[galaxy-dev] Galaxy workflow with variable inputs

[Dave Walton]

I'm curious if there is a way to create a workflow as follows (or if anyone
else thinks this is a good idea, or for that matter has a good suggestion of
another solution):

1) User selects N groomed fastq files and puts them in a history

2) User selects a workflow that allows them to select the N files, and then
passes each of them to a two step process that first runs them through
tophat, and the resulting bam file through cufflinks.

3) At the other end of the workflow would be a merge module that would take
one of the 3 output files from cufflinks from each run, and does some sort
of aggregation or transformation step on all the resulting data.

Any input would be greatly appreciated.

Thanks,

Dave


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Re: [galaxy-dev] Galaxy workflow with variable inputs

[Dave Walton]

Okay, so I'm caught up on my Galaxy Dev reading, and now realize that the
thread on calling workflows programmatically is discussing what I need to
do.

I would still be curious to know if something is planned for the Galaxy
workflow interface, that would allow you go configure a workflow to take
multiple inputs, run the workflow for each of these inputs, and then allow
me to pass the end result of the workflows to a single "merging" or
"aggregating" tool.  However, in the meantime, I'm going to try the api
interface to workflows and see if that means my near term needs.

Thanks,

Dave


On 3/18/11 11:23 AM, "Dave Walton"  wrote:

> I'm curious if there is a way to create a workflow as follows (or if anyone
> else thinks this is a good idea, or for that matter has a good suggestion of
> another solution):
> 
> 1) User selects N groomed fastq files and puts them in a history
> 
> 2) User selects a workflow that allows them to select the N files, and then
> passes each of them to a two step process that first runs them through
> tophat, and the resulting bam file through cufflinks.
> 
> 3) At the other end of the workflow would be a merge module that would take
> one of the 3 output files from cufflinks from each run, and does some sort
> of aggregation or transformation step on all the resulting data.
> 
> Any input would be greatly appreciated.
> 
> Thanks,
> 
> Dave
> 
> 
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Re: [galaxy-dev] Running a workflow programatically

[Dave Walton]

When is this functionality expected to make it into galaxy-dist?

Thanks,

Dave


On 3/16/11 6:07 PM, "Dannon Baker"  wrote:

> That's not actually what I expected, but I see what's going on here.  The
> workflows API expects explicit "Input Dataset" steps for mapping datasets, add
> one of those and connect it to your fastq step and see if it has inputs
> showing up for you to map to at that point.
> 
> Do note that the input step id expected is actually the workflow step_id, not
> the "Step 1" "Step 2", etc numbers that you'll see in the run workflow page.
> 
> -Dannon
> 
> On Mar 16, 2011, at 6:01 PM, Darren Brown wrote:
> 
>> Ah ok, and you are right there is something wrong there.  The inputs
>> dictionary is empty:
>> 
>> inputs: {}
>> 
>> However this seems kind of odd, because I do need to specify history
>> inputs for the workflow through the web ui.
>> 
>> On Wed, Mar 16, 2011 at 2:55 PM, Dannon Baker  wrote:
>>> On Mar 16, 2011, at 5:43 PM, Darren Brown wrote:
>>> 
 However, when I run a workflow from the command line:
 
 python /mnt/galaxy/galaxy_dist/scripts/api/workflow_execute.py
   /api/workflows 38247d270c7cb1bb
 'hist_id=38247d270c7cb1bb' '1=hda=30fc17ce78176bfb'
>>> 
>>> My hunch is that the step id '1' in this line is probably your issue. To
>>> list workflow details in the api, you can use the scripts/api/display.py
>>> 
>>> So, for your workflow there,
>>> 
>>> python /mnt/galaxy/galaxy_dist/scripts/api/display.py 
>>> http://localhost:8080/api/workflows/38247d270c7cb1bb
>>> 
>>> Check that with the workflow in question and see what it returns as the
>>> inputs dictionary.
>>> 
>>> -Dannon
>>> 
> 
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Re: [galaxy-dev] Recommended Specs for Production System

[Dave Walton]

This is very close to our config, except -
We run all of this on a 4 core Virtual Machine running SUSE Linux Enterprise
Server 11 (x86_64) with 16 GB of memory.

Instead of SGE our HPC cluster uses Torque/Moab for scheduling.

Also, we've set up a separate IO Node for upload of data files from the file
system and FTP (correct me if I mis-spoke Glen).

Also, instead of apache we run nginx for our httpd server as it was easy to
get off-loading of file upload and download working with that server.

We're not seeing a heavy load from users at this point, but this has worked
pretty well for us so far.

Hope this helps,

Dave


On 4/8/11 10:21 AM, "Assaf Gordon"  wrote:

> Assaf Gordon wrote, On 04/08/2011 10:07 AM:
>> Processes:
>> 
>> The servers processes that you should plan for are:
>> 1 galaxy process for job-runner
>> 2 or 3 galaxy processes for web-fronts
>> 1 process of postgres
>> 1 process of apache
>> optionally 1 process of galaxy-reports
>> you'll also want to leave some free CPUs for SSH access, CRON jobs and other
>> peripherals.
>> Postgres & apache are multithreaded, but it usually balances out with light
>> load on the web/DB front from galaxy (even with 30 users).
>> So all in all, I'd recommend reserving 5 to 8 CPU cores to just galaxy and
>> daemons (reserving means: never using those cores for galaxy jobs).
>> You can do with less cores, but then response times might suffer (and it's
>> annoying when you click "show saved histories" and the page takes 20 seconds
>> to load...).
>> 
> Forgot to mention SGE/PBS: you definitely want to use them (even if you're
> using a single machine),
> because the local job runner doesn't take into account multi-threaded programs
> when scheduling jobs.
> So another core is needed for the SGE scheduler daemons (sge_qmaster and
> sge_execd).
> 
> 
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Re: [galaxy-dev] Output file naming / dataset's label

[Dave Walton]

I get it now!!

I did my Rename Dataset/output_file with a variable ${input}.  

I chose that because I thought that would give me the name of the input file to 
that module, which I'm looking to carry on through out the run of my workflow 
(though actually I'd like the file name minus the file extension, but that's 
another problem). 

When I did this, I ended up with a field "Input" at the top of my workflow form 
when I went to run it.  I typed a value in and sure enough, all my output files 
now contained what I typed into the field.

So, this is certainly useful, but the question I have, and I believe it's what 
Matthew is getting at too is:

Is there anyway to access the value of fields that are part of the workflow.  
Taking the "Input Dataset" example, that is an input file that goes into my 
next module.  I'd like to grab the name of that input file, and then append it 
with a new extension.  So if the module is grooming fastq, I'd like to grab my 
file name that is given to the fastq groomer, and append ".fastqsanger" to it, 
and have that be my output file name.

Is this possible?

Thanks,

Dave

On Apr 13, 2011, at 11:20 AM, Dannon Baker wrote:

> Ahh, I understand your confusion now.  The previous bit you pointed out 
> was an error indeed, but not the one you were running into.  The 
> variable name should be whatever you want it to be, it doesn't have to 
> map to an existing value like "Input Dataset", but there's an issue with 
> the way the tags are handled for parameter replacement that causes a 
> failure when the name contains spaces.  Instead of ${Input Dataset}, try 
> ${input_dataset}.  I have a fix for this that should be available in the 
> near future, as part of a larger set of changes that should make 
> parameters much more accessible.
> 
> 
> 
> On 04/13/2011 10:11 AM, Matthew Conte wrote:
>> Hi Dannon,
>> 
>> Sorry, I guess I still don't quite get it.  So I should keep the Input
>> Dataset name the default which is "Input Dataset".  In the next subsequent
>> step in the workflow I then edit step actions Rename Dataset/output_file
>> with "${Input Dataset} groomed", for example.  This gives me the same error
>> as before.  It is still unclear to me what the actual variable name is for
>> the input dataset so that I can use it to rename output in later steps.  Do
>> you have an example workflow that uses the input data set name to name the
>> output of downstream workflow steps that you could share with me as an
>> example so I can see the usage?  Even a simple two step workflow would do.
>> 
>> Thanks again,
>> Matt
>> 
>> On Wed, Apr 13, 2011 at 6:09 AM, Dannon Baker  wrote:
>> 
>>> The input dataset steps do not use workflow parameters as they don't
>>> actually create output datasets, but rather act as more of a temporary
>>> handle.  Remove the parameter tags from the input steps and just referring
>>> to those same parameter names in the subsequent steps you wanted to use them
>>> with should work and I think will allow you to do what you want.
>>> 
>>> Thank you for pointing out the error though, this should definitely be more
>>> gracefully handled and supported with some help text in the editor, I'll see
>>> what I can do about that.  Let me know if this doesn't get up and running
>>> and I'll do what I can to help!
>>> 
>>> -Dannon
>>> 
>>> 
>>> 
>>> 
>>> On 04/12/2011 06:20 PM, Matthew Conte wrote:
>>> 
 I'd like to do the same thing that Tanguy described.  I'm trying to figure
 out the syntax to this within the workflow editor, but can't quite get it
 right.  In your example Dannon, would you just set ${dataset_name} as the
 "Name" for your "Input dataset" to capture the input dataset name as a
 variable? When I do that and then try to run the workflow I get the
 following error:
 
 Error -: 'dataset_name'
 URL: http://localhost:8080/galaxy/workflow/run?id=f597429621d6eb2b
 File
 
 '/path-to-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 '/path-to-galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py',
 line 80 in __call__
   return self.application(environ, start_response)
 File
 '/path-to-galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
 line 632 in __call__
   return self.application(environ, start_response)
 File '/path-to-galaxy-dist/lib/galaxy/web/framework/base.py', line 145 in
 __call__
   body = method( trans, **kwargs )
 File '/path-to-galaxy-dist/lib/galaxy/web/controllers/workflow.py', line
 1397 in run
   incoming=kwargs )
 File '/path-to-galaxy-dist/lib/galaxy/web/framework/__init__.py', line 650
 in fill_template
   return self.fill_template_mako( filename, **kwargs )
 File '/path-to-galaxy-dist/lib/galaxy/web/framework/__init__.py', line 661
 in fill_template_mako
   return template.render( **d

[galaxy-dev] Workflow variables and the workflow API

[Dave Walton]

I'm working on a module that involves calling a workflow multiple times over a 
set of data.

The workflow has a "variable" that I use for renaming output files.

I see, using the workflow_execute.py example how to pass in file names, but I 
don't see how to pass in a value for this variable.

When I do a "./display.py  
http://jaxgalaxydev01/api/workflows/" I see the two input data 
files I would expect, but I don't see this variable.

ex: 
Member Information
--
url: /api/workflows/
inputs: {'207': {'value': '', 'label': 'Input Dataset'}, '211': {'value': '', 
'label': 'Input Dataset'}}
id: 
name: Single-end RNA Seq with grooming v 2.0 (imported from uploaded file)


Is there anyway to get at this variable so I can set it when I call a workflow 
through the API?

Thanks,

Dave
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Re: [galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

[Dave Walton]

I've essentially asked the same question of the list in the past and gotten no 
real response.

I have the same interest, but from a workflow perspective.

* A module that allows me to select multiple datafiles (say fastq files)
* Then pass each data file to a separate instance of a workflow that runs 
tophat and cufflinks
* then another module that takes the final outputs of each of the workflow runs 
and sends them to a final module that merges results.

I am attempting to implement something like this using the API, though the API 
is still pretty green from my perspective.

I think functionality like this built into the workflow editor would be a great 
addition.

Dave

On Apr 15, 2011, at 8:14 AM, Leandro Hermida wrote:

> Hi everyone,
> 
> I was wondering what would be the way in Galaxy to program the following:
> 
> - User clicks on a tool and form is displayed
> - They use a select multi menu in the form to pick lets say X multiple 
> datasets from their history
> - When they click submit the tool launches X number of jobs in the history, 
> on for each of the datasets selected.
> 
> I have a common use case where users have to manually run the same tool over 
> and over again with the same parameters for each dataset of interest in their 
> history.  I would be great to be able programmatically or otherwise with 
> Galaxy to be able to use one form and multi select the datasets and then 
> launch the parallel jobs in one go.
> 
> regards,
> Leandro
> 
> 


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Re: [galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

[Dave Walton]

Leandro,

As far as I can tell there are no real docs for the API.   The best I’ve been 
able to find is what’s under the scripts/api directory.  I believe the API is 
still considered a “beta” at best.

Galaxy team, are there any updates on the API, documentation plans, etc?

Thanks,

Dave


On 4/15/11 1:14 PM, "Leandro Hermida"  wrote:

Hi Dave,

Thanks for the feedback, this to me would be a very useful feature to be able 
to spawn multiple same jobs or workflows from one tool form using different 
input datasets selected with multi select and all other form parameters being 
the same.

Where are the docs and information for the Galaxy API? Wondering if I could 
program this exact functionality in the script that the tool would execute.

thanks,
Leandro

On Fri, Apr 15, 2011 at 4:28 PM, Dave Walton  wrote:
I've essentially asked the same question of the list in the past and gotten no 
real response.

I have the same interest, but from a workflow perspective.

* A module that allows me to select multiple datafiles (say fastq files)
* Then pass each data file to a separate instance of a workflow that runs 
tophat and cufflinks
* then another module that takes the final outputs of each of the workflow runs 
and sends them to a final module that merges results.

I am attempting to implement something like this using the API, though the API 
is still pretty green from my perspective.

I think functionality like this built into the workflow editor would be a great 
addition.

Dave

On Apr 15, 2011, at 8:14 AM, Leandro Hermida wrote:

> Hi everyone,
>
> I was wondering what would be the way in Galaxy to program the following:
>
> - User clicks on a tool and form is displayed
> - They use a select multi menu in the form to pick lets say X multiple 
> datasets from their history
> - When they click submit the tool launches X number of jobs in the history, 
> on for each of the datasets selected.
>
> I have a common use case where users have to manually run the same tool over 
> and over again with the same parameters for each dataset of interest in their 
> history.  I would be great to be able programmatically or otherwise with 
> Galaxy to be able to use one form and multi select the datasets and then 
> launch the parallel jobs in one go.
>
> regards,
> Leandro
>
> 



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Re: [galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

[Dave Walton]

Is the server below down?  I'm trying to get there this morning and having
no luck...

https://wiki.nbic.nl/index.php/NBIC_Galaxy_Hackathon_project#Loop_over_files
_in_a_directory

Dave


On 4/15/11 12:16 PM, "Pieter Neerincx"  wrote:

> Hi, 
> 
> You're not alone with this request! Unfortunately I wasn't able to join the
> 2-day Galaxy Hackathon, but I heard from a colleague who just came back that
> this was one of the topics they worked on. At the end of the hackathon they
> had a working prototype:
> 
> https://wiki.nbic.nl/index.php/NBIC_Galaxy_Hackathon_project#Loop_over_files_i
> n_a_directory
> 
> Since they had only 2 days, it will need some polish, but I heard this hack
> already made it into the development branch of Galaxy, so we may see something
> like this in the near future :)
> 
> Cheers,
> 
> Pi
> 
> On Apr 15, 2011, at 4:28 PM, Dave Walton wrote:
> 
>> I've essentially asked the same question of the list in the past and gotten
>> no real response.
>> 
>> I have the same interest, but from a workflow perspective.
>> 
>> * A module that allows me to select multiple datafiles (say fastq files)
>> * Then pass each data file to a separate instance of a workflow that runs
>> tophat and cufflinks
>> * then another module that takes the final outputs of each of the workflow
>> runs and sends them to a final module that merges results.
>> 
>> I am attempting to implement something like this using the API, though the
>> API is still pretty green from my perspective.
>> 
>> I think functionality like this built into the workflow editor would be a
>> great addition.
>> 
>> Dave
>> 
>> On Apr 15, 2011, at 8:14 AM, Leandro Hermida wrote:
>> 
>>> Hi everyone,
>>> 
>>> I was wondering what would be the way in Galaxy to program the following:
>>> 
>>> - User clicks on a tool and form is displayed
>>> - They use a select multi menu in the form to pick lets say X multiple
>>> datasets from their history
>>> - When they click submit the tool launches X number of jobs in the history,
>>> on for each of the datasets selected.
>>> 
>>> I have a common use case where users have to manually run the same tool over
>>> and over again with the same parameters for each dataset of interest in
>>> their history.  I would be great to be able programmatically or otherwise
>>> with Galaxy to be able to use one form and multi select the datasets and
>>> then launch the parallel jobs in one go.
>>> 
>>> regards,
>>> Leandro
>>> 
>>> 
>> 
>> 
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> 
> -
> mobile: +31 6 143 66 783
> e-mail: pieter.neeri...@gmail.com
> skype:  pieter.online
> -
> 


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[galaxy-dev] No Menu after submitting workflow

[Dave Walton]

I'm getting inconsistent behavior when I run a workflow.

I have one workflow,that when I run it, the green box indicating my workflow
has been submitted shows up in the middle panel with Tools to the left,
histories to the right, and menu above.

For another workflow, I submit it successfully, but the green box ends up on
a page with nothing but the green box.  No tools, no history, no menus.

Both of these are being done using the same browser session (running firefox
on a mac).

Thanks,

Dave


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Re: [galaxy-dev] No Menu after submitting workflow

[Dave Walton]

ca0c4ad2bb39 is the last upstream change set in our fork (Glen is planning
to update our fork with the latest dist later this week).

Neither workflow does history destinations.
Both histories have multiple inputs going to varying tools in the workflow.
Both histories rename outputs.

One workflow does tool hiding for modules that don't generate output (this
is the one that behaved strangely in galaxy).

The one that behaves strangely (doesn't have the message appear in the
middle panel) is essentially the same workflow as the first, but with more
steps, additional side paths, and quite a few more output files.

When Glen updates to the latest dist, I'll try to reproduce the problem.

Dave


On 4/19/11 3:08 PM, "Dannon Baker"  wrote:

> Dave,
> 
> What revision of galaxy are you running (hg tip)?  We've made a few
> changes quite recently to running workflows, though I haven't seen any
> errors like this yet.
> 
> Also, what's different about the two workflows (history destinations,
> multiple-inputs, rename actions, etc.)?
> 
> -Dannon
> 
> On 04/19/2011 03:01 PM, Dave Walton wrote:
>> I'm getting inconsistent behavior when I run a workflow.
>> 
>> I have one workflow,that when I run it, the green box indicating my workflow
>> has been submitted shows up in the middle panel with Tools to the left,
>> histories to the right, and menu above.
>> 
>> For another workflow, I submit it successfully, but the green box ends up on
>> a page with nothing but the green box.  No tools, no history, no menus.
>> 
>> Both of these are being done using the same browser session (running firefox
>> on a mac).
>> 
>> Thanks,
>> 
>> Dave
>> 
>> 
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Re: [galaxy-dev] Display BAM with IGV

[Dave Walton]

I’m getting this same error and I’m running nginx as a proxy server.  Is there 
a specfic parameter we should be aware of to allow partial gets?  I don’t see 
anything in the wiki page for setting up the ProductionServer.

Thanks,

Dave


On 4/27/11 12:33 PM, "Daniel Blankenberg"  wrote:

Hi Alex,

Displaying BAM files at external applications usually requires an http server 
that supports partial gets. Unfortunately, the current lightweight http server 
that is built into Galaxy does not support these advanced http options.  
However, this limitation can be overcome by using a proxy server that is able 
to handle http1.1 requests. Please see "Using a Proxy server" at 
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer for 
help on setting this up.

Thanks for using Galaxy,

Dan


On Apr 27, 2011, at 10:06 AM, Alexander Graf wrote:

Hello all,
I just updated our local copy of Galaxy and just wanted to try the new IGV 
display application.
When I try to display a BAM file with the local IGV or the web IGV I encounter 
following error complaining about the Null content-length.
Has any of you encountered the same problem? Do I miss something?
Thanks in advance

Alex


INFO [2011-04-27 16:00:14,440]  [TrackManager.java:225] [Thread-6]  Loading1 
resources.
ERROR [2011-04-27 16:00:14,589]  [SeekableHTTPStream.java:59] [Thread-6]  Null 
content-length for: 
http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bam
ERROR [2011-04-27 16:00:14,590]  [TrackLoader.java:821] [Thread-6]  Error 
loading sam track
java.lang.RuntimeException: Error loading file: 
http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bam
 NULL content-length
at org.broad.igv.util.SeekableHTTPStream.(SeekableHTTPStream.java:60)
at 
org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:42)
at 
org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.java:129)
at 
org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.java:70)
at 
org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryReader.java:80)
at 
org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryReader.java:97)
at 
org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java:75)
at 
org.broad.igv.sam.AlignmentDataManager.(AlignmentDataManager.java:69)
at 
org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.java:54)
at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761)
at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143)
at org.broad.igv.track.TrackManager.load(TrackManager.java:271)
at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241)
at org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282)
at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148)
at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88)
at org.broad.igv.main.CommandListener.processGet(CommandListener.java:193)
at org.broad.igv.main.CommandListener.run(CommandListener.java:93)
at java.lang.Thread.run(Thread.java:636)
ERROR [2011-04-27 16:00:14,592]  [TrackLoader.java:211] [Thread-6]  
java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: 
http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bam
 NULL content-length



___

  Alexander Graf

Laboratory of Functional Genome Analysis
Gene Center, University of Munich (LMU)
Feodor-Lynen-Strasse 25; 81377 Munich; Germany
email: g...@lmb.uni-muenchen.de
Internet: www.lafuga.de/genomics.htm 
 ___

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Re: [galaxy-dev] Display BAM with IGV

[Dave Walton]

Could someone who has successfully gotten the IGV tool to work using NGINX as 
your proxy, tell me if there was anything specific they needed to do with their 
NGINX or galaxy config to get it working?

Thanks,

Dave


On 4/27/11 9:07 PM, "Dave Walton"  wrote:

I’m getting this same error and I’m running nginx as a proxy server.  Is there 
a specfic parameter we should be aware of to allow partial gets?  I don’t see 
anything in the wiki page for setting up the ProductionServer.

Thanks,

Dave


On 4/27/11 12:33 PM, "Daniel Blankenberg"  wrote:

Hi Alex,

Displaying BAM files at external applications usually requires an http server 
that supports partial gets. Unfortunately, the current lightweight http server 
that is built into Galaxy does not support these advanced http options.  
However, this limitation can be overcome by using a proxy server that is able 
to handle http1.1 requests. Please see "Using a Proxy server" at 
https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer for 
help on setting this up.

Thanks for using Galaxy,

Dan


On Apr 27, 2011, at 10:06 AM, Alexander Graf wrote:

Hello all,
I just updated our local copy of Galaxy and just wanted to try the new IGV 
display application.
When I try to display a BAM file with the local IGV or the web IGV I encounter 
following error complaining about the Null content-length.
Has any of you encountered the same problem? Do I miss something?
Thanks in advance

Alex


INFO [2011-04-27 16:00:14,440]  [TrackManager.java:225] [Thread-6]  Loading1 
resources.
ERROR [2011-04-27 16:00:14,589]  [SeekableHTTPStream.java:59] [Thread-6]  Null 
content-length for: 
http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bam
ERROR [2011-04-27 16:00:14,590]  [TrackLoader.java:821] [Thread-6]  Error 
loading sam track
java.lang.RuntimeException: Error loading file: 
http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bam
 NULL content-length
at org.broad.igv.util.SeekableHTTPStream.(SeekableHTTPStream.java:60)
at 
org.broad.igv.util.SeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:42)
at 
org.broad.igv.sam.reader.BAMHttpQueryReader.loadHeader(BAMHttpQueryReader.java:129)
at 
org.broad.igv.sam.reader.BAMHttpQueryReader.getHeader(BAMHttpQueryReader.java:70)
at 
org.broad.igv.sam.reader.BAMHttpQueryReader.getSequenceNames(BAMHttpQueryReader.java:80)
at 
org.broad.igv.sam.reader.CachingQueryReader.getSequenceNames(CachingQueryReader.java:97)
at 
org.broad.igv.sam.AlignmentDataManager.initChrMap(AlignmentDataManager.java:75)
at 
org.broad.igv.sam.AlignmentDataManager.(AlignmentDataManager.java:69)
at 
org.broad.igv.sam.AlignmentDataManager.getDataManager(AlignmentDataManager.java:54)
at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:761)
at org.broad.igv.track.TrackLoader.load(TrackLoader.java:143)
at org.broad.igv.track.TrackManager.load(TrackManager.java:271)
at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241)
at org.broad.igv.main.CommandExecutor.loadFiles(CommandExecutor.java:282)
at org.broad.igv.main.CommandExecutor.hget(CommandExecutor.java:148)
at org.broad.igv.main.CommandExecutor.execute(CommandExecutor.java:88)
at org.broad.igv.main.CommandListener.processGet(CommandListener.java:193)
at org.broad.igv.main.CommandListener.run(CommandListener.java:93)
at java.lang.Thread.run(Thread.java:636)
ERROR [2011-04-27 16:00:14,592]  [TrackLoader.java:211] [Thread-6]  
java.lang.RuntimeException: java.lang.RuntimeException: Error loading file: 
http://localhost:8080/display_application/a1f8a55a946ee078/igv_bam/local/454edf2520b73a7e/data/galaxy_a1f8a55a946ee078.bam
 NULL content-length



___

  Alexander Graf

Laboratory of Functional Genome Analysis
Gene Center, University of Munich (LMU)
Feodor-Lynen-Strasse 25; 81377 Munich; Germany
email: g...@lmb.uni-muenchen.de
Internet: www.lafuga.de/genomics.htm <http://www.lafuga.de/genomics.htm>
 ___

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[galaxy-dev] More on multiple inputs to a workflow

[Dave Walton]

So we loaded the change set that was developed at the hack-a-thon to our
instance of galaxy.  For the case where I have a directory of input files,
where I want to run the same workflow for each, this change works great.

There is one new issue I see, that I'd be interested in input on, and an old
issue that I'd like a status on.

First the new...  So I have a workflow that does analysis on paired end mRNA
Seq data.  My workflow for single end works great, but with paired end, I
can see an obvious way to submit two lists of files (one for the forward and
one for the reverse), which can then be submitted to a series of the same
workflow.  Once I've chosen the forward to allow selection of multiple input
files, the option to allow the reverse to also allow selection of multiple
input files becomes disabled.  This makes perfect sense, as, unless you've
implemented it to associate pairs of files together, this probably wouldn't
work anyway.  Is there anyone out there working on a solution to this?  If
not, does anyone have suggestion as to how we could make it work?

Now the old... A while back I suggested that it would be useful while
editing a workflow, if there were a way to grab the name of an input file as
a variable, and then use this variable in naming all later output files
(this way I can propagate a sample name all the way through the workflow).
Especially in a case where we are using the option to select multiple files
to run the same workflow, this feature is very important.  Is anyone working
on this?  If not, could someone point me in the right direction if I were to
start trying to implement this feature?

Thanks,

Dave


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[galaxy-dev] Concatenation as first step in workflow

[Dave Walton]

We have samples that span multiple lanes of our sequencer, that are the same
sample.

We'd like to have workflows where the first step is to concatenation the
fastq files for one sample, and then feed it to the rest of our workflow
(for RNA Seq).

Unfortunately, when I use the Concatenation module as the first step in my
worflow, it doesn't have the "Add New Dataset" button appear when running
the workflow, and I don't see a way to force it in the workflow editor to
"Set at runtime".  

Is this a bug?  Is there a fix forthcoming?

Sure I could do this concatenation as a stand-alone module first and then
run the workflow separately with my new fastq file, but for my users I'd
rather it be part of the workflow.

Thanks,

Dave


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Re: [galaxy-dev] Wrapper generator.

[Dave Walton]

An alternative might be to have something like GenePattern has.  It's not as
seamless for the person who wants the wrapper as what's been suggested here,
but it's easier than creating a lengthy XML file.

GenePattern has an HTML Form interface for entering all the components of
your tool, including the command-line you want to expose and the parameters
you want to make available, and then it generates the back-end.

There are definite down-sides to this.  I've never tested what keeps the
tool in GenePattern from letting you do destructive things.

Dave


On 5/13/11 9:41 AM, "Peter Cock"  wrote:

> On Fri, May 13, 2011 at 2:12 PM, J. F. J. Laros  wrote:
>> Hi Pieter,
>> 
>> Thanks for the reply, but from the looks of it, this is a way to incorporate
>> webservice clients into galaxy. What I want is slightly different.
>> 
>> I'm talking about adding a normal command line tool (an aligner for example)
>> but I'm not willing to write a wrapper each time (the wrapper for BWA for
>> example is 327 lines). If a computer readable description of the interface
>> exists, this description can be used to generate a python wrapper. I
>> mentioned
>> WSDL because this also gives a description of an interface, but any
>> equivalent
>> description would of course be fine.
>> 
>> Ideally, such a description is maintained by the developer of the tool in
>> question.
>> 
>> With kind regards,
>> Jeroen.
> 
> How many tools can you name that come with such a machine readable
> file describing their command line interface?
> 
> I can think of only one - the EMBOSS tool suite and their ACD files
> (used internally by EMBOSS to generate the command line help,
> documentation, and do the command line option parsing).
> 
> Unfortunately I don't think there is an easy answer - even if wrapping
> a tool where all the input and output formats are already supported in
> Galaxy.
> 
> Peter
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Re: [galaxy-dev] More on multiple inputs to a workflow

[Dave Walton]

Thanks very much Dannon.

I will at least take a look at the code and see what is involved.  The
scientists here at the Lab consider this to be fairly important
functionality (in both cases).

I'll let you know if I move ahead and start to implement it.

Thanks again,

Dave


On 5/13/11 9:30 AM, "Dannon Baker"  wrote:

> On May 9, 2011, at 10:49 AM, Dave Walton wrote:
>> First the new...  So I have a workflow that does analysis on paired end mRNA
>> Seq data.  My workflow for single end works great, but with paired end, I
>> can see an obvious way to submit two lists of files (one for the forward and
>> one for the reverse), which can then be submitted to a series of the same
>> workflow.  Once I've chosen the forward to allow selection of multiple input
>> files, the option to allow the reverse to also allow selection of multiple
>> input files becomes disabled.  This makes perfect sense, as, unless you've
>> implemented it to associate pairs of files together, this probably wouldn't
>> work anyway.  Is there anyone out there working on a solution to this?  If
>> not, does anyone have suggestion as to how we could make it work?
> 
> We did consider the case of paired reads, as well as the possibility of
> allowing for the product of all input dataset lists as we implemented multiple
> inputs at the hackathon, but chose to focus on the most commonly requested use
> case of a single ranged input for simplicity.  The enhancement that you want
> to make isn't something I currently have on my list to add, though you're more
> than welcome to have a go at it.  To make it work, you'd have to modify the
> run workflow template ( templates/workflow/run.mako ), as well as the run
> workflow controller ( lib/galaxy/web/controllers/workflow.py ) to handle the
> new logic.
> 
> 
>> Now the old... A while back I suggested that it would be useful while
>> editing a workflow, if there were a way to grab the name of an input file as
>> a variable, and then use this variable in naming all later output files
>> (this way I can propagate a sample name all the way through the workflow).
>> Especially in a case where we are using the option to select multiple files
>> to run the same workflow, this feature is very important.  Is anyone working
>> on this?  If not, could someone point me in the right direction if I were to
>> start trying to implement this feature?
> 
> 
> This is something I've wanted to add as a part of a larger set of enhancement
> to the workflow parameters interface.  I believe we talked about this before,
> as it seems familiar to me, but even now you could approximate some of the
> functionality you're looking for with workflow parameters.  Another tool for
> managing the outputs of these large multi-input workflow runs is the "Send
> Results to New History" option in the run workflow interface.  When used in
> combination with multiple inputs, this option actually generates a new
> numbered history for *each* separate workflow run, so "Sample Processing Run
> 1", "Sample Processing Run 2" and so on.  All that said, if you wanted to
> implement this, you'd want to look at the run workflow template as well as the
> editor template (templates/workflow/editor.mako).
> 
> Good luck, and definitely let us know if you end up writing something that
> you'd like to contribute back,
> 
> -Dannon


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[galaxy-dev] Database/Build

[Dave Walton]

I'd like to get a better understanding of the point of the database/build
attribute, and pose the question of when is the appropriate time to have it
set?

In our case at the Jackson Laboratory, the most common build is  NCBI37/MM9.

However, the feeling of many folks here, is that this should not be set on
our fastq files.  The only place we really run into trouble is with
cufflinks.  If you haven't set the db when you get to cufflinks you'll get
an error.

Our suggestion is that there should be one of two options:

1)  Tophat has the ability to set the database of the output files based on
the genome that was selected for alignment.

2)  There should be a module that can be plugged into a workflow that would
set the database of the file prior to passing the file to cufflinks (or any
other two that requires the database attribute to be set).

We are curious if anyone else is running into this issue, and how it is
being solved.

We're thinking about hacking the Tophat wrapper, but I wanted to check with
others before I did this.

Thanks,

Dave


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[galaxy-dev] Error getting to http://galaxy/user/create on local instance

[Dave Walton]

We upgraded our Galaxy instance to the current Dist build at the end of last
week.   Since then we've had a couple new users attempt to create accounts.
When they go to the create user page (http://galaxy.jax.org/user/create)
they get a 500 Server Error.

The message in the error log is:
10.30.34.254 - - [24/May/2011:15:54:24 -0400] "GET /user/create HTTP/1.0"
500 - "http://galaxy/user/login"; "Mozilla/5.0 (Macintosh; U; Intel Mac OS X
10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2"
Error - : create() takes at least 3 arguments
(2 given)


Glen is traveling to the Galaxy Community Conference, he's the one that did
the upgrade, but as far as I know, he did a pretty straight forward upgrade.

Did something change, in configuration of the create user page?

Any thoughts what might be causing this?

Thanks,

Dave


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Re: [galaxy-dev] Error getting to http://galaxy/user/create on local instance

[Dave Walton]

Greg,

We've tried just reloading the browser and that didn't do anything.

As for deleting the cached templates, on our development server I tried
deleting everything under the database/compiled_templates directory (I even
restarted my server) and it appeared to have no affect.  We still get the
error message.  Maybe I misunderstood you.

The only cache related variable in my universe_wsgi files is
"static_cache_time = 360".

Thanks,

Dave


On 5/24/11 4:27 PM, "Greg Von Kuster"  wrote:

> Hello Dave,
> 
> The index method signature of the user controller changed, so this is a
> template cache issue.  It may work to simply have your users refresh their
> Galaxy masthead ( the top menu banner that includes the login in the User
> pop-up ).  
> 
> However, sometimes this isn't enough to clear the cache, so you can fix things
> for sure by deleting the cached templates in
> ~//database/compiled_templates/user assuming you have not changed the setting
> for the template cache in your universe_wsgi.ini file.  If you have, delete
> the files in the user directory where you have them stored.
> 
> Greg Von Kuster
> 
> 
> 
> On May 24, 2011, at 4:02 PM, Dave Walton wrote:
> 
>> We upgraded our Galaxy instance to the current Dist build at the end of last
>> week.   Since then we've had a couple new users attempt to create accounts.
>> When they go to the create user page (http://galaxy.jax.org/user/create)
>> they get a 500 Server Error.
>> 
>> The message in the error log is:
>> 10.30.34.254 - - [24/May/2011:15:54:24 -0400] "GET /user/create HTTP/1.0"
>> 500 - "http://galaxy/user/login"; "Mozilla/5.0 (Macintosh; U; Intel Mac OS X
>> 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2"
>> Error - : create() takes at least 3 arguments
>> (2 given)
>> 
>> 
>> Glen is traveling to the Galaxy Community Conference, he's the one that did
>> the upgrade, but as far as I know, he did a pretty straight forward upgrade.
>> 
>> Did something change, in configuration of the create user page?
>> 
>> Any thoughts what might be causing this?
>> 
>> Thanks,
>> 
>> Dave
>> 
>> 
>> ___
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>> 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
> 
> 
> 


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Re: [galaxy-dev] Error getting to http://galaxy/user/create on local instance

[Dave Walton]

Greg.

We do not use the "template_cache_path" in our config.  I deleted all the
files in ~/database/compiled_templates and restarted my server.  I still get
the error (even with a shift reload of my browser).  I've tried it (on the
Mac) with Firefox 3.5.2, Safari 5.0.5 and Google Chrome 11.0.696.71

We run two totally separate instances of Galaxy, on different virtual
machines.  One for testing, development of tools and deploying new versions
of galaxy, and one for production, where our scientists do their analysis.
Each of these servers run 4 instances of the "galaxy process".  3 Web
applications and 1 job runner.

We get the error on both servers, but I'm doing all of this troubleshooting
on our development server.

This behavior is occuring for any user who tries to create a new galaxy
account (so the original user who reported the problem, and myself as I test
it.  I can ask others to try if you think that will help).

I mentioned the browsers I've tried it with above.  I've not tried it from a
windows box, but can, again, if you think that will help.

We are running whatever version of galaxy-dist was available about a week
and a half ago, which is when Glen did the upgrade.

Thanks,

Dave


On 5/24/11 11:29 PM, "Greg Von Kuster"  wrote:

> Hi Dave,
> 
> If you do not have a template_cache_path config setting in universe_wsgi.ini,
> then your cached templates are stored in the default directory of
> ~/database/compiled_templates.
> 
> Deleting your cached templates in ~/database/compiled_templates should have
> corrected the problem, assuming there are no other issues within your Galaxy
> environment, so let's begin down the path of determining the cause.
> 
> You mention your "development server" in your response.  Are you running only
> 1 Galaxy instance, or more than 1?
> 
> Is the behavior occurring for all of your users or just a few?  Does it occur
> with different browsers, or is it related to a certain browser brand?
> 
> What version of Galaxy are your running?
> 
> Thanks Dave,
> 
> Greg Von Kuster
> 
> On May 24, 2011, at 6:06 PM, Dave Walton wrote:
> 
>> Greg,
>> 
>> We've tried just reloading the browser and that didn't do anything.
>> 
>> As for deleting the cached templates, on our development server I tried
>> deleting everything under the database/compiled_templates directory (I even
>> restarted my server) and it appeared to have no affect.  We still get the
>> error message.  Maybe I misunderstood you.
>> 
>> The only cache related variable in my universe_wsgi files is
>> "static_cache_time = 360".
>> 
>> Thanks,
>> 
>> Dave
>> 
>> 
>> On 5/24/11 4:27 PM, "Greg Von Kuster"  wrote:
>> 
>>> Hello Dave,
>>> 
>>> The index method signature of the user controller changed, so this is a
>>> template cache issue.  It may work to simply have your users refresh their
>>> Galaxy masthead ( the top menu banner that includes the login in the User
>>> pop-up ).  
>>> 
>>> However, sometimes this isn't enough to clear the cache, so you can fix
>>> things
>>> for sure by deleting the cached templates in
>>> ~//database/compiled_templates/user assuming you have not changed the
>>> setting
>>> for the template cache in your universe_wsgi.ini file.  If you have, delete
>>> the files in the user directory where you have them stored.
>>> 
>>> Greg Von Kuster
>>> 
>>> 
>>> 
>>> On May 24, 2011, at 4:02 PM, Dave Walton wrote:
>>> 
>>>> We upgraded our Galaxy instance to the current Dist build at the end of
>>>> last
>>>> week.   Since then we've had a couple new users attempt to create accounts.
>>>> When they go to the create user page (http://galaxy.jax.org/user/create)
>>>> they get a 500 Server Error.
>>>> 
>>>> The message in the error log is:
>>>> 10.30.34.254 - - [24/May/2011:15:54:24 -0400] "GET /user/create HTTP/1.0"
>>>> 500 - "http://galaxy/user/login"; "Mozilla/5.0 (Macintosh; U; Intel Mac OS X
>>>> 10.6; en-US; rv:1.9.1.2) Gecko/20090729 Firefox/3.5.2"
>>>> Error - : create() takes at least 3 arguments
>>>> (2 given)
>>>> 
>>>> 
>>>> Glen is traveling to the Galaxy Community Conference, he's the one that did
>>>> the upgrade, but as far as I know, he did a pretty straight forward
>>>> upgrade.
>>>> 
>>>> Did something change, in configuration of the create use

Re: [galaxy-dev] Error getting to http://galaxy/user/create on local instance

[Dave Walton]

Just removed user.pyc and restarted the server.  Did not resolve the problem.

Dave


On 5/26/11 8:09 AM, "Greg Von Kuster"  wrote:

Hi Glen,

I've never seen this before, but perhaps your user controller is using an old 
version ( I'm just grasping here, because this is pretty obscure behavior ).  
Try deleting the following file - make sure it is the .pyc file.

~/lib/galaxy/web/controllers/user.pyc

The user controller contains the code that generates the you may create one 
<http://galaxy.jax.org/user/create>  link, but the current versions of this 
controller is using the new method signature as well, so the only thing I can 
think of is that your compiled version ( user.pyc ) is old.

Let us know if this doesn't resolve the issue.

Thanks!

On May 26, 2011, at 7:39 AM, Glen Beane wrote:

I just checked,

Using the User->Register menu works,  however we require our users to log in so 
when they go to galaxy.jax.org <http://galaxy.jax.org/>  they are redirected to 
a login page if they are not already logged in.  That page has the text "This 
installation of Galaxy has been configured such that only users who are logged 
in may use it. If you don't already have an account, you may create one 
<http://galaxy.jax.org/user/create> ."  , and "you may create one" links to 
http://galaxy.jax.org/user/create.  clicking on the link results in the error.

-glen


On May 26, 2011, at 4:00 AM, Greg Von Kuster wrote:

Hello Dave,

Can you clarify how your users are accessing the following URL

http://galaxy.jax.org/user/create

I originally assumed they were using the Galaxy UI to register by clicking the 
"Register" link on the "User" popup menu.  However, perhaps they are just 
pointing their browser to the URL.  Is this the case?  If so, why are you not 
clicking on the menu link?

If it is the case that your users are entering the address in their browsers 
rather than using the normal Galaxy UI, then the address should include an 
additional request param as is shown here:

http://galaxy.jax.org/user/create?cntrller=user

Greg


~/
On May 25, 2011, at 1:46 PM, Dave Walton wrote:

Greg.

We do not use the "template_cache_path" in our config.  I deleted all the
files in ~/database/compiled_templates and restarted my server.  I still get
the error (even with a shift reload of my browser).  I've tried it (on the
Mac) with Firefox 3.5.2, Safari 5.0.5 and Google Chrome 11.0.696.71

We run two totally separate instances of Galaxy, on different virtual
machines.  One for testing, development of tools and deploying new versions
of galaxy, and one for production, where our scientists do their analysis.
Each of these servers run 4 instances of the "galaxy process".  3 Web
applications and 1 job runner.

We get the error on both servers, but I'm doing all of this troubleshooting
on our development server.

This behavior is occuring for any user who tries to create a new galaxy
account (so the original user who reported the problem, and myself as I test
it.  I can ask others to try if you think that will help).

I mentioned the browsers I've tried it with above.  I've not tried it from a
windows box, but can, again, if you think that will help.

We are running whatever version of galaxy-dist was available about a week
and a half ago, which is when Glen did the upgrade.

Thanks,

Dave


On 5/24/11 11:29 PM, "Greg Von Kuster"  wrote:

Hi Dave,

If you do not have a template_cache_path config setting in universe_wsgi.ini,
then your cached templates are stored in the default directory of
~/database/compiled_templates.

Deleting your cached templates in ~/database/compiled_templates should have
corrected the problem, assuming there are no other issues within your Galaxy
environment, so let's begin down the path of determining the cause.

You mention your "development server" in your response.  Are you running only
1 Galaxy instance, or more than 1?

Is the behavior occurring for all of your users or just a few?  Does it occur
with different browsers, or is it related to a certain browser brand?

What version of Galaxy are your running?

Thanks Dave,

Greg Von Kuster

On May 24, 2011, at 6:06 PM, Dave Walton wrote:

Greg,

We've tried just reloading the browser and that didn't do anything.

As for deleting the cached templates, on our development server I tried
deleting everything under the database/compiled_templates directory (I even
restarted my server) and it appeared to have no affect.  We still get the
error message.  Maybe I misunderstood you.

The only cache related variable in my universe_wsgi files is
"static_cache_time = 360".

Thanks,

Dave


On 5/24/11 4:27 PM, "Greg Von Kuster"  wrote:

Hello Dave,

The index method signature of the user controller changed, so this is a
template cache issue.  It may work to simply have your users 

[galaxy-dev] Display names accessible from Tool XML?

[Dave Walton]

I'm building a tool that needs the "display name" of a file inside the
output of the tool.

To clarify, I have a tool that merges gene expression  result from cufflinks
for many samples.  It generates a "matrix" tab-delimited file that provides
the results with genes or transcript down one axis and samples across the
other with intensity values in the cells of the matrix.

I have already built into my galaxy server the ability to carry meaningful
sample names from the original input file all the way through to the output
of the final output of the cufflinks step of my workflow (this is
functionality I've already offered up to the galaxy team to include, and can
explain at a later date).

Okay, so the problem I have is from the XML, I want to be able to pass my
command-line script both the physical file names  so the files can be
parsed, but I also want to be able to pass the script the "display name" to
use as the sample names for the columns in the file.

Is there a way using the metadata to grab this from the input?  I see that I
can do something like input.metadata.dbkey and get the database key, but I
can't find a way to do anything like input.metadata.name or
input.metadata.display_name to give me what I want.

My example XML file is below.

Thanks,

Dave


  merges multiple cufflinks expression output files (gene or
transcript) into a single matrix formatted file (id by sample, with
intensity values)
  
cuff_exp_2_matrix_new.py
  $input1.metadata.display_name
  $input1
  $output1
  #for $i in $inputs
${i.input.metadata.display_name}
${i.input}
  #end for
  
  


  

  
  

  
  

**What it does**

This is a Jackson Laboratory custom tool for taking the output for several
runs of
cufflinks, where each run represents a sample, and merging these results
into a file
that contains a matrix of gene/transcript id by sample, with the cells of
the matrix
filled with the intensity values.  The end result is a file that is easily
imported
into R or other tools for expression analysis.

  



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Re: [galaxy-dev] Display names accessible from Tool XML?

[Dave Walton]

I figured it out!

The mistake I was making was assuming that I needed to use the "metadata"
attribute.  I found in the "Data" base class that there is a display_name
method.

So instead in my xml I just used the syntax $input.display_name and I got
exactly what I was looking for.

Are things like this documented somewhere?  I couldn't find it in the wiki,
and it took digging into the code and quite a bit of trial and error to
figure it out.

Thanks,

Dave


On 6/16/11 9:08 AM, "Dave Walton"  wrote:

> I'm building a tool that needs the "display name" of a file inside the
> output of the tool.
> 
> To clarify, I have a tool that merges gene expression  result from cufflinks
> for many samples.  It generates a "matrix" tab-delimited file that provides
> the results with genes or transcript down one axis and samples across the
> other with intensity values in the cells of the matrix.
> 
> I have already built into my galaxy server the ability to carry meaningful
> sample names from the original input file all the way through to the output
> of the final output of the cufflinks step of my workflow (this is
> functionality I've already offered up to the galaxy team to include, and can
> explain at a later date).
> 
> Okay, so the problem I have is from the XML, I want to be able to pass my
> command-line script both the physical file names  so the files can be
> parsed, but I also want to be able to pass the script the "display name" to
> use as the sample names for the columns in the file.
> 
> Is there a way using the metadata to grab this from the input?  I see that I
> can do something like input.metadata.dbkey and get the database key, but I
> can't find a way to do anything like input.metadata.name or
> input.metadata.display_name to give me what I want.
> 
> My example XML file is below.
> 
> Thanks,
> 
> Dave
> 
> 
>   merges multiple cufflinks expression output files (gene or
> transcript) into a single matrix formatted file (id by sample, with
> intensity values)
>   
> cuff_exp_2_matrix_new.py
>   $input1.metadata.display_name
>   $input1
>   $output1
>   #for $i in $inputs
> ${i.input.metadata.display_name}
> ${i.input}
>   #end for
>   
>   
>  help="Need to add more files? Use controls below."/>
> 
>   
> 
>   
>   
> 
>   
>   
> 
> **What it does**
> 
> This is a Jackson Laboratory custom tool for taking the output for several
> runs of
> cufflinks, where each run represents a sample, and merging these results
> into a file
> that contains a matrix of gene/transcript id by sample, with the cells of
> the matrix
> filled with the intensity values.  The end result is a file that is easily
> imported
> into R or other tools for expression analysis.
> 
>   
> 
> 
> 
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[galaxy-dev] Selective storage of galaxy files

[Dave Walton]

Dear Galaxy developers,

Our institution is trying solve our storage problem (we need lots,
especially for NGS data, and someone needs to fund it).  What we would like
to be able to do, is based on some criteria control in what location a file
gets written to disk.

This criteria could be an individual user, a role or group they belong to,
or a project the file is associated with.

What we'd like to know are the following 3 things:
1) Is anyone already working on something like this?

2) Are there other institutions that would be interested in this type of
functionality?

3) If we were to attempt to implement this ourselves, would anyone be
interested in giving us some input with respect to how to implement and how
to make it generic enough to meet the needs of most institutions?  If we're
going to do it, we'll need to be able to produce an estimate of what the
effort would be like so that we could get institutional funding to develop
the functionality.

Thanks for any input you can provide.

Dave

--
Dave Walton
Computational Sciences
The Jackson Laboratory
Bar Harbor, Maine


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Re: [galaxy-dev] Display BAM with IGV

[Dave Walton]

Minor correction.  It wasn't commented out...

# Force everyone to log in (disable anonymous access).
require_login = True

But yes, changing to
Require_login = False

Fixed the problem.

Thanks Iry.

Dave


On 9/1/11 8:42 AM, "Iry Witham"  wrote:

> Hi Nate,
> 
> We have found the solution to our/this issue.  The way we have our
> Galaxy instance configured is to have users required to log on.  So in the
> universe.wsgi.webapp.ini file we had set the User and Security settings to:
> 
> # Force everyone to log in (disable anonymous access).
> #require_login = True
> 
> This was where we found the issue.  We have changed the settings as
> follows and we can now view BAM files through IGV:
> 
> # Force everyone to log in (disable anonymous access).
> require_login = False
> #require_login = True
> 
> Thanks for all of you assistance.
> 
> Iry
> 
> 
> On 8/29/11 2:50 PM, "Nate Coraor"  wrote:
> 
>> Iry Witham wrote:
>>> Hi Nate,
>>> 
>>> I have been able to get this to work on a Mac and Windows XP within
>>> limited guide lines.  The following are what I had to do to make it work:
>>> 
>>> My Mac is now running Java 1.6.0_26, Firefox 3.6.20, Google Crome
>>> ver.13.0.782.215 and Safari 5.1 (6534.50).  In addition I have installed Max
>>> OS 10.6.8 Supplemental Update 1.0.  My PC is running Windows XP SP3 with
>>> Java 1.6.0_26, Firefox 3.6.20 and IE8.  Windows updates are at current
>>> levels.  I have not tested this on Windows 7.
>>> 
>>> I am currently able to run the IGV-web tool from Galaxy via Firefox, Crome
>>> and Safari on the Mac and IE8 only on Windows.  When I use either Firefox or
>>> Crome on Windows I get the following error.
>>> 
>>> 
>>> ERROR [2011-08-24 09:22:40,169]  [TrackLoader.java:211]
>>> [SwingWorker-pool-20352093-thread-1]  java.lang.RuntimeException:
>>> java.lang.RuntimeException: Error loading file:
>>> http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908
>>> 0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length
>>> 
>>> ERROR [2011-08-24 09:22:40,169]  [TrackManager.java:245]
>>> [SwingWorker-pool-20352093-thread-1]  Error loading tracks
>>> 
>>> org.broad.igv.exceptions.DataLoadException: An error occurred while
>>> loading:
>>> http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908
>>> 0aa/data/galaxy_afa21414c9c9e7eb.bamjava.lang.RuntimeException: Error
>>> loading file: 
>>> http://galaxy/display_application/afa21414c9c9e7eb/igv_bam/web/8e5efb082c908
>>> 0aa/data/galaxy_afa21414c9c9e7eb.bam NULL content-length
>>> 
>>> at org.broad.igv.track.TrackLoader.load(TrackLoader.java:212)
>>> 
>>> at org.broad.igv.track.TrackManager.load(TrackManager.java:271)
>>> 
>>> at org.broad.igv.track.TrackManager.loadResources(TrackManager.java:241)
>>> 
>>> at 
>>> org.broad.igv.ui.IGVMainFrame$StartupWorker.doInBackground(IGVMainFrame.java
>>> :2775)
>>> 
>>> at com.jidesoft.utils.SwingWorker$1.call(Unknown Source)
>>> 
>>> at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
>>> 
>>> at java.util.concurrent.FutureTask.run(Unknown Source)
>>> 
>>> at com.jidesoft.utils.SwingWorker.run(Unknown Source)
>>> 
>>> at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown
>>> Source)
>>> 
>>> at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
>>> 
>>> at java.lang.Thread.run(Unknown Source)
>>> 
>>> This error appears to be different from the original, at least in
>>> details though the results are the same.  I am also going to post this with
>>> IGV support.
>> 
>> Hi Iry,
>> 
>> If you get anything back from the IGV folks please post a followup.
>> Since IGV runs in the local JVM, that it works with one browser and not
>> another on the same system doesn't make a lot of sense.
>> 
>> --nate
>> 
>>> 
>>> Thanks,
>>> Iry
>>> 
>>> 
>>> On 8/15/11 2:46 PM, "Nate Coraor"  wrote:
>>> 
 Iry Witham wrote:
> Hi Nate,
> 
> I have checked the nginx.conf file and they comply to the
> documentation:
> 
>  #  added to allow nginx to handle file downloads
> location /_x_accel_redirect/ {
> internal;
> alias /;
> 
> I have also confirmed that the universe_wsgi.ini file contains the
> following:
> 
> And the following to the [app:main] section of universe_wsgi.ini:
> nginx_x_accel_redirect_base = /_x_accel_redirect
> 
> Iry
 
 This will need some in-depth debugging, then.
 
 If you access Galaxy directly via the port of its built-in web server
 (by default, 8080), and request to display a dataset, does it set the
 X-Accel-Redirect header in the response?
 
 If you access the same dataset via the nginx address but rename the
 underlying disk file, do you get an error message from nginx or from
 Galaxy?
 
 --nate
 
> 
> On 8/15/11 10:46 AM, "Nate Coraor"  wrote:
> 
>> Iry Witham wrote:
>

Re: [galaxy-dev] Setting the output label based on input parameters?

[Dave Walton]

This is similar to something we've done for workflows in our instance of
Galaxy.  Dannon actually suggested I push a copy of my changes out so he can
review them and potentially add them to galaxy central.  I've been
delinquent in doing this push.  It's not exactly what you are talking about
but similar (IMHO)...  If folks are interested in this functionality I'll
get off my butt and make the time to share the changes.

In brief, here's what I did:

The change is totally isolated to lib/galaxy/jobs/actions/post.py in the
RenameDatasetAction.execute method.

I have introduced syntax similar to the ${variable} syntax that is used for
creating workflow variables.

In my case the syntax is as follows:
#{inputs_file_variable | option 1 | option n}
where: 
 input_file_variable = is the name of a module input variable
 |  = the delimiter for added options. Optional if no options.
 options = basename, upper, lower
 basename = keep all of the file name except the extension
(everything before the final ".")
 upper = force the file name to upper case
 lower = force the file name to lower case
 suggested additions:
 "replace" option so you can replace a portion of the name,
 support multiple #{name} in one rename action...

The choice of the character "#" instead of "$" was relatively arbitrary...
It was that or "!" actually.

So an example might be:
I have a workflow with an Input Dataset and a FASTQ Groomer.
In the FASTQ Groomer I select "Rename Dataset" "output_file" and then in the
"New output name:" field I might type:
#{input_file | basename | upper}.fastqsanger

Assume the original input file name to the Input Dataset was
s_1_1_PWDxNOD.txt
The variable in the FastQ Groomer module for that file is "input_file".
When I run the workflow, the resulting output file from the groomer would be
"S_1_1_PWDXNOD.fastqsanger"

A much simpler example might just be "#{input_file}.fastqsanger".  This is
perfectly legal syntax, but the downside is if you have a lengthy workflow
and you are continually appending new extentions, you could end up with
something like "s_1_1_PWDxNOD.fastqsanger.bam.gex.tab".

Like the first of the two suggested additions I mention above, I could see
you deciding to add more possible operations in addition to basename, upper,
lower and replace. 

The concept of the markup I used for adding the operations was taken from
"Liquid markup" (https://github.com/tobi/liquid/wiki/liquid-for-designers).

I welcome any feedback and am more than happy to share the code back to the
galaxy community.

Dave

On 8/29/11 6:20 PM, "Ross"  wrote:

> Most times I need a user supplied label substring. I'm not sure how
> else to conditionally set a string to a predetermined value other than
> with boolean true/false strings or select parameter values.
> 
> One even more ugly option is to use a (strictly speaking now
> deprecated) post job exec hook to change the output dataset name based
> on some logic - but if the boolean works, I'd recommend moving on :)
> 
> On Tue, Aug 30, 2011 at 7:56 AM, Nikhil Joshi  wrote:
>> Hi Ross,
>> 
>> Yes, I did try that... but what I want is string parameter that changes
>> based on whether or not you've checked a checkbox (or a way to change the
>> label of the output based on whether or not the checkbox was checked).  So
>> my idea below did work, but it seems like a hack.  Which is why I was
>> wondering if there was a better way.
>> 
>> - Nik.
>> 
>> On Mon, Aug 29, 2011 at 2:55 AM, Ross  wrote:
>>> 
> On Thu, Aug 25, 2011 at 6:34 AM, SHAUN WEBB 
> wrote:
>> 
>> I meant to say label="${input}" or label="${input.value}.
>> 
>>> 
>>> Nikhil, did you try as Shaun and others have suggested? Any available
>>> string parameter can be used in a label as far as I can tell.
>>> 
>>> This is a common idiom - ask for a string ('title') to describe the
>>> job/output for posterity, then in an output:
>>> 
>>> >> label="${title}.myext"/>
>>> 
>>> There's even a built in ${on_string} if you just want the file name
>>> plus some history ids?
>>> 
>>> 
>>> On Mon, Aug 29, 2011 at 6:54 PM, Nikhil Joshi  wrote:
 It looks like the Cheetah syntax only is parsed within the 
 tags so I figured out a way to do it... but it seems hackish.  I
 basically changed the string values of truevalue and falsevalue within
 the
 parameter to be an English sentence that would become the label for the
 output.  I.e., in the input section:
 
 >>> falsevalue="Unfiltered Reads Fasta" label="Filter reads?"/>
 
 and in the output section:
 
 
 
 This seems wrong to do, but it does work.  If anyone has a better
 method,
 please let me know!
 
 - Nik.
 
 On Thu, Aug 25, 2011 at 2:36 PM, Nikhil Joshi 
 wrote:
> 
> It's actually a boolean checkbox. so I basically want the label to
> change based upon whether or not the checkbox is checked.  Is there any
> w

Re: [galaxy-dev] Setting the output label based on input parameters?

[Dave Walton]

This is a big part of the reason we did this.

I will push it out for the galaxy team to look at.  If for some reason the 
don't approve it I can share our change directly with you.

Dave

On Sep 1, 2011, at 6:39 PM, "Ross"  wrote:

> FWIW: This sounds like a useful idea to me.
> 
> My users are struggling with output names currently being generated by
> complex workflows where many tools do something like
> label="${tool.name} on ${on_string}: reordered ${outputFormat}" - that
> might be ok for a single step but after traveling through a few of
> those, the base name (which we routinely use for metadata needed at
> some final amalgamation step, such as experimental condition) is hard
> to find in all the cruft.
> 
> 
> 
> On Thu, Sep 1, 2011 at 11:16 PM, Dave Walton  wrote:
>> This is similar to something we've done for workflows in our instance of
>> Galaxy.  Dannon actually suggested I push a copy of my changes out so he can
>> review them and potentially add them to galaxy central.  I've been
>> delinquent in doing this push.  It's not exactly what you are talking about
>> but similar (IMHO)...  If folks are interested in this functionality I'll
>> get off my butt and make the time to share the changes.
>> 
>> In brief, here's what I did:
>> 
>> The change is totally isolated to lib/galaxy/jobs/actions/post.py in the
>> RenameDatasetAction.execute method.
>> 
>> I have introduced syntax similar to the ${variable} syntax that is used for
>> creating workflow variables.
>> 
>> In my case the syntax is as follows:
>> #{inputs_file_variable | option 1 | option n}
>> where:
>> input_file_variable = is the name of a module input variable
>> |  = the delimiter for added options. Optional if no options.
>> options = basename, upper, lower
>> basename = keep all of the file name except the extension
>>(everything before the final ".")
>> upper = force the file name to upper case
>> lower = force the file name to lower case
>>  suggested additions:
>> "replace" option so you can replace a portion of the name,
>> support multiple #{name} in one rename action...
>> 
>> The choice of the character "#" instead of "$" was relatively arbitrary...
>> It was that or "!" actually.
>> 
>> So an example might be:
>> I have a workflow with an Input Dataset and a FASTQ Groomer.
>> In the FASTQ Groomer I select "Rename Dataset" "output_file" and then in the
>> "New output name:" field I might type:
>> #{input_file | basename | upper}.fastqsanger
>> 
>> Assume the original input file name to the Input Dataset was
>> s_1_1_PWDxNOD.txt
>> The variable in the FastQ Groomer module for that file is "input_file".
>> When I run the workflow, the resulting output file from the groomer would be
>> "S_1_1_PWDXNOD.fastqsanger"
>> 
>> A much simpler example might just be "#{input_file}.fastqsanger".  This is
>> perfectly legal syntax, but the downside is if you have a lengthy workflow
>> and you are continually appending new extentions, you could end up with
>> something like "s_1_1_PWDxNOD.fastqsanger.bam.gex.tab".
>> 
>> Like the first of the two suggested additions I mention above, I could see
>> you deciding to add more possible operations in addition to basename, upper,
>> lower and replace.
>> 
>> The concept of the markup I used for adding the operations was taken from
>> "Liquid markup" (https://github.com/tobi/liquid/wiki/liquid-for-designers).
>> 
>> I welcome any feedback and am more than happy to share the code back to the
>> galaxy community.
>> 
>> Dave
>> 
>> On 8/29/11 6:20 PM, "Ross"  wrote:
>> 
>>> Most times I need a user supplied label substring. I'm not sure how
>>> else to conditionally set a string to a predetermined value other than
>>> with boolean true/false strings or select parameter values.
>>> 
>>> One even more ugly option is to use a (strictly speaking now
>>> deprecated) post job exec hook to change the output dataset name based
>>> on some logic - but if the boolean works, I'd recommend moving on :)
>>> 
>>> On Tue, Aug 30, 2011 at 7:56 AM, Nikhil Joshi  wrote:
>>>> Hi Ross,
>>>> 
>>>> Yes, I did try that... but what I want is string parameter that changes
>>>> based on whether or not you've checked

[galaxy-dev] Multiple Workflows broken?

[Dave Walton]

We just upgraded our Galaxy server last week to the one from change-set 
b258de1e6cea.

We have several workflows that leverage the ability to select multiple input 
files, that in turn launches an instance of the workflow per input file.

When I use these workflows, it now only runs a single instance of the workflow.

Is this feature broken?  Did we miss something in our upgrade?  Is it by chance 
fixed in one of the releases that have come out over the last couple weeks?

Thanks,

Dave
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Re: [galaxy-dev] Multiple Workflows broken?

[Dave Walton]

After some digging I just found an archived email from Dannon where it looks 
like the problem I reported is fixed.  In an email from Jan 8th entitled 
“multiple file input not taken into account in workflows”, Dannon said it was 
fixed in:

changeset 6368:52de9815a7c4.

If this is correct, please disregard this email and except my apology for 
reporting a known issue.

Dave

On 1/30/12 2:20 PM, "Dave Walton"  wrote:

We just upgraded our Galaxy server last week to the one from change-set 
b258de1e6cea.

We have several workflows that leverage the ability to select multiple input 
files, that in turn launches an instance of the workflow per input file.

When I use these workflows, it now only runs a single instance of the workflow.

Is this feature broken?  Did we miss something in our upgrade?  Is it by chance 
fixed in one of the releases that have come out over the last couple weeks?

Thanks,

Dave


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Re: [galaxy-dev] [Newsletter] Re: Interested in speaking with other institutions deploying Galaxy locally?

[Dave Walton]

JAX would be interested in this.

Dave

From: Ryan Golhar 
mailto:ngsbioinformat...@gmail.com>>
Date: Friday, April 27, 2012 3:14 PM
To: Ann Black-Ziegelbein mailto:annbl...@eng.uiowa.edu>>
Cc: "galaxy-dev@lists.bx.psu.edu" 
mailto:galaxy-dev@lists.bx.psu.edu>>
Subject: [Newsletter] Re: [galaxy-dev] Interested in speaking with other 
institutions deploying Galaxy locally?

This is a great idea.

On Fri, Apr 27, 2012 at 2:45 PM, Ann Black-Ziegelbein 
mailto:annbl...@eng.uiowa.edu>> wrote:
Hi everyone -

Here at the University of Iowa we are working on deploying Galaxy locally for 
campus wide access.  I am interested in forming a community of other 
institutions trying to deploy Galaxy locally and mange/operate it on a broad 
level.  Is anyone else?   If there is enough interest, possibly we could have  
a community conference call every other month to have an open discussion on how 
we are all deploying galaxy, customizations we are making, problems we are 
encountering, bugs, and any add-on operations management for galaxy being 
developed, etc.

Would love to hear from others operating Galaxy or in process of standing up a 
local deployment.

Thanks!

Ann Black-Ziegelbein
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The information in this email, including attachments, may be confidential and 
is intended solely for the addressee(s). If you believe you received this email 
by mistake, please notify the sender by return email as soon as possible.
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[galaxy-dev] Cannot see data when selecting "Display Data in Browser"

[Dave Walton]

I'm seeing some weird behavior in our local galaxy instance and am wondering if 
anyone has seen anything similar.

I have a custom tool that I've written that generates a tab-delimted file.  
When I click on the item name in the history, I can see the contents in the 
"preview" window.  However, when I click on the eye (Display Data in Browser), 
it comes up empty.  Same thing if I download the file.  However, if I go to the 
database directory to examine the file on disk, the content is exactly what I 
would expect.  The permissions on the file are galaxy user/group and the file 
has permissions of 644.

I don't see any reason why I shouldn't be able to view or download this file 
through galaxy.

Any ideas?

Thanks,

Dave

---
Dave Walton
Manager Scientific Computing
The Jackson Laboratory
Bar Harbor, Maine
dave.wal...@jax.org

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