[galaxy-dev] UnicodeDecodeError
Hello everybody, currently I have some trouble with the following kind of error: UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 155: ordinal not in range(128) We have encountered it twice now. The first time it was related to a shared library, which could not be opened anymore because of this error. So we deleted the library and set it up again. The second time it was related to a workflow. Clicking on Run caused this error to appear, while editing still worked. This time I saved the error message and you can find it attached to this mail. The cause of the error was a sign in a renaming step inside the workflow (the was part of the new name). After removing the everything worked again. However, when using the in a history item, it works without a problem. Unfortunately I cannot reproduce the error currently on my machine. The computer that caused it was a Mac. Should we just try to avoid any special characters or is this actually a bug which could be fixed? Best regards, Sarah 10.1.4.162 - - [09/Jun/2011:10:56:28 +0200] GET /workflow/run?id=91cc5a0bc3008f7d HTTP/1.1 500 - http://solweb2/workflow/list_for_run; Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.16) Gecko/20110319 Firefox/3.6.16 Error - type 'exceptions.UnicodeDecodeError': 'ascii' codec can't decode byte 0xe2 in position 155: ordinal not in range(128) URL: http://solweb2/workflow/run?id=91cc5a0bc3008f7d File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1397 in run incoming=kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 650 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 661 in fill_template_mako return template.render( **data ) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/template.py', line 133 in render return runtime._render(self, self.callable_, args, data) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 364 in _render _render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data)) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/galaxy/galaxy_server/database/compiled_templates/base.mako.py', line 40 in render_body __M_writer(unicode(next.body())) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 255 in lambda return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/galaxy/galaxy_server/database/compiled_templates/workflow/run.mako.py', line 226 in render_body __M_writer(unicode(do_inputs( module.get_runtime_inputs(type_filter), step.state.inputs, errors.get( step.id, dict() ), , step ))) File '/galaxy/galaxy_server/database/compiled_templates/workflow/run.mako.py', line 39 in do_inputs return render_do_inputs(context.locals_(__M_locals),inputs,values,errors,prefix,step,other_values) File '/galaxy/galaxy_server/database/compiled_templates/workflow/run.mako.py', line 391 in render_do_inputs __M_writer(unicode(row_for_param( input, values[ input.name ], other_values, errors, prefix, step ))) File '/galaxy/galaxy_server/database/compiled_templates/workflow/run.mako.py', line 297 in row_for_param return render_row_for_param(context,param,value,other_values,error_dict,prefix,step) File '/galaxy/galaxy_server/database/compiled_templates/workflow/run.mako.py', line 466 in render_row_for_param __M_writer(unicode(param.get_html_field( t, value, other_values ).get_html( str(step.id) + | + prefix ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 155: ordinal not in range(128) CGI Variables - CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_CHARSET: 'ISO-8859-1,utf-8;q=0.7,*;q=0.7' HTTP_ACCEPT_ENCODING: 'gzip,deflate' HTTP_ACCEPT_LANGUAGE: 'en-us,en;q=0.5' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: 'galaxysession=f611411aa8a0c6655dce25cc8ce7931696473135a41884694eefb704cf34d98429880ec7e01926f8' HTTP_HOST: 'solweb2' HTTP_REFERER:
Re: [galaxy-dev] bowtie on localgalaxy
On 06/09/2011 02:47 PM, Arun Selvam wrote: Hi, I am new to galaxy, I just downloaded and installed galaxy on my MAC system. I also download bowtie , and it is working perfectly on the command line. But am not able to see the bowtie option under mapping in the galaxy menu. Are you sure, you did not comment'out it in the 'tool_conf.xml'? Do you get an error in the log file after restart, following the line: galaxy.tools DEBUG 2011-06-09 15:08:52,316 Loaded tool: bowtie_wrapper 1.1.2 Regards, Hans Do I have to do another modifications like move into particular folder or create some files or set path ? Could anyone please help me on this ? Thank you Arun ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] galaxy-dev] format=input
I added an example taken from trim.seqs.xml in the Mothur metagenomics
tool_suite to:
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
The following will create datasets in the history panel, setting the output data type to
be the same as that of an input dataset named by the format_source attribute.
Note that a conditional name is not included, so 2 separate conditional blocks should not
contain parameters with the same name.
inputs
!-- fasta may be an aligned fasta that subclasses Fasta --
param name=fasta type=data format=fasta label=fasta - Sequences/
conditional name=qual
param name=add type=select label=Trim based on a quality file? help=
option value=nono/option
option value=yesyes/option
/param
when value=no/
when value=yes
!-- qual454, qualsolid, qualillumina --
param name=qfile type=data format=qual label=qfile - a quality file/
/when
/conditional
/inputs
outputs
data format_source=fasta name=trim_fasta label=${tool.name} on ${on_string}:
trim.fasta/
data format_source=qfile name=trim_qual label=${tool.name} on ${on_string}:
trim.qual
filter(qual['add'] == 'yes')/filter
/data
/outputs
On 6/9/11 2:39 AM, Peter Cock wrote:
On Wed, Jun 8, 2011 at 9:59 PM, Jim Johnsonjohns...@umn.edu wrote:
It went into galaxy-central:
$ hg log -pr 5082
changeset: 5082:a86e1fa82a89
user:Kanwei Likan...@gmail.com
date:Thu Feb 17 15:35:07 2011 -0500
summary: Add a format_source attribute to the ToolConfig output data
element [JJ Johnson]. Closes #470
...
And I should have put an example in:
https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
Oh right - better late than never ;)
On the bright side because this commit was a while ago, it has
already been included in the stable Galaxy releases.
Thanks for this, I can think of several of my own tools where this
will work much more cleanly than the current solution using
change_format andwhen.
Regards,
Peter
___
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:
http://lists.bx.psu.edu/
Re: [galaxy-dev] User list and disk space?
On Tue, May 17, 2011 at 2:21 PM, Nate Coraor n...@bx.psu.edu wrote: Peter Cock wrote: That sounds really useful - it is something that you plan on adding to Galaxy officially? Yes, I'm working on adding a lot of user- and admin- side access to various numbers about disk usage (used by histories, used by deleted data, etc. and disk quotas. I hope to have this done shortly after the GCC. Thanks, --nate Hi Nate, Since you're looking at this kind of thing, would the Saved Histories page be worth updating to show the size on disk of each history? As a Galaxy user that seems moderately useful - although perhaps more of interest to Galaxy admins? Peter ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Passing username to drmaa.py
Chorny, Ilya wrote: I am trying to figure out how to pass the current user name to drama.py. I have had little success so far. None of the environmental variables contain any current user information. Any thoughts? Thanks, Ilya Hi Ilya, You can use $__user_email__ in the command template in the tool's configuration, if you need it there. In the drmaa.py code itself, you can use the '.user' property on the job wrapper to get the email address. --nate Ilya Chorny Ph.D. Bioinformatics - Intern icho...@illumina.commailto:icho...@illumina.com 858-202-4582 ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] use external authentication bare username as email address without appending any email domain
Leandro Hermida wrote: Hi, Is it possible to tell Galaxy to use the bare username passed back by external authentication as the email address without appending any domain? It seems to complain if it isn't in email address format and asks you to set up a domain to append in universe.wsgi. I would like to use the bare username as the email address since it works fine as an email address in for example any Active Directory-based organization and also in many non-academic organizations it is preferred not to use the email addresses as the ID. Hi Leandro, If you're using any of Galaxy's mail services, your SMTP server would also need to be able to accept mail to users with no domain. That said, you should be able to hack lib/galaxy/web/framework/middleware/remoteuser.py to do what you want. Specifically, remove/comment the conditional: if not environ[ 'HTTP_REMOTE_USER' ].count( '@' ): --nate thanks in advance, Leandro ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] Fwd: [galaxy-user] Galaxy tool error report from joh...@ibms.sinica.edu.tw
John, Questions about local installs are best directed to galaxy-dev, so I've moved the question to this list. While executing cuffcompare, I encountered this error message: Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output' I was practicing RNA-seq analysis steps on newly installed galaxy to test if i could easily analyze my data. I could run cufflinks and cuffdiff through galaxy, but i'm unable to run cuffcompare. how should i solve this problem? thanks a lot! A recent change set has made Cuffcompare compatible with v1.0.3: https://bitbucket.org/galaxy/galaxy-central/changeset/f4b98c453389 You'll need to update your Galaxy instance with this change set for Cuffcompare to work; also note that the change set is in galaxy-central, not galaxy-dist. Best, J.___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Defining new file formats in Galaxy (for new tool wrappers)
Hi Peter, On Jun 9, 2011, at 12:02 PM, Peter Cock wrote: Is there anything documented about the built-in format conversion within the Galaxy core, rather than tools. No, not currently - except for a few details in various slide presentations. Nothing forma though. We're trying to keep up on some of this documentation, so hopefully we'll have something soon. Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] use external authentication bare username as email address without appending any email domain
Hi Nate, Thank so much for the instructions :) , yes this is what I would want to do as Galaxy was adding an empty @ after the username. Yep in a Windows domain environment the bare username (sAMAccountName) is also an email nickname and works with the Exchange server when you use SMTP services. thank a lot, Leandro On Thu, Jun 9, 2011 at 6:54 PM, Nate Coraor n...@bx.psu.edu wrote: Leandro Hermida wrote: Hi, Is it possible to tell Galaxy to use the bare username passed back by external authentication as the email address without appending any domain? It seems to complain if it isn't in email address format and asks you to set up a domain to append in universe.wsgi. I would like to use the bare username as the email address since it works fine as an email address in for example any Active Directory-based organization and also in many non-academic organizations it is preferred not to use the email addresses as the ID. Hi Leandro, If you're using any of Galaxy's mail services, your SMTP server would also need to be able to accept mail to users with no domain. That said, you should be able to hack lib/galaxy/web/framework/middleware/remoteuser.py to do what you want. Specifically, remove/comment the conditional: if not environ[ 'HTTP_REMOTE_USER' ].count( '@' ): --nate thanks in advance, Leandro ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] CSV import of Sample information Error
Joe, Try editing your Sample Form Definition, changing the Field name value from the default of 1_field_name to be your desired agctac. Then, your csv file with the line Sample1,Library1,Lib1Folder1,History,Workflow,agctac should work. Greg On Jun 9, 2011, at 6:03 PM, Joe Cruz wrote: Hey Greg, I got it to work by filling the field names with their default names, but I thought you could fill out the entire sample forms, including the field names, with the csv file. For example: Sample1,Library1,Lib1Folder1,History,Workflow,1_field_name The above works when imported, filling out the sample name, library, folder, history, and workflow fields but leaving 1_field_name (barcode field in this case) empty. We wish this next example to work,which I currently get the '1_field_name' error: Sample1,Library1,Lib1Folder1,History,Workflow,agctac Currently we have clients fill out a spreadsheet for the samples they intend to submit, since many submit multiple samples and most of the time have the same parameters for all of them. We wish to convert their completed spreadsheet into a csv file and then import it into galaxy so they dont' have to fill out all the fields repetitively. joe On Thu, Jun 9, 2011 at 3:20 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Joe, Sorry you've bumped into problems - we know we're lacking on documentation for the sample tracking stuff currently. I believe this new issue is due to a field named differently in your Sample FormDefinition vs your csf file. In looking at this, I found a slightly incorrect description of the csv file layout on our Add Samples page, which I've corrected. In the Sample FormDefinition, the default name for a field is 1_field_name, 2_field_name, etc. Below is a screen capture that show this. However, the csv file you sent me previously includes the following: SampleName1,library1,library1_folder1,history1,workflow1,sampleType1,conc,runType,readLength The csv layout is as follows ( I've correct the incorrect FieldValue1, etc to be Field1Name, etc. The csv file must be in the following format: SampleName,DataLibraryName,DataLibraryFolderName,HistoryName,WorkflowName,Field1Name,Field2name.. The Field1Name, Field2Name values in your csv file must match the value in the Field name form field in the screen shot below. After making this change, let me know if you bump into any other problems. Thanks for you patience on this, Greg sample_form.tiff On Jun 9, 2011, at 12:32 PM, Joe Cruz wrote: Hey Greg, Unfortunately after pulling your changeset I got a new error related to '1_field_name'. Here is the error traceback: URL: http://localhost:8080/requests_common/add_samples?cntrller=requestsid=f2db41e1fa331b3e File '/home/jcruz/galaxy-central/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/jcruz/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/jcruz/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/jcruz/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/jcruz/galaxy-central/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/jcruz/galaxy-central/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/home/jcruz/galaxy-central/lib/galaxy/web/framework/__init__.py', line 84 in decorator return func( self, trans, *args, **kwargs ) File '/home/jcruz/galaxy-central/lib/galaxy/web/controllers/requests_common.py', line 831 in add_samples return self.__import_samples( trans, cntrller, request, displayable_sample_widgets, libraries, workflows, **kwd ) File '/home/jcruz/galaxy-central/lib/galaxy/web/controllers/requests_common.py', line 1163 in __import_samples sample_copy_select_field=sample_copy_select_field ) File '/home/jcruz/galaxy-central/lib/galaxy/web/framework/__init__.py', line 661 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/jcruz/galaxy-central/lib/galaxy/web/framework/__init__.py', line 672 in fill_template_mako return template.render( **data ) File '/home/jcruz/galaxy-central/eggs/Mako-0.2.5-py2.6.egg/mako/template.py', line 133 in render return runtime._render(self, self.callable_, args, data) File '/home/jcruz/galaxy-central/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 364 in _render _render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data)) File
