Re: [galaxy-dev] How to be an admin?
Hi Tobias, Maybe your Galaxy is running in daemon mode. If that is the case, if you do 'ps aux | grep universe' you will see something like: python ./scripts/paster.py serve universe_wsgi.ini --daemon You should first stop the daemon. Or you kill it, or you type in the galaxy home './run.sh stop'. Check again via ps to assure yourself the daemon has stopped. Now, start galaxy again. HTH, Marc -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Tobias Hohenaur Sent: Tuesday, April 09, 2013 3:59 PM To: Dannon Baker Cc: Galaxy Dev Subject: Re: [galaxy-dev] How to be an admin? Thank you for hinting the reload option. I opened the universe_wsgi.ini in the galaxy-dist folder and changed the port to 8081, the host to 0.0.0.0, then saved. The server reloads, but the changes have not taken effect. It is still at 127.0.0.1 and 8080... As far as I can see there is no other universe_wsgi.ini file except one that is calles universe_wsgi.ini sample. - Original Message - From: Dannon Baker dannon.ba...@gmail.com To: Tobias Hohenaur hohena...@brain.riken.jp Cc: Peter Cock p.j.a.c...@googlemail.com,Galaxy Dev galaxy-dev@lists.bx.psu.edu Date: 2013-04-09 22:47:04 Subject: Re: [galaxy-dev] How to be an admin? Yeah, if you're running it with just `run.sh`, that should work fine. One thing you can do if you're going to be tweaking a bunch of settings would be to run it with the reload option enabled `run.sh --reload`. When you change the port in universe_wsgi.ini in the galaxy directory, kill the server and restart, in the log at the end you should see something like: serving on 0.0.0.0:new port view at http://127.0.0.1:new port If you're not seeing that, I'd verify that you're editing the correct universe_wsgi.ini. Perhaps you have multiple galaxies installed somehow? On Tue, Apr 9, 2013 at 9:39 AM, Tobias Hohenaur hohena...@brain.riken.jpwrote: I just hit ctrl c in the terminal to stop. Is that enough? - Original Message - From: Dannon Baker dannon.ba...@gmail.com To: Tobias Hohenaur hohena...@brain.riken.jp Cc: Peter Cock p.j.a.c...@googlemail.com,Galaxy Dev galaxy-dev@lists.bx.psu.edu Date: 2013-04-09 22:30:38 Subject: Re: [galaxy-dev] How to be an admin? How is it that you're restarting the server? It might be useful to check galaxy's log to see what's going on -- this would be paster.log in your galaxy directory or perhaps the foreground of the terminal you're executing galaxy from. -Dannon On Tue, Apr 9, 2013 at 9:25 AM, Tobias Hohenaur hohena...@brain.riken.jpwrote: That does not help. Actually, I tried to change random things in the universe_wsgi.ini, like setting the port to 8081, but none of the changes take effect when I restart the server. I am confused... - Original Message - From: Peter Cock p.j.a.c...@googlemail.com To: Tobias Hohenaur hohena...@brain.riken.jp Cc: galaxy-dev@lists.bx.psu.edu Date: 2013-04-07 23:28:31 Subject: Re: [galaxy-dev] How to be an admin? On Sun, Apr 7, 2013 at 1:27 PM, Tobias Hohenaur hohena...@brain.riken.jp wrote: Hello, I just installed and updated a local instance of Galaxy on my mac. I then created a user and set the according username (email) as admin in the universe_wsgi.ini file. When I save and restart the server no admin panel appears. What am I doing wrong? Thank you very much for your help! Tobias Make sure you are logged in, and that the email address of your Galaxy account matches the universe_wsgi.ini setting exactly (case may be important). Also the setting used to have problems with extra white space (but I think that was fixed). 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby
Re: [galaxy-dev] REST API: upload of dataset to history possible ?
Thanks John. Not sure what I am doing wrong, but in my hands it does not work. No errors but there is no file upload either. ToolsClient toolsClient = galaxyInstance.getToolsClient(); ClientResponse result = toolsClient.fileUploadRequest(history.getId(), txt, whatIsAdbKey?, new File(C:\\Users\\mlogghe\\Documents\\bb3d562ec52a9fc5.yml)); System.out.println(result.getClientResponseStatus()); In paster.log I also do not see any evidence that upload_handler is called. Regards, Marc -Original Message- From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John Chilton Sent: Thursday, April 04, 2013 3:40 PM To: Marc Logghe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] REST API: upload of dataset to history possible ? On Tue, Apr 2, 2013 at 5:23 AM, Marc Logghe marc.log...@ablynx.com wrote: Hi, Is it currently possible to upload an input dataset to a history via the REST API ? This has been possible since pull request 94: https://bitbucket.org/galaxy/galaxy-central/pull-request/94/enable-upload-of-files-to-history-through/diff. The idea is to use the tools API and to invoke the upload1 tool. I imagine this is a little tricky to do with the bioblend Python library right now, but the blend4j Java library has a high-level helper function (ToolsClient.fileUploadRequest) to make this pretty simple: https://github.com/jmchilton/blend4j/blob/master/src/main/java/com/github/jmchilton/blend4j/galaxy/ToolsClient.java -John Or should one use a library dataset instead ? But in the latter case, only an admin can upload data, right ? Thanks, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] REST API
Hi, I just knew I was missing something crucial here ... Finally I found at the bottom of the Tools list (when you are in workflow editing mode) a section called 'Workflow control' having a single entry: 'Inputs'. Thought it could be useful to share my 'Aha-Erlebnis' :) Now it is perfectly possible to run a workflow using the CLI. Cheers, Marc From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Marc Logghe Sent: Monday, April 01, 2013 11:25 PM To: Dannon Baker Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] REST API Hi Dannon, Thanks for the reply. From: Dannon Baker [mailto:dannon.ba...@gmail.com] Sent: Monday, April 01, 2013 11:02 PM To: Marc Logghe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] REST API Hey Marc, Yep, the '38' in this case is the step id shown just after steps, but it would be an id listed in that 'inputs' dict. The inputs dictionary should be a list of all the Input Dataset steps for the workflow -- yours just doesn't have any and you'll need to add these to be able to map input datasets to the correct workflow input steps. I am afraid I don't quite understand. In my case, the single step workflow accepts fasta as input. If you say that it is currently not possible to pass 'set-at-runtime' parameters how do you pass the fasta then ? I mean, what changes to the workflow need to be done in order to make it possible to pass a command line argument like '38=hda=03501d7626bd192f' ? I'am pretty much confused ... Think I keep on missing something crucial here. Regards, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] REST API: upload of dataset to history possible ?
Hi, Is it currently possible to upload an input dataset to a history via the REST API ? Or should one use a library dataset instead ? But in the latter case, only an admin can upload data, right ? Thanks, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] REST API
Hi Dannon, Thanks for the reply. From: Dannon Baker [mailto:dannon.ba...@gmail.com] Sent: Monday, April 01, 2013 11:02 PM To: Marc Logghe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] REST API Hey Marc, Yep, the '38' in this case is the step id shown just after steps, but it would be an id listed in that 'inputs' dict. The inputs dictionary should be a list of all the Input Dataset steps for the workflow -- yours just doesn't have any and you'll need to add these to be able to map input datasets to the correct workflow input steps. I am afraid I don't quite understand. In my case, the single step workflow accepts fasta as input. If you say that it is currently not possible to pass 'set-at-runtime' parameters how do you pass the fasta then ? I mean, what changes to the workflow need to be done in order to make it possible to pass a command line argument like '38=hda=03501d7626bd192f' ? I'am pretty much confused ... Think I keep on missing something crucial here. Regards, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] blend4j
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Marc Logghe
Sent: Thursday, February 28, 2013 10:25 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] blend4j
Hi all,
Is this the correct forum to post blend4j issues ? Apologies if this is not the
case.
I was trying to run a custom workflow via blend4j, according to
https://github.com/jmchilton/blend4j
In my hands, the call to workflowDetails.getInputs() returns an empty Map. I
believe the corresponding REST request looks like:
/galaxy/api/workflows/workflow id?key=API key
In the JSON response, the 'inputs' attribute is empty indeed ({url:
/galaxy/api/workflows/f09437b8822035f7, inputs: {}, ...).
I do not understand why this is the case because 2 steps require inputs to be
set at runtime. Via the Galaxy web interface those required parameters can be
set and the workflow is running smoothly.
Or has the term 'inputs' nothing to do with 'parameters' ?
Please allow me to come back to this. I now realize that the workflow needs 2
inputs (instead of parameters). As far as I understand, for the moment it is
not possible to pass parameter values via the REST API without tempering with
the JSON strings themselves.
But dataset inputs should be supported. In my case, step 1 and step 2 need the
same dataset as input.
According to this snippet taken from the blend4j page (shown below), the
workflow should provide you with the input ids (here workflowInput1Id and
workflowInput2Id).
The issue is I don't have a clue what these input ids are, since in my hands
workflowDetails.getInputs() returns an empty collection. Do you need to add
metadata/attributes to the workflow in order to have these input IDs returned ?
final WorkflowDetails workflowDetails =
workflowsClient.showWorkflow(matchingWorkflow.getId());
String workflowInput1Id = null;
String workflowInput2Id = null;
for(final Map.EntryString, WorkflowInputDefinition inputEntry :
workflowDetails.getInputs().entrySet()) {
final String label = inputEntry.getValue().getLabel();
if(label.equals(WorkflowInput1)) {
workflowInput1Id = inputEntry.getKey();
}
if(label.equals(WorkflowInput2)) {
workflowInput2Id = inputEntry.getKey();
}
}
final WorkflowInputs inputs = new WorkflowInputs();
inputs.setDestination(new
WorkflowInputs.ExistingHistory(matchingHistory.getId()));
inputs.setWorkflowId(matchingWorkflow.getId());
inputs.setInput(workflowInput1Id, new
WorkflowInputs.WorkflowInput(input1Id, WorkflowInputs.InputSourceType.HDA));
inputs.setInput(workflowInput2Id, new
WorkflowInputs.WorkflowInput(input2Id, WorkflowInputs.InputSourceType.HDA));
final WorkflowOutputs output = workflowsClient.runWorkflow(inputs);
System.out.println(Running workflow in history + output.getHistoryId());
for(String outputId : output.getOutputIds()) {
System.out.println( Workflow writing to output id + outputId);
}
Regards,
Marc
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[galaxy-dev] blend4j
Hi all,
Is this the correct forum to post blend4j issues ? Apologies if this is not the
case.
I was trying to run a custom workflow via blend4j, according to
https://github.com/jmchilton/blend4j
In my hands, the call to workflowDetails.getInputs() returns an empty Map. I
believe the corresponding REST request looks like:
/galaxy/api/workflows/workflow id?key=API key
In the JSON response, the 'inputs' attribute is empty indeed ({url:
/galaxy/api/workflows/f09437b8822035f7, inputs: {}, ...).
I do not understand why this is the case because 2 steps require inputs to be
set at runtime. Via the Galaxy web interface those required parameters can be
set and the workflow is running smoothly.
Or has the term 'inputs' nothing to do with 'parameters' ?
Regards,
Marc
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Re: [galaxy-dev] blend4j
-Original Message-
From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John Chilton
Sent: Thursday, February 28, 2013 11:27 PM
To: Marc Logghe
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] blend4j
This is not a blend4j issue, it is more of a Galaxy API issue. I think
it is essentially a known problem that you cannot specify runtime
parameters for workflow, only data inputs. Here the relevant piece of
Galaxy code:
inputs = {}
for step in latest_workflow.steps:
if step.type == 'data_input':
inputs[step.id] = {'label':step.tool_inputs['name'], 'value':}
else:
pass
# Eventually, allow regular tool parameters to be
inserted and modified at runtime.
# p = step.get_required_parameters()
I think the meantime, the work around is not define these are workflow
parameters but instead hard code some values, and then pull down,
rewrite, and reupload a new workflow for each execution:
WorkflowsClient client = galaxyInstance.getWorkflowsClient();
String workflowJson = client.exportWorkflow(originalWorkflowId);
// modify workflow json
Workflow importedWorkflow = client.importWorkflow(workflowJson);
String importedWorkflowId = importedWorkflow.getId();
It is not pretty obviously. They are pretty good about responding to
API pull requests so if you have the time to fix the Galaxy code
itself I think everyone would appreciate that fix.
-John
Hi John
Thanks for the quick answer; I'll give it a try.
Regarding the fix: you need to give me some time, started with a python
tutorial only 2 days ago ;-)
Regards,
Marc
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[galaxy-dev] Filter tool: how to override automatic guessing of column types ?
Hi, I have an issue with filtering using the Filter tool in the sense that the first line is considered invalid and I think it has to do with the automatic guessing of column types. The condition is like: c4 !='XXX' The value of c4 for the first line is 'NA' When the paster.log is checked one can see that the last argument for filtering.py are the column types: str,str,int,int,int . As you can see for whatever reason, the system thinks c4 is an int, it should be 'str'. Indeed, most values for that field look like numbers but they should be treated as string types. In an attempt to override the guessing, a custom tabular type was defined in lib/galaxy/datatypes/tabular.py as such: class CloneAdminTable( Tabular ): Tabular format Clone Administration column_names = ['Name', 'SeqInAlignment', 'Family', 'Animal/library', 'NR Cluster'] column_types = ['str','str','int','str','int'] def display_peek( self, dataset ): Returns formated html of peek return Tabular.make_html_table( self, dataset, column_names=self.column_names ) But that seems not to help very much; the system still guesses the column types. Any idea how to solve this ? Thanks and regards, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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] Filter tool: how to override automatic guessing of column types ?
From: Daniel Blankenberg [mailto:d...@bx.psu.edu] Sent: Friday, February 22, 2013 4:44 PM To: Marc Logghe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Filter tool: how to override automatic guessing of column types ? Hi Marc, Ah, I think I see the issue here, and it has to do with an assumption being made that the first line is a undeclared header, which in your case is wrong. Can you trying adding to your set_meta: kwd['skip'] = 0 and then restart your sever and then create a new dataset with your tool? OK, got it to work. Guess I combined both of your suggestions in a way. It ended up looking like this: def set_meta( self, dataset, overwrite = True, skip = None, max_data_lines = None, max_guess_type_data_lines = None, **kwd ): dataset.metadata.columns = 5 dataset.metadata.column_types = ['str','str','int','str','int'] It might have worked after all in one of the previous attempts but I did not create a new dataset. I did like you suggested and now it works. Thanks a lot, you saved my day ! Regards, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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] workflow input param issue
Hi, I have a workflow that basically needs a select parameter as input. 2 steps in the workflow actually need the very same input. I don't think there is a (easy) way to let the user only input the parameter once and that it is passed to both steps. Anyhow, currently - as a workaround and not very user friendly - the user needs to input the very same parameter twice, for each step where that parameter is required. The first issue however, is that as soon as the first parameter is set, the second is set as well apparently (they have the same name, that could explain) which is fine, but not to the chosen one, eg. both are kind of reset to default. No errors or something, simply reset, which makes it impossible to enter the parameter. Next, I hoped to solve the issue by upgrading galaxy to the most recent version. This was not the case since the workflow did not run at all anymore, which brings me to the second issue (see exception dump below). Any ideas anyone ? Thanks and regards, Marc Error - type 'exceptions.AttributeError': 'list' object has no attribute 'output_name' URL: http://smith:8889/workflow/run?id=4b187121143038ff File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 1523 in run enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults) File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 836 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py', line 847 in fill_template_mako return template.render( **data ) File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/home/galaxy/galaxy-dev/database/compiled_templates/base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py', line 171 in render_body __M_writer(unicode(do_inputs( tool.inputs, step.state.inputs, errors.get( step.id, dict() ), , step, None, used_accumulator ))) File '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py', line 40 in do_inputs return render_do_inputs(context.locals_(__M_locals),inputs,values,errors,prefix,step,other_values,already_used) File '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py', line 435 in render_do_inputs __M_writer(unicode(row_for_param( input, values[ input.name ], other_values, errors, prefix, step, already_used ))) File '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py', line 338 in row_for_param return render_row_for_param(context,param,value,other_values,error_dict,prefix,step,already_used) File '/home/galaxy/galaxy-dev/database/compiled_templates/workflow/run.mako.py', line 498 in render_row_for_param __M_writer(unicode(conn.output_name)) AttributeError: 'list' object has no attribute 'output_name' THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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] workflow input param issue
Hi John,
Your patch works indeed. Issues--
Thanks,
Marc
-Original Message-
From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John Chilton
Sent: Monday, December 03, 2012 2:58 PM
To: Marc Logghe
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] workflow input param issue
I am really very sorry about that. It seems this must be related to my pull
request fixing multiple input tool parameters. I have spent some time this
morning trying to reproduce your error, but I cannot.
That said I think I can fix it, this patch should work:
diff --git a/templates/workflow/run.mako b/templates/workflow/run.mako index
c7cd138..175f148 100644
--- a/templates/workflow/run.mako
+++ b/templates/workflow/run.mako
@@ -243,9 +243,12 @@ if wf_parms:
%if isinstance( param, DataToolParameter ):
%if ( prefix + param.name ) in step.input_connections_by_name:
%
-conn = step.input_connections_by_name[ prefix
+ param.name ]
+conns = step.input_connections_by_name[
prefix + param.name ]
+if not isinstance(conns, list):
+conns = [conns]
+vals = [Output dataset '%s' from step %d %
(conn.output_name, int(conn.output_step.order_index)+1
%
-Output dataset '${conn.output_name}' from step
${int(conn.output_step.order_index)+1}
+${,.join(vals)}
%else:
## FIXME: Initialize in the controller
%
Can you apply the patch and tell me if it works? Probably a similar fix needs
to be applied to display.mako also, but I want to be able to recreate the
problem first or at least verify this fixes it.
-John
On Mon, Dec 3, 2012 at 4:45 AM, Marc Logghe marc.log...@ablynx.com wrote:
Hi,
I have a workflow that basically needs a select parameter as input. 2
steps in the workflow actually need the very same input. I don't think
there is a
(easy) way to let the user only input the parameter once and that it
is passed to both steps.
Anyhow, currently - as a workaround and not very user friendly - the
user needs to input the very same parameter twice, for each step where
that parameter is required.
The first issue however, is that as soon as the first parameter is
set, the second is set as well apparently (they have the same name,
that could
explain) which is fine, but not to the chosen one, eg. both are kind
of reset to default. No errors or something, simply reset, which makes
it impossible to enter the parameter.
Next, I hoped to solve the issue by upgrading galaxy to the most
recent version. This was not the case since the workflow did not run
at all anymore, which brings me to the second issue (see exception dump
below).
Any ideas anyone ?
Thanks and regards,
Marc
Error - type 'exceptions.AttributeError': 'list' object has no
attribute 'output_name'
URL: http://smith:8889/workflow/run?id=4b187121143038ff
File
'/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/exceptions/err
ormiddleware.py',
line 143 in __call__
app_iter = self.application(environ, start_response)
File
'/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/recursive.py',
line 80 in __call__
return self.application(environ, start_response)
File
'/home/galaxy/galaxy-dev/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions
.py',
line 632 in __call__
return self.application(environ, start_response)
File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/base.py', line
160 in __call__
body = method( trans, **kwargs )
File
'/home/galaxy/galaxy-dev/lib/galaxy/webapps/galaxy/controllers/workflo
w.py',
line 1523 in run
enable_unique_defaults=trans.app.config.enable_unique_workflow_default
s)
File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py',
line
836 in fill_template
return self.fill_template_mako( filename, **kwargs )
File '/home/galaxy/galaxy-dev/lib/galaxy/web/framework/__init__.py',
line
847 in fill_template_mako
return template.render( **data )
File
'/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/template.py',
line 296 in render
return runtime._render(self, self.callable_, args, data)
File
'/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 660 in _render
**_kwargs_for_callable(callable_, data))
File
'/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 692 in _render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File
'/home/galaxy/galaxy-dev/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 718 in _exec_template
callable_(context, *args, **kwargs)
File
'/home/galaxy/galaxy-dev/database/compiled_templates/base.mako.py',
line 42 in render_body
__M_writer(unicode(next.body()))
File
'/home/galaxy/galaxy-dev/database
Re: [galaxy-dev] collapse FASTA
Hi, If you have EMBOSS installed you should try degapseq. Galaxy emboss tools are available in the tool shed. HTH, Marc From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Deepthi Theresa [deepthither...@gmail.com] Sent: Thursday, September 27, 2012 9:45 PM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] collapse FASTA Hi Galaxy team, I tried to do collapse FASTA sequences for removing the duplicate reads. but error occured due to the lowercase letters at both the ends of the sequences. Is there any option available to clean my reads? some of my reads contains hyphen too. Thanks, D. -- Deepthi Theresa Thomas Kannanayakal 1919 University Drive NW, Apt. No. E104 T2N 4K7 Calgary, Alberta Canada Ph: (403) 483 7409, (403) 618 5956 Email: deepthither...@gmail.commailto:deepthither...@gmail.com THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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] concatenate datasets: how to fixate first dataset
Hi, In a workflow the last step is 'concatenate datasets' where the results table (dataset 2) is concatenated to a table header (dataset 1). Issue is that whenever the workflow is run, the table header dataset is required input at runtime. Is there a way to fixate that e.g. making it the input not necessary at runtime but take it from shared datasets or something ? Btw: I did try to first publish dataset 1 hoping that this would solve the problem but unfortunately it does not. Or is there another way to add a header in such a way that the users should not be taking care of it themselves ? Regards, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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] concatenate datasets: how to fixate first dataset
From: ja...@taylorlab.org [mailto:ja...@taylorlab.org] On Behalf Of James Taylor Sent: Wednesday, September 19, 2012 12:36 PM To: Marc Logghe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] concatenate datasets: how to fixate first dataset No, but this is a good idea that can be implemented as a new type of workflow module (fixed data set, like input dataset but specified at workflow build time). Can you file an issue in bitbucket describing how you would like this feature to work? Thanks! Done: https://bitbucket.org/galaxy/galaxy-central/issue/821/fixed-dataset Cheers, Marc On Wednesday, September 19, 2012, Marc Logghe wrote: Hi, In a workflow the last step is 'concatenate datasets' where the results table (dataset 2) is concatenated to a table header (dataset 1). Issue is that whenever the workflow is run, the table header dataset is required input at runtime. Is there a way to fixate that e.g. making it the input not necessary at runtime but take it from shared datasets or something ? Btw: I did try to first publish dataset 1 hoping that this would solve the problem but unfortunately it does not. Or is there another way to add a header in such a way that the users should not be taking care of it themselves ? Regards, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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] password param type
Hi, Kind of feature request: parameter of type 'password' so that an entered password is not shown in the html form nor in the logs. Or is there already a way to achieve this that I missed out ? Cheers, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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] dynamic update of tool data files
Hi all, I am wondering what is the best way to dynamically update tool data files without having to restart Galaxy. The context is as follows. A cron job is regularly creating new blast databases (or in general: e.g. tool data needed to fill a dropdown list). The same cron job could be adapted so that the corresponding galaxy tool data file is updated as well. But I don't think it is possible to make Galaxy aware of the new data without restarting, is it ? Or should one follow the root of shared library datasets ? But then, how to configure a tool so that this dataset is used (without manual import into a history ?) Thanks, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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] Upload File: how to see all registered formats ?
Hi Greg, That is great, I`ll give it a try. Thank a lot, Marc From: Greg Von Kuster [g...@bx.psu.edu] Sent: Tuesday, August 14, 2012 10:38 PM To: Marc Logghe Cc: Björn Grüning; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Upload File: how to see all registered formats ? Hello Marc, This issue has been resolve din change set 7491:a7a0a5962648, which will be included in the next Galaxy release. It is also currently available in the Galaxy central repository in case you track that repository. The datatypes registry will load any changes you've made to the datatypes_conf.xml file installed with the emboss_datatypes tool shed repository (or any other repository that includes this file). SO display_in_upload will now function correctly for the installed proprietary datatypes. Thanks for reporting this issue, and sorry for the inconvenience. Greg Von Kuster On Aug 3, 2012, at 4:53 PM, Marc Logghe wrote: Hi Greg, You'll need to add the display_in_upload attribute to your local version of the datatypes_conf.xml file installed with your emboss_datatypes repository from the tool shed. I'am afraid this does not work. At least not in my hands. Like I indicated before, it seems like the upload tool does not take the tool shed emboss_datatypes into account, with or without the display_in_upload attribute set. It seems to work only if you transfer the entire data type definition line to the main galaxy datatypes_conf.xml That is the workaround I currently use. Marc This may result in a merge at some point if the contents of the datatypes_conf.xml file changes in the emboss_datatypes repository in the main tool shed and you pull the updates to your local repository. Greg Von Kuster Hi Björn, I think the issue is that the genbank datatype is coming in via the tool shed and is not taken into account by the upload tool. The genbank datatype is defined in shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/emboss_datatypes/a89163f31369/emboss_datatypes/datatypes_conf.xml I have added the display_in_upload attribute in the latter file for the genbank datatype, restarted Galaxy but the type did not appear in the selection. Should the genbank datatype be added to the main galaxy datatypes_conf.xml ? Or is it better to explicitly add the emboss' datatypes_conf.xml to the universe_wsgi.ini (but this will break the tool shed update system, right) ? Thanks, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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] genbank data type
Hi all, The last few days I have been experimenting with a local Galaxy installation. Via the tool shed, emboss and emboss_datatypes were installed. Next, a custom tool was added for which a rich sequence is needed as input. I was hoping to achieve this as such: param name=input type=data format=genbank label=Annotated sequences/ As a test, a genbank was created using EMBOSS's newseq and output format genbank was chosen (the history indicates the format is 'genbank', so that's fine). However, it seems not to be recognized as valid input for our custom tool. Guess I'm overlooking something obvious ? Regards, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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] genbank data type
From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Marc Logghe Sent: Friday, August 03, 2012 9:22 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] genbank data type Hi all, The last few days I have been experimenting with a local Galaxy installation. Via the tool shed, emboss and emboss_datatypes were installed. Next, a custom tool was added for which a rich sequence is needed as input. I was hoping to achieve this as such: param name=input type=data format=genbank label=Annotated sequences/ As a test, a genbank was created using EMBOSS's newseq and output format genbank was chosen (the history indicates the format is 'genbank', so that's fine). However, it seems not to be recognized as valid input for our custom tool. Guess I'm overlooking something obvious ? Regards, Marc Mmm, issue disappeared by itself. Love these kind of issues ;-) Cheers, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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] Upload File: how to see all registered formats ?
Hi again, Emboss_datatypes is installad via tool shed. The 'View datatypes registry' in the Adminstration page, shows all registered data types, including the emboss ones, like e.g. genbank. However, the 'Upload File' tool does not show genbank in the 'File Format' dropdown. How can one configure the upload1 tool so that all registered formats are listed ? I don't understand the from_parameter hocus-pocus in this line (upload.xml): options from_parameter=tool.app.datatypes_registry.upload_file_formats transform_lines=[ quot;%s%s%squot; % ( line, self.separator, line ) for line in obj ] The workaround which is used up to now is upload genbank sequences as txt format and change the format later via the history. But that is a 2-step operation, guess there should be a way taking only 1 step ? Regards, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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] Upload File: how to see all registered formats ?
Hi Björn, I think the issue is that the genbank datatype is coming in via the tool shed and is not taken into account by the upload tool. The genbank datatype is defined in shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/emboss_datatypes/a89163f31369/emboss_datatypes/datatypes_conf.xml I have added the display_in_upload attribute in the latter file for the genbank datatype, restarted Galaxy but the type did not appear in the selection. Should the genbank datatype be added to the main galaxy datatypes_conf.xml ? Or is it better to explicitly add the emboss' datatypes_conf.xml to the universe_wsgi.ini (but this will break the tool shed update system, right) ? Thanks, Marc -Original Message- From: Björn Grüning [mailto:bjoern.gruen...@pharmazie.uni-freiburg.de] Sent: Friday, August 03, 2012 4:14 PM To: Marc Logghe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Upload File: how to see all registered formats ? Hi Marc, please have a look at the datatypes_conf.xml file in your galaxy directory. There should be something like that: datatype extension=wsf type=galaxy.datatypes.wsf:SnpFile display_in_upload=true/ Try to add 'display_in_upload=true' to the genbank datatype. The 'good' solution would be to define a datatype genbank, with a sniff function, so that galaxy can guess the filetype when you are uploading it. Please find attached my first attempt for that. Im working on some datatypes and converteres, but its not ready yet :( Cheers, Bjoern Hi again, Emboss_datatypes is installad via tool shed. The ‘View datatypes registry’ in the Adminstration page, shows all registered data types, including the emboss ones, like e.g. genbank. However, the ‘Upload File’ tool does not show genbank in the ‘File Format’ dropdown. How can one configure the upload1 tool so that all registered formats are listed ? I don’t understand the from_parameter hocus-pocus in this line (upload.xml): options from_parameter=tool.app.datatypes_registry.upload_file_formats transform_lines=[ quot;%s%s%squot; % ( line, self.separator, line ) for line in obj ] The workaround which is used up to now is upload genbank sequences as txt format and change the format later via the history. But that is a 2-step operation, guess there should be a way taking only 1 step ? Regards, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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/ -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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] Upload File: how to see all registered formats ?
Hi Greg, You'll need to add the display_in_upload attribute to your local version of the datatypes_conf.xml file installed with your emboss_datatypes repository from the tool shed. I'am afraid this does not work. At least not in my hands. Like I indicated before, it seems like the upload tool does not take the tool shed emboss_datatypes into account, with or without the display_in_upload attribute set. It seems to work only if you transfer the entire data type definition line to the main galaxy datatypes_conf.xml That is the workaround I currently use. Marc This may result in a merge at some point if the contents of the datatypes_conf.xml file changes in the emboss_datatypes repository in the main tool shed and you pull the updates to your local repository. Greg Von Kuster Hi Björn, I think the issue is that the genbank datatype is coming in via the tool shed and is not taken into account by the upload tool. The genbank datatype is defined in shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/emboss_datatypes/a89163f31369/emboss_datatypes/datatypes_conf.xml I have added the display_in_upload attribute in the latter file for the genbank datatype, restarted Galaxy but the type did not appear in the selection. Should the genbank datatype be added to the main galaxy datatypes_conf.xml ? Or is it better to explicitly add the emboss' datatypes_conf.xml to the universe_wsgi.ini (but this will break the tool shed update system, right) ? Thanks, Marc THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at abl...@ablynx.com. Thank you for your co-operation. NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V. ___ 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/
