Re: [galaxy-dev] Components
On Tue, Jun 7, 2011 at 9:24 AM, Mariette jmari...@toulouse.inra.fr wrote: Thanks for the answer, so I tryed to write a wrapper, but the main script is not recognize. When I'm calling my wrapper in the xml file, I don't have to specify the full path but then from my wrapper if I want to call my main script I can't if this one is not on the PATH ? the wrapper current directory is the job_working_directory, there is anyway to access my main script just like it's done for the wrapper ? Generally put the wrapper script next to your tool XML file, and don't prefix it with any path in the command tag in the XML, e.g. /opt/galaxy/tools/mariette/my_tool.xml /opt/galaxy/tools/mariette/my_tool.sh (or my_tool.py or my_tool.pl etc depending on what language you used) Your wrapper script then has to call the real executable, and the normal way to do this on Unix is to have it on the PATH. You could also hard code an absolute path. 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] Components
On Tue, Jun 7, 2011 at 10:56 AM, Mariette jmari...@toulouse.inra.fr wrote: Thanks for the answer, Still considering the number of outputed files problem. In my script I know that if a cleaning option is set 2 other files will be created, so I check if the option is asked by the user and try this : outputs data name=log format=txt / #if $clean_pairends.clean_pairends_select==y: data name=output format=input/ #end if /outputs but this is not working ... there is a way to do what I want ? thx Jerome The #if stuff is Cheetah syntax, and only applies within the command tag - not to the XML file in general. You probably want a conditional output using when, see: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Components
Thanks for the answer, so I tryed to write a wrapper, but the main script is not recognize. When I'm calling my wrapper in the xml file, I don't have to specify the full path but then from my wrapper if I want to call my main script I can't if this one is not on the PATH ? the wrapper current directory is the job_working_directory, there is anyway to access my main script just like it's done for the wrapper ? thanks for your answer, Jerome Peter Cock a écrit : On Mon, Jun 6, 2011 at 2:45 PM, Mariette jmari...@toulouse.inra.fr wrote: Hi everyone, I'm new in galaxy and I want to create a component, so I have multiple questions. The component executes a script which takes different formats : fasta|fastq|sff. As output it takes a folder, to do so I used the extra_files_path attribute of an output data (--out='$output.extra_files_path'). The result file is stored in this folder with the log file and should be in the same format as the input one. I wrote the xml file and it works just fine, however as it's a folder there is no way to use the result file(s) for further analysis. How can I manage this ? I use a wrapper script which moves the output file from the sub-directory to the location Galaxy requested. Regarding the file format, if you only have one input file you can use format=input, otherwise use the change_format tag in the XML. Also it can happen that there is more than 1 file outputted, how can I manage multiple outputs ? An other question about the input format, I have an option to the script to specify the format. I saw there is auto-format detection routines in galaxy, there is a way so I can call them to automatically complete this option ? Normally the wrapper specifies the output format explicitly. 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/ ___ 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] Components
Thanks for the answer, Still considering the number of outputed files problem. In my script I know that if a cleaning option is set 2 other files will be created, so I check if the option is asked by the user and try this : outputs data name=log format=txt / #if $clean_pairends.clean_pairends_select==y: data name=output format=input/ #end if /outputs but this is not working ... there is a way to do what I want ? thx Jerome Peter Cock a écrit : On Tue, Jun 7, 2011 at 9:24 AM, Mariette jmari...@toulouse.inra.fr wrote: Thanks for the answer, so I tryed to write a wrapper, but the main script is not recognize. When I'm calling my wrapper in the xml file, I don't have to specify the full path but then from my wrapper if I want to call my main script I can't if this one is not on the PATH ? the wrapper current directory is the job_working_directory, there is anyway to access my main script just like it's done for the wrapper ? Generally put the wrapper script next to your tool XML file, and don't prefix it with any path in the command tag in the XML, e.g. /opt/galaxy/tools/mariette/my_tool.xml /opt/galaxy/tools/mariette/my_tool.sh (or my_tool.py or my_tool.pl etc depending on what language you used) Your wrapper script then has to call the real executable, and the normal way to do this on Unix is to have it on the PATH. You could also hard code an absolute path. 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/ ___ 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] Adding Link to Sequencing Requests Page
Hello Everyone, I would like to add a link to the Sequencing Requests page and modify it further in the future but I'm unsure of how to go about doing that, since there is no static html file for the webpage (at least none that I can find) and I'm a newbie when it comes to web application development. I appreciate your help and patience. joe ___ 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] CSV import of Sample information Error
Hello Everyone, I wanted to ask if anyone has experience successfully importing sample information through a csv file. I know there is an issue already created for csv file import, which I left a comment earlier: https://bitbucket.org/galaxy/galaxy-central/issue/398/csv-import-of-sample-information-is-broken#comment-510683 \ but my bug doesn't seem to deal with an 'Invalid Request ID' as the issue above states. This is the error I get: URL: http://localhost/requests_common/add_samples?cntrller=requestsid=a65cf3ca8eb85be3 File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 84 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/controllers/requests_common.py', line 829 in add_samples return self.__import_samples( trans, cntrller, request, displayable_sample_widgets, libraries, **kwd ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/controllers/requests_common.py', line 1109 in __import_samples sample_copy_select_field=sample_copy_select_field ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 650 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 661 in fill_template_mako return template.render( **data ) File '/home/galaxy1/galaxy-dist/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/galaxy1/galaxy-dist/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 '/home/galaxy1/galaxy-dist/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 '/home/galaxy1/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/home/galaxy1/galaxy-dist/database/compiled_templates/base.mako.py', line 40 in render_body __M_writer(unicode(next.body())) File '/home/galaxy1/galaxy-dist/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 '/home/galaxy1/galaxy-dist/database/compiled_templates/requests/common/ add_samples.mako.py', line 164 in render_body __M_writer(unicode(render_samples_grid( cntrller, request, displayable_sample_widgets, action='edit_samples', adding_new_samples=True, encoded_selected_sample_ids=[], render_buttons=False, grid_header=grid_header ))) File '/home/galaxy1/galaxy-dist/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 '/home/galaxy1/galaxy-dist/database/compiled_templates/requests/common/ common.mako.py', line 749 in render_render_samples_grid sample_widget_history = sample_widget[ 'history' ] KeyError: 'history' I greatly appreciate your help and patience. Thanks, joe ___ 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] Components
So I tryed an other way to access the value :
data name=out_pe_fasta format=fasta
filter${clean_pairends.clean_pairends_select} == y/filter
/data
but it's not working either ... I tryed to add a label to the data like
this :
data name=out_pe_fasta format=fasta
label=${clean_pairends.clean_pairends_select}
filter${clean_pairends.clean_pairends_select} == y/filter
/data
the data file is created with a label n ! Is it not weird ?
Jerome
Mariette a écrit :
Thanks this is what I was looking for !!
I succeded to make it work when checking the value on a simple param
using the name like this
inputs
param name=qual_file type=data format=qual optional=true
label=Quality reads file (if input is a fasta) /
/input
...
outputs
data name=out_qual format=qual
filterqual_file != None/filter
/data
/outputs
however when I'm in a conditional tag like this, I tryed :
inputs
conditional name=clean_pairends
param name=clean_pairends_select type=select label=Clean
pairends
option value=yYes/option
option selected=true value=nNo/option
/param
when value=y
param name=border_limit type=integer size=10
value=70 label=Minimal length between the spacer and the read
extremity/
param name=missmatch type=integer size=10 value=10
label=Limit of missmatch/
/when
when value=n
/when
/conditional
/input
...
outputs
data name=out_pe_fasta format=fasta
filterclean_pairends.clean_pairends_select == y/filter
/data
but it's not working ... it looks like between filter tag I should
provide a python test, am I missing something ?
thx,
Jerome
Peter Cock a écrit :
On Tue, Jun 7, 2011 at 11:38 AM, Mariette jmari...@toulouse.inra.fr
wrote:
I can only see the usage of the when tag into the outputs
to change format, is that correct ?
On re-reading the wiki page, yes, I think you are right. I should have
said filter with data, as in tools/filters/sff_extractor.xml
Peter
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Re: [galaxy-dev] question/bug with cuffcompare wrapper
Assaf, Thanks for the very helpful information. We largely sync our tool wrappers to the tool version used on our public server. We're currently running v1.0.1 of Cufflinks on main; hence, as you discovered, the wrappers are compatible with that version of Cufflinks but (sadly) incompatible with newer versions. If you modify the Cufflinks/compare/diff wrappers to be compatible with 1.0.2/3, please either put them in the toolshed or send them to me and I'll incorporate them into the Galaxy code base. Thanks, J. On Jun 6, 2011, at 2:42 PM, Assaf Gordon wrote: Hi, It seems the cuffcompare XML wrapper expects a file named cc_output to contain the transcript accuracy report. I guess it worked with versions 0.9.3 and 1.0.1, but at least in version 1.0.2, this file is now named cc_output.stats, and the transcript accuracy file is empty. so the XML wrapper is compatible with 1.0.1 but not really with 1.0.2/3 (Unless I missed something in the XML/python/cuffcompare execution chain). Also, Notice that starting version 1.0.2 they've added an option to normalize by either total number of reads or by number of reads that matched the given GTF file. To make matters worse, cufflinks defaults to normalizing to total reads, and cuffdiff defaults to normalizing by GTF-matching reads. The options are called --total-hits-norm and --compatible-hits-norm. There's no way for users to specify either of those in Galaxy, so running cufflinks/cuffdiff might give unexpected results (not that there are any expected results, but still...) Just something to think about when you work on the next version of cufflinks wrappers. -gordon ___ 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] question/bug with cuffcompare wrapper
Hi all, Jeremy Goecks wrote, On 06/07/2011 01:25 PM: If you modify the Cufflinks/compare/diff wrappers to be compatible with 1.0.2/3, please either put them in the toolshed or send them to me and I'll incorporate them into the Galaxy code base. We are actually working on customized version of those tools, with parameters which better suit our needs, I'm happy to share. They are far from stable, so no tool-shed yet. The XML's are here: http://cancan.cshl.edu/labmembers/gordon/files/cshl_rnaseq_tools_2011-06-07.tar.bz2 They use Cufflinks 1.0.3, but also require a small patch to Galaxy (included in the tarball), to add our $input.tag labeling hack. Without this patch, you'll need to modify the output labels and the --label parameter of cuffdiff (with this patch, it calculates the labels automatically). See the working interface go here: http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_cufflinks http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_cuffcompare http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_cuffdiff http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_cuffdiff_replicates Comments are always welcomed, -gordon ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] loading tool options depending on initial parameter
Hello,
I am working on a tool that should load a set of selected files from a
group folder. The interface should only display the files in the
selected group folder.
I tried to use the code below to read the files as options from an
external .xml file in the tool-data directory based on the group
selected in the first step but I run into 2 problems:
- How can I pass the information from the parameter group to
from_file.
- Even if I hardcode the xml file to be read from tool-data,
the options do not show up. In the tool annotation profiler certain meta
data of the input dataset are required for the options to be displayed
but in my case I do not start without input dataset.
inputs
page
param name=group type=select label=Group help=Select
your group
option value=group1_files.xmlgroup1/option
option value=group2_files.xmlgroup2/option
/param
/page
page
param name=selectedfiles type=drill_down
display=checkbox hierarchy=recurse multiple=true label=Choose
files to upload help= from_file=${group}/
/page
/inputs
Thanks for your help in advance
Tim
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Re: [galaxy-dev] CuffDiff output mis-named ?
Based on the naming convention of the other outputs (and the output files from cuffdiff), I think the label of the first one should be renamed to CDS Expression only (assuming the relevant input file cds_exp.diff). Correct. That said, I've been planning to reorder and rename the Cuffdiff outputs for a while now; changes in are galaxy-central changeset 5650:dc97d0a852cb Thanks, 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] CSV import of Sample information Error
Hello Joe, Can you send me your csv file? Thanks! On Jun 7, 2011, at 10:45 AM, Joe Cruz wrote: Hello Everyone, I wanted to ask if anyone has experience successfully importing sample information through a csv file. I know there is an issue already created for csv file import, which I left a comment earlier: https://bitbucket.org/galaxy/galaxy-central/issue/398/csv-import-of-sample-information-is-broken#comment-510683\ but my bug doesn't seem to deal with an 'Invalid Request ID' as the issue above states. This is the error I get: URL: http://localhost/requests_common/add_samples?cntrller=requestsid=a65cf3ca8eb85be3 File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 84 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/controllers/requests_common.py', line 829 in add_samples return self.__import_samples( trans, cntrller, request, displayable_sample_widgets, libraries, **kwd ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/controllers/requests_common.py', line 1109 in __import_samples sample_copy_select_field=sample_copy_select_field ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 650 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 661 in fill_template_mako return template.render( **data ) File '/home/galaxy1/galaxy-dist/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/galaxy1/galaxy-dist/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 '/home/galaxy1/galaxy-dist/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 '/home/galaxy1/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/home/galaxy1/galaxy-dist/database/compiled_templates/base.mako.py', line 40 in render_body __M_writer(unicode(next.body())) File '/home/galaxy1/galaxy-dist/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 '/home/galaxy1/galaxy-dist/database/compiled_templates/requests/common/add_samples.mako.py', line 164 in render_body __M_writer(unicode(render_samples_grid( cntrller, request, displayable_sample_widgets, action='edit_samples', adding_new_samples=True, encoded_selected_sample_ids=[], render_buttons=False, grid_header=grid_header ))) File '/home/galaxy1/galaxy-dist/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 '/home/galaxy1/galaxy-dist/database/compiled_templates/requests/common/common.mako.py', line 749 in render_render_samples_grid sample_widget_history = sample_widget[ 'history' ] KeyError: 'history' I greatly appreciate your help and patience. Thanks, joe ___ 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/ 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] CSV import of Sample information Error
For my sample forms I have fields for Sample type, concentration, run type, and read length. I greatly appreciate your help Greg. If you have any other questions let me know. Thanks, Joe On Tue, Jun 7, 2011 at 2:56 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Joe, Can you send me your csv file? Thanks! On Jun 7, 2011, at 10:45 AM, Joe Cruz wrote: Hello Everyone, I wanted to ask if anyone has experience successfully importing sample information through a csv file. I know there is an issue already created for csv file import, which I left a comment earlier: https://bitbucket.org/galaxy/galaxy-central/issue/398/csv-import-of-sample-information-is-broken#comment-510683 \ but my bug doesn't seem to deal with an 'Invalid Request ID' as the issue above states. This is the error I get: URL: http://localhost/requests_common/add_samples?cntrller=requestsid=a65cf3ca8eb85be3 File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy1/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 84 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/controllers/requests_common.py', line 829 in add_samples return self.__import_samples( trans, cntrller, request, displayable_sample_widgets, libraries, **kwd ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/controllers/requests_common.py', line 1109 in __import_samples sample_copy_select_field=sample_copy_select_field ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 650 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/galaxy1/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 661 in fill_template_mako return template.render( **data ) File '/home/galaxy1/galaxy-dist/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/galaxy1/galaxy-dist/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 '/home/galaxy1/galaxy-dist/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 '/home/galaxy1/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/home/galaxy1/galaxy-dist/database/compiled_templates/base.mako.py', line 40 in render_body __M_writer(unicode(next.body())) File '/home/galaxy1/galaxy-dist/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 '/home/galaxy1/galaxy-dist/database/compiled_templates/requests/common/ add_samples.mako.py', line 164 in render_body __M_writer(unicode(render_samples_grid( cntrller, request, displayable_sample_widgets, action='edit_samples', adding_new_samples=True, encoded_selected_sample_ids=[], render_buttons=False, grid_header=grid_header ))) File '/home/galaxy1/galaxy-dist/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 '/home/galaxy1/galaxy-dist/database/compiled_templates/requests/common/ common.mako.py', line 749 in render_render_samples_grid sample_widget_history = sample_widget[ 'history' ] KeyError: 'history' I greatly appreciate your help and patience. Thanks, joe ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu SampleName1,client1DataLib,folder1,testHistory,testWorkflow,sampleType1,conc,runType,readLength ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions
