.0.1', 52260) Traceback (most recent call last): ) Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread ---------------------------------------- Exception happened during processing of request from (---------------------------------------- File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread Exception happened during processing of request from'127.0.0.1' , ('127.0.0.1'52264, 52262---------------------------------------- ) Exception happened during processing of request from ('127.0.0.1'---------------------------------------- , ) Traceback (most recent call last): Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread Exception happened during processing of request from 52261('127.0.0.1', ---------------------------------------- )Exception happened during processing of request from Traceback (most recent call last): 52263('127.0.0.1') File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread Traceback (most recent call last): , 52265) File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread Traceback (most recent call last): File "/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request self.finish_request(request, client_address) self.finish_request(request, client_address) self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request self.finish_request(request, client_address) File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request 127.0.0.1 - - [27/Feb/2014:16:59:36 -0700] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:20020/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:27.0) Gecko/20100101 Firefox/27.0" self.RequestHandlerClass(request, client_address, self) self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ self.RequestHandlerClass(request, client_address, self) self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ self.finish() self.RequestHandlerClass(request, client_address, self) self.finish() self.RequestHandlerClass(request, client_address, self) self.finish() File "/usr/lib/python2.7/SocketServer.py", line 693, in finish File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ File "/usr/lib/python2.7/SocketServer.py", line 693, in finish File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.7/SocketServer.py", line 693, in finish File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ File "/usr/lib/python2.7/SocketServer.py", line 640, in __init__ self.finish() self.finish() File "/usr/lib/python2.7/SocketServer.py", line 693, in finish self.wfile.flush() self.wfile.flush() File "/usr/lib/python2.7/SocketServer.py", line 693, in finish self.wfile.flush() self.finish() File "/usr/lib/python2.7/SocketServer.py", line 693, in finish File "/usr/lib/python2.7/socket.py", line 303, in flush File "/usr/lib/python2.7/socket.py", line 303, in flush self.wfile.flush() self.finish() self.wfile.flush() File "/usr/lib/python2.7/socket.py", line 303, in flush self.wfile.flush() File "/usr/lib/python2.7/SocketServer.py", line 693, in finish File "/usr/lib/python2.7/socket.py", line 303, in flush File "/usr/lib/python2.7/socket.py", line 303, in flush File "/usr/lib/python2.7/socket.py", line 303, in flush self.wfile.flush() File "/usr/lib/python2.7/socket.py", line 303, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) self._sock.sendall(view[write_offset:write_offset+buffer_size]) self._sock.sendall(view[write_offset:write_offset+buffer_size]) self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe error: [Errno 32] Broken pipe self._sock.sendall(view[write_offset:write_offset+buffer_size]) ---------------------------------------- self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe error: [Errno 32] Broken pipe error: [Errno 32] Broken pipe ---------------------------------------- self._sock.sendall(view[write_offset:write_offset+buffer_size]) ---------------------------------------- error: [Errno 32] Broken pipe ---------------------------------------- ---------------------------------------- error: [Errno 32] Broken pipe ----------------------------------------

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