Re: [galaxy-dev] survey

[Hans-Rudolf Hotz]

On 12/02/2013 11:14 PM, Philippe Moncuquet wrote:

Hi,

I hope this is relevant to the dev list but if it is not please let me know.

I was trying to estimate active users out of our registered users. I
ended counting users that had a job during the last month. How would you
guys do ?


I assume, you are also using the 'report tools'?

In general it is difficult to do the estimate, ie what is the difference 
between a user who does 5 jobs every month and a user who does 50 jobs 
at once and then never uses Galaxy again?


Hence, I would count the total number of jobs. Although, again, the 
number could be misleading, as there are 'big' jobs and 'small' jobs 
which use different amounts of compute resources, and so on




During this process I also wanted to see how we were doing in comparison
to other instance. I set up a simple survey and would greatly appreciate
if instance admin would take 2 min to complete it. I will publish
results here (or maybe to some more relevant place, let me know) at the
end of the month.

https://fr.surveymonkey.com/s/CD6NN88



done.


Regards, Hans-Rudolf



Regards,
Philip


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[galaxy-dev] hierarchical ObjectStore - noatime

[Bjoern Gruening]

Hi,

we want to put some more hard drives into your Galaxy Server. And we
plan to use the hierarchical ObjectStore for that purpose. 
The new discs will be type="distributed" id="primary" and the old disc
will become type="disk" id="secondary". If I understood correctly the
old disc is them in some read-only state and will not touched until the
primary discs are full or not working ...

Is it save to mount the old discs or all discs with noatime, to get a
small performance gain? Is Galaxy using noatime?

Thanks,
Bjoern

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Re: [galaxy-dev] [Galaxy-ZBIT] Help needed in Galaxy Uploading files.

[El-Sayed Hegazy]

Dear Dr Johannes,Alot of thanks for you but i already sent the same issue to 
galaxy-dev@lists.bx.psu.edu  the galaxy mailing list without reply 
i am so sorry for disturbance Best Regards,


https://www.mcpvirtualbusinesscard.com/VBCServer/elsayedhegazy/interactivecardEl-Sayed
 HegazyIT Manager at ALHAYAH LabsBioinformatician - Software developer Mobile: 
+2 0100 6 99 88 36e-mail: elsayedheg...@live.com  

> Date: Tue, 3 Dec 2013 10:15:22 +0100
> From: johannes.eich...@uni-tuebingen.de
> To: elsayedheg...@live.com
> CC: andrae...@eng.ucsd.edu
> Subject: Re: [Galaxy-ZBIT] Help needed in Galaxy Uploading files.
> 
> Dear Mr. Hegazy,
> 
> please note that we only provide support for the customized Galaxy
> instance hosted at http://webservices.cs.uni-tuebingen.de.
> 
> If you have any questions considering the main Galaxy instance which
> also offers the NGS TOOLBOX BETA (https://usegalaxy.org) please contact
> the core development team by joining the galaxy mailing list
> (galaxy-dev@lists.bx.psu.edu) as described here:
> http://wiki.galaxyproject.org/MailingLists#Posting_a_Question
> 
> Kind regards,
> Johannes
> 
> 
> On 12/03/2013 08:37 AM, El-Sayed Hegazy wrote:
> > Dear Dr Andreas,When i using Galaxy website and then go to Analyze data 
> > section and navigate through tools i found NGS tool box used for Next 
> > Generation Sequencing data analysis from Quality control like Groomer and 
> > trimming and filtering and then we can make mapping and more with Illumina 
> > RAW data files Its actually part of Galaxy services Called NGS tool box 
> > Beta 
> > I need to clarify what i miss ?
> > Alot of thanks for you 
> > Best Regards, 
> > https://www.mcpvirtualbusinesscard.com/VBCServer/elsayedhegazy/interactivecardEl-Sayed
> >  HegazyIT Manager at ALHAYAH LabsBioinformatician - Software developer 
> > Mobile: +2 0100 6 99 88 36e-mail: elsayedheg...@live.com  
> > 
> >> Date: Mon, 2 Dec 2013 09:28:10 -0800
> >> From: andrae...@eng.ucsd.edu
> >> To: elsayedheg...@live.com; gal...@listserv.uni-tuebingen.de
> >> CC: mahef...@gmail.com
> >> Subject: Re: [Galaxy-ZBIT] Help needed in Galaxy Uploading files.
> >>
> >> Dear El-Sayed Hegazy,
> >>
> >> Due to the long Thanksgiving weekend I could not reply to you earlier. 
> >> Thank you for your patience. I now downloaded your file and had a look 
> >> into it. What I realized from your e-mail is that you are interested in 
> >> next generation sequencing, NGS, which is actually not part of our 
> >> services. We do not provide any tools that facilitate handling this kind 
> >> of data. So, I would like to know what you intended to do with your 
> >> file; i.e., to which tool did you like to upload it and what was your 
> >> envisaged analysis?
> >>
> >> Thanks
> >>
> >> -- 
> >> Dr. Andreas Draeger
> >> University of California, San Diego, La Jolla, CA 92093-0412, USA
> >> Bioengineering Dept., Systems Biology Research Group, Office #2506
> >> Phone: +1-858-534-9717, Fax: +1-858-822-3120, twitter: @dr_drae
> >>
> >   
> > 
> > 
> > 
> > ___
> > Galaxy mailing list
> > gal...@listserv.uni-tuebingen.de
> > https://listserv.uni-tuebingen.de/mailman/listinfo/galaxy
> > 
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Re: [galaxy-dev] hierarchical ObjectStore - noatime

[Dannon Baker]

On Tue, Dec 3, 2013 at 5:49 AM, Bjoern Gruening
wrote:

> The new discs will be type="distributed" id="primary" and the old disc
> will become type="disk" id="secondary". If I understood correctly the
> old disc is them in some read-only state and will not touched until the
> primary discs are full or not working ...
>

Correct -- the default HierarchicalObjectStore always writes new files to
the first ObjectStore but can read through to any of them.  Probably worth
noting that, with this base implementation (that could easily be extended
to do whatever you'd prefer), when the first objectstore gets full it still
won't attempt to write to the second.


> Is it save to mount the old discs or all discs with noatime, to get a
> small performance gain? Is Galaxy using noatime?
>

I do believe we're using it, but Nate would be better able to comment on
the actual performance gain we see.
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Re: [galaxy-dev] tiff files in galaxy

[Carl Eberhard]

Hi, Robert

As far as I know, all browsers besides Safari aren't set up to render tiff
files by default. Are you using Safari to display the files in Galaxy?

There are extensions for Firefox and Chrome that will allow you to display
these files. Would that be an option?

As a side note: creating, saving, and manipulating images and thumbnails
would require Galaxy including a server side image processing library as a
dependency. I'd like to do this at some point in the future as it would
allow us other advantages too.

Thanks,
Carl


On Thu, Nov 21, 2013 at 4:17 PM, Robert Baertsch wrote:

> Do you know a fast way to open large tiff files in galaxy ? The sniffer
> recognizes the type, but clicking on the eyeball on a large 82mb file just
> hangs.
> Downloading the file and opening in preview does work but it is clunky.
> Perhaps storing a low res version that would be display when clicking the
> eyeball would speed access.
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Re: [galaxy-dev] Interacting with output views in Galaxy

[Carl Eberhard]

Hello, Stephen

Although still under initial development, you may want to look into the
visualization registry for the infrastructure to render the region and
allow the user to interact with it:
http://wiki.galaxyproject.org/VisualizationsRegistry
http://wiki.galaxyproject.org/Events/GCC2013/Abstracts#Events.2FGCC2013.2FAbstracts.2FTalks.How_to_Create_Your_Own_Web-based.2C_Interactive_Visualizations_for_Galaxy

In a nutshell, it allows you to configure and include a link from the
history panel to a custom page that you create with the mako templating
system and the javascript you'll need for the interactivity. Galaxy
resources (like your initial dataset) are parsed for you and available in
the template.

For the other half of the problem: creating new data from the interaction
of the user, you'll want to look into the tools API (which is what
Trackster uses). Still somewhat rough, there have been improvements to it
lately that should allow you to run a tool based on user input and keep the
chain of reproducibility.

Two things to note:
1. I'd recommend not using the upload tool via the API: not because it
doesn't work but because adding arbitrary data this way won't be
reproducible.
2. Both the visualizations registry and the tools API are still under
development. Feel free to contact me on IRC, email, or the mailing lists if
you have any trouble though.

I hope that helps and let me know if I can provide any more information,
Carl



On Fri, Nov 29, 2013 at 7:11 AM, Stephen Taylor  wrote:

> Hi,
>
> I was wondering, if anyone could point me to any resources and that allow
> the user to interact with the view of the output of a tool in Galaxy. So
> for example, I would like to load an image, draw a region of interest (ROI)
> (probably via some js routine) and then store that information in a file,
> generating an input in the History view. This input could then be used for
> further analysis.
>
> I guess Trackster does something like this, but I don't know if its
> routines are generic enough to handle this type of interaction.
>
> Thanks for any info!
>
> Steve
>
>
>
>
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Re: [galaxy-dev] hierarchical ObjectStore - noatime

[Nate Coraor]

Hi Björn,

atime is definitely not used by Galaxy, and we have generally disabled it
on all filesystems we mount.

--nate


On Tue, Dec 3, 2013 at 8:10 AM, Dannon Baker  wrote:

> On Tue, Dec 3, 2013 at 5:49 AM, Bjoern Gruening  > wrote:
>
>> The new discs will be type="distributed" id="primary" and the old disc
>> will become type="disk" id="secondary". If I understood correctly the
>> old disc is them in some read-only state and will not touched until the
>> primary discs are full or not working ...
>>
>
> Correct -- the default HierarchicalObjectStore always writes new files to
> the first ObjectStore but can read through to any of them.  Probably worth
> noting that, with this base implementation (that could easily be extended
> to do whatever you'd prefer), when the first objectstore gets full it still
> won't attempt to write to the second.
>
>
>> Is it save to mount the old discs or all discs with noatime, to get a
>> small performance gain? Is Galaxy using noatime?
>>
>
> I do believe we're using it, but Nate would be better able to comment on
> the actual performance gain we see.
>
>
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Re: [galaxy-dev] hierarchical ObjectStore - noatime

[Björn Grüning]

Thanks for the info Nate and Dannon!

Bjoern

> Hi Björn,
> 
> 
> atime is definitely not used by Galaxy, and we have generally disabled
> it on all filesystems we mount.
> 
> 
> --nate
> 
> 
> On Tue, Dec 3, 2013 at 8:10 AM, Dannon Baker 
> wrote:
> On Tue, Dec 3, 2013 at 5:49 AM, Bjoern Gruening
>  wrote:
> The new discs will be type="distributed" id="primary"
> and the old disc
> will become type="disk" id="secondary". If I
> understood correctly the
> old disc is them in some read-only state and will not
> touched until the
> primary discs are full or not working ...
> 
> 
> Correct -- the default HierarchicalObjectStore always writes
> new files to the first ObjectStore but can read through to any
> of them.  Probably worth noting that, with this base
> implementation (that could easily be extended to do whatever
> you'd prefer), when the first objectstore gets full it still
> won't attempt to write to the second.
> 
>  
> Is it save to mount the old discs or all discs with
> noatime, to get a
> small performance gain? Is Galaxy using noatime?
> 
> 
> I do believe we're using it, but Nate would be better able to
> comment on the actual performance gain we see.
> 
>  
> 
> ___
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> in your mail client.  To manage your subscriptions to this
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> 
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>   http://galaxyproject.org/search/mailinglists/
> 
> 



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Re: [galaxy-dev] tiff files in galaxy

[Robert Baertsch]

I was planning to use server code to tile the large images and then use one of 
a number of JavaScript   libraries to render.  Any browser should work without 
extensions . Jim did this with visigene in the genome browser years ago. 
- Robert 

> On Dec 3, 2013, at 9:16 AM, Carl Eberhard  wrote:
> 
> Hi, Robert
> 
> As far as I know, all browsers besides Safari aren't set up to render tiff 
> files by default. Are you using Safari to display the files in Galaxy?
> 
> There are extensions for Firefox and Chrome that will allow you to display 
> these files. Would that be an option?
> 
> As a side note: creating, saving, and manipulating images and thumbnails 
> would require Galaxy including a server side image processing library as a 
> dependency. I'd like to do this at some point in the future as it would allow 
> us other advantages too.
> 
> Thanks,
> Carl 
> 
> 
>> On Thu, Nov 21, 2013 at 4:17 PM, Robert Baertsch  
>> wrote:
>> Do you know a fast way to open large tiff files in galaxy ? The sniffer 
>> recognizes the type, but clicking on the eyeball on a large 82mb file just 
>> hangs.
>> Downloading the file and opening in preview does work but it is clunky. 
>> Perhaps storing a low res version that would be display when clicking the 
>> eyeball would speed access.
>> ___
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
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>> 
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>>   http://galaxyproject.org/search/mailinglists/
> 
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Re: [galaxy-dev] tiff files in galaxy

[James Taylor]

VisiGene only sends gif and jpeg over the wire.

--
James Taylor, Associate Professor, Biology/CS, Emory University


On Tue, Dec 3, 2013 at 12:59 PM, Robert Baertsch  wrote:
> I was planning to use server code to tile the large images and then use one
> of a number of JavaScript   libraries to render.  Any browser should work
> without extensions . Jim did this with visigene in the genome browser years
> ago.
> - Robert
>
> On Dec 3, 2013, at 9:16 AM, Carl Eberhard  wrote:
>
> Hi, Robert
>
> As far as I know, all browsers besides Safari aren't set up to render tiff
> files by default. Are you using Safari to display the files in Galaxy?
>
> There are extensions for Firefox and Chrome that will allow you to display
> these files. Would that be an option?
>
> As a side note: creating, saving, and manipulating images and thumbnails
> would require Galaxy including a server side image processing library as a
> dependency. I'd like to do this at some point in the future as it would
> allow us other advantages too.
>
> Thanks,
> Carl
>
>
> On Thu, Nov 21, 2013 at 4:17 PM, Robert Baertsch 
> wrote:
>>
>> Do you know a fast way to open large tiff files in galaxy ? The sniffer
>> recognizes the type, but clicking on the eyeball on a large 82mb file just
>> hangs.
>> Downloading the file and opening in preview does work but it is clunky.
>> Perhaps storing a low res version that would be display when clicking the
>> eyeball would speed access.
>> ___
>> 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:
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>>
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>>   http://galaxyproject.org/search/mailinglists/
>
>
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Re: [galaxy-dev] tiff files in galaxy

[Dannon Baker]

If you wanted to implement fancier tiling and display for tiff, the
extension point for this would be in the datatype's display_data method.
 You can use this to do whatever you'd like, displaying an intermediate
page with relevant code for tiling, etc.  See datatypes/tabular.py's
display_data method for an example of the chunking tabular display.


On Tue, Dec 3, 2013 at 12:59 PM, Robert Baertsch wrote:

> I was planning to use server code to tile the large images and then use
> one of a number of JavaScript   libraries to render.  Any browser should
> work without extensions . Jim did this with visigene in the genome browser
> years ago.
> - Robert
>
> On Dec 3, 2013, at 9:16 AM, Carl Eberhard  wrote:
>
> Hi, Robert
>
> As far as I know, all browsers besides Safari aren't set up to render tiff
> files by default. Are you using Safari to display the files in Galaxy?
>
> There are extensions for Firefox and Chrome that will allow you to display
> these files. Would that be an option?
>
> As a side note: creating, saving, and manipulating images and thumbnails
> would require Galaxy including a server side image processing library as a
> dependency. I'd like to do this at some point in the future as it would
> allow us other advantages too.
>
> Thanks,
> Carl
>
>
> On Thu, Nov 21, 2013 at 4:17 PM, Robert Baertsch wrote:
>
>> Do you know a fast way to open large tiff files in galaxy ? The sniffer
>> recognizes the type, but clicking on the eyeball on a large 82mb file just
>> hangs.
>> Downloading the file and opening in preview does work but it is clunky.
>> Perhaps storing a low res version that would be display when clicking the
>> eyeball would speed access.
>> ___
>> 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/
>>
>
>
> ___
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[galaxy-dev] Installing DeepTools on Cloudman 2.0

[Mohammad Heydarian]

Hello,
I recently discovered the DeepTools program and have been looking forward
to using it with Galaxy Cloudman. Today I attempted to load DeepTools from
the Galaxy tool shed on my freshly started Galaxy Cloudman 2.0 instance and
got the following error:
Internal Server ErrorGalaxy was unable to sucessfully complete your request

URL:
http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=8aa7aee9b90e1791&changeset_revisions=1ee0b1ecf500
Module galaxy.web.framework.middleware.error:*149* in __call__
>>  
>> 
app_iter *=* self*.*application*(*environ*,* sr_checker*)*
Module paste.recursive:*84* in __call__
>>  
>> 
*return* self*.*application*(*environ*,* start_response*)*
Module paste.httpexceptions:*633* in __call__
>>  
>> 
*return* self*.*application*(*environ*,* start_response*)*
Module galaxy.web.framework.base:*132* in __call__
>>  
>> 
*return* self*.*handle_request*(* environ*,* start_response *)*
Module galaxy.web.framework.base:*190* in handle_request
>>  
>> 
body *=* method*(* trans*,* kwargs *)*
Module galaxy.web.framework:*221* in decorator
>>  
>> 
*return* func*(* self*,* trans*,* ***args*,* kwargs *)*
Module galaxy.webapps.galaxy.controllers.admin_toolshed:*896* in
prepare_for_install
>>  
>> 
common_install_util*.*get_dependencies_for_repository*(* trans*,*
tool_shed_url*,* repo_info_dict*,*includes_tool_dependencies *)*
Module tool_shed.util.common_install_util:*84* in
get_dependencies_for_repository
>>  
>> 
installed_rd*,* missing_rd *=*
get_installed_and_missing_repository_dependencies_for_new_install*(*trans*,*
 repo_info_tuple *)*
Module tool_shed.util.common_install_util:*190* in
get_installed_and_missing_repository_dependencies_for_new_install
>>  
>> 
tool_shed*,* name*,* owner*,* changeset_revision*,*
prior_installation_required *=*suc*.*parse_repository_dependency_tuple*(*
rd_tup *)*
Module tool_shed.util.shed_util_common:*1106* in
parse_repository_dependency_tuple
>>  
>> 
prior_installation_required *=* str*(* prior_installation_required *)*
*UnboundLocalError: local variable 'prior_installation_required' referenced
before assignment*
I got this error when I tried to install either of the three revisions of
the tool. Am I doing something wrong?


Any guidance is appreciated! Thanks in advance!

Cheers,
Mo Heydarian

PhD candidate
The Johns Hopkins School of Medicine
Department of Biological Chemistry
725 Wolfe Street
402 Biophysics
Baltimore, MD 21205
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Re: [galaxy-dev] Installing DeepTools on Cloudman 2.0

[Björn Grüning]

Hi Mohammed,

that seems to be a old Tool Shed bug that is already fixed. Which Galaxy
version are you running. Can you update to a more recent version?

Thanks for using Galaxy and deepTools,
Bjoern

> Hello,
> I recently discovered the DeepTools program and have been looking
> forward to using it with Galaxy Cloudman. Today I attempted to load
> DeepTools from the Galaxy tool shed on my freshly started Galaxy
> Cloudman 2.0 instance and got the following error:
> 
> Internal Server Error
> Galaxy was unable to sucessfully complete your request
> URL: 
> http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=8aa7aee9b90e1791&changeset_revisions=1ee0b1ecf500
> Module galaxy.web.framework.middleware.error:149 in __call__
> >>  app_iter = self.application(environ, sr_checker)
> Module paste.recursive:84 in __call__
> >>  return self.application(environ, start_response)
> Module paste.httpexceptions:633 in __call__
> >>  return self.application(environ, start_response)
> Module galaxy.web.framework.base:132 in __call__
> >>  return self.handle_request( environ, start_response )
> Module galaxy.web.framework.base:190 in handle_request
> >>  body = method( trans, **kwargs )
> Module galaxy.web.framework:221 in decorator
> >>  return func( self, trans, *args, **kwargs )
> Module galaxy.webapps.galaxy.controllers.admin_toolshed:896 in 
> prepare_for_install
> >>  common_install_util.get_dependencies_for_repository( trans, 
> >> tool_shed_url, repo_info_dict,includes_tool_dependencies )
> Module tool_shed.util.common_install_util:84 in 
> get_dependencies_for_repository
> >>  installed_rd, missing_rd = 
> >> get_installed_and_missing_repository_dependencies_for_new_install(trans, 
> >> repo_info_tuple )
> Module tool_shed.util.common_install_util:190 
> inget_installed_and_missing_repository_dependencies_for_new_install
> >>  tool_shed, name, owner, changeset_revision, prior_installation_required 
> >> =suc.parse_repository_dependency_tuple( rd_tup )
> Module tool_shed.util.shed_util_common:1106 in 
> parse_repository_dependency_tuple
> >>  prior_installation_required = str( prior_installation_required )
> UnboundLocalError: local variable 'prior_installation_required'
> referenced before assignment
> 
> 
> I got this error when I tried to install either of the three revisions
> of the tool. Am I doing something wrong?
> 
> 
> 
> 
> Any guidance is appreciated! Thanks in advance!
> 
> 
> Cheers, 
> Mo Heydarian
> 
> PhD candidate 
> The Johns Hopkins School of Medicine
> Department of Biological Chemistry 
> 725 Wolfe Street
> 402 Biophysics
> Baltimore, MD 21205



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Re: [galaxy-dev] Installing DeepTools on Cloudman 2.0

[Mohammad Heydarian]

Hi Bjorn,
Thanks for the quick response.

I am running version: 10201:ebe87051fadf, when I updated to the latest
version, I was able to start the install of DeepTools.  The tool seemed to
be installing but when I went to refresh the page, I was greeted with this
message: "Initializing repository installation failed".  Checking on the
progress of the installation with the "monitor installing tool shed
repositories" page, shows that most of the repositories are "Installing
tool dependencies" (yellow box) or "Installed, missing both tool and
repository dependencies" (gray box). This is the case even after ~ two
hours.

I am glad to clarify if my description was unclear, or even share the cloud
instance.

Thanks in advance for any help!

Cheers,
Mo Heydarian

PhD candidate
The Johns Hopkins School of Medicine
Department of Biological Chemistry
725 Wolfe Street
402 Biophysics
Baltimore, MD 21205


On Tue, Dec 3, 2013 at 1:37 PM, Björn Grüning <
bjoern.gruen...@pharmazie.uni-freiburg.de> wrote:

> Hi Mohammed,
>
> that seems to be a old Tool Shed bug that is already fixed. Which Galaxy
> version are you running. Can you update to a more recent version?
>
> Thanks for using Galaxy and deepTools,
> Bjoern
>
> > Hello,
> > I recently discovered the DeepTools program and have been looking
> > forward to using it with Galaxy Cloudman. Today I attempted to load
> > DeepTools from the Galaxy tool shed on my freshly started Galaxy
> > Cloudman 2.0 instance and got the following error:
> >
> > Internal Server Error
> > Galaxy was unable to sucessfully complete your request
> > URL:
> http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=8aa7aee9b90e1791&changeset_revisions=1ee0b1ecf500
> > Module galaxy.web.framework.middleware.error:149 in __call__
> > >>  app_iter = self.application(environ, sr_checker)
> > Module paste.recursive:84 in __call__
> > >>  return self.application(environ, start_response)
> > Module paste.httpexceptions:633 in __call__
> > >>  return self.application(environ, start_response)
> > Module galaxy.web.framework.base:132 in __call__
> > >>  return self.handle_request( environ, start_response )
> > Module galaxy.web.framework.base:190 in handle_request
> > >>  body = method( trans, **kwargs )
> > Module galaxy.web.framework:221 in decorator
> > >>  return func( self, trans, *args, **kwargs )
> > Module galaxy.webapps.galaxy.controllers.admin_toolshed:896 in
> prepare_for_install
> > >>  common_install_util.get_dependencies_for_repository( trans,
> tool_shed_url, repo_info_dict,includes_tool_dependencies )
> > Module tool_shed.util.common_install_util:84 in
> get_dependencies_for_repository
> > >>  installed_rd, missing_rd =
> get_installed_and_missing_repository_dependencies_for_new_install(trans,
> repo_info_tuple )
> > Module tool_shed.util.common_install_util:190
> inget_installed_and_missing_repository_dependencies_for_new_install
> > >>  tool_shed, name, owner, changeset_revision,
> prior_installation_required =suc.parse_repository_dependency_tuple( rd_tup )
> > Module tool_shed.util.shed_util_common:1106 in
> parse_repository_dependency_tuple
> > >>  prior_installation_required = str( prior_installation_required )
> > UnboundLocalError: local variable 'prior_installation_required'
> > referenced before assignment
> >
> >
> > I got this error when I tried to install either of the three revisions
> > of the tool. Am I doing something wrong?
> >
> >
> >
> >
> > Any guidance is appreciated! Thanks in advance!
> >
> >
> > Cheers,
> > Mo Heydarian
> >
> > PhD candidate
> > The Johns Hopkins School of Medicine
> > Department of Biological Chemistry
> > 725 Wolfe Street
> > 402 Biophysics
> > Baltimore, MD 21205
>
>
>
>
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[galaxy-dev] Announcing the Galaxy Deployment Catalog!

[Dave Clements]

Hello all,

*I am pleased to formally announce the Galaxy Deployment Catalog
*, a place to describe
individual Galaxy deployments, and to learn how others in the community are
implementing Galaxy in production environments.

If you have a Galaxy deployment then please take a few minutes to describe
your instance to the community.  There are two ways to do this.

*Use the Wiki Template*

Go to the "Using the Wiki" section of the catalog home
page,
enter a CamelCase name for your deplloyment, click "Create ...," and then
edit, preview, and save the page. Voilà, an entry for your deployment now
exists in the catalog.


*Use the Google Form*

Fill out this Google Form .  In a week or two,
a deployment catalog page will be programmatically created and you will
receive an email.


The wiki method requires a wiki login, but gives you control over how the
page appears. The Google form is easier.

Thanks a bunch, and please let me know if you have any questions.

Dave C.

PS: The form submission method was inspired by (stolen from?) Philip
Moncuquet's post
 earlier
this week.

-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://wiki.galaxyproject.org/
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Re: [galaxy-dev] Installing DeepTools on Cloudman 2.0

[Björn Grüning]

Am Dienstag, den 03.12.2013, 16:19 -0500 schrieb Mohammad Heydarian:
> Hi Bjorn,
> Thanks for the quick response. 
> 
> 
> I am running version: 10201:ebe87051fadf, when I updated to the latest
> version, I was able to start the install of DeepTools.  The tool
> seemed to be installing but when I went to refresh the page, I was
> greeted with this message: "Initializing repository installation
> failed".  

That one should not scare you. Its not an error, I need to fill a trello
card about that. But it nothing to worry about. 

> Checking on the progress of the installation with the "monitor
> installing tool shed repositories" page, shows that most of the
> repositories are "Installing tool dependencies" (yellow box) or
> "Installed, missing both tool and repository dependencies" (gray box).
> This is the case even after ~ two hours. 

Probably due to the error before. Can you please visit the deepTools
repository and choose the 'repair repository' under 'repository
actions'. That should fix all previous errors. You can also remove and
reinstall deepTools and all packages in the 'Installing' state. 

Hope that helps!
Bjoern

> 
> I am glad to clarify if my description was unclear, or even share the
> cloud instance.
> 
> 
> Thanks in advance for any help!
> 
> 
> Cheers, 
> Mo Heydarian
> 
> PhD candidate 
> The Johns Hopkins School of Medicine
> Department of Biological Chemistry 
> 725 Wolfe Street
> 402 Biophysics
> Baltimore, MD 21205
> 
> 
> On Tue, Dec 3, 2013 at 1:37 PM, Björn Grüning
>  wrote:
> Hi Mohammed,
> 
> that seems to be a old Tool Shed bug that is already fixed.
> Which Galaxy
> version are you running. Can you update to a more recent
> version?
> 
> Thanks for using Galaxy and deepTools,
> Bjoern
> 
> > Hello,
> > I recently discovered the DeepTools program and have been
> looking
> > forward to using it with Galaxy Cloudman. Today I attempted
> to load
> > DeepTools from the Galaxy tool shed on my freshly started
> Galaxy
> > Cloudman 2.0 instance and got the following error:
> >
> > Internal Server Error
> > Galaxy was unable to sucessfully complete your request
> > URL:
> 
> http://ec2-54-226-209-68.compute-1.amazonaws.com/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=8aa7aee9b90e1791&changeset_revisions=1ee0b1ecf500
> > Module galaxy.web.framework.middleware.error:149 in __call__
> > >>  app_iter = self.application(environ, sr_checker)
> > Module paste.recursive:84 in __call__
> > >>  return self.application(environ, start_response)
> > Module paste.httpexceptions:633 in __call__
> > >>  return self.application(environ, start_response)
> > Module galaxy.web.framework.base:132 in __call__
> > >>  return self.handle_request( environ, start_response )
> > Module galaxy.web.framework.base:190 in handle_request
> > >>  body = method( trans, **kwargs )
> > Module galaxy.web.framework:221 in decorator
> > >>  return func( self, trans, *args, **kwargs )
> > Module galaxy.webapps.galaxy.controllers.admin_toolshed:896
> in prepare_for_install
> > >>
>  common_install_util.get_dependencies_for_repository( trans,
> tool_shed_url, repo_info_dict,includes_tool_dependencies )
> > Module tool_shed.util.common_install_util:84 in
> get_dependencies_for_repository
> > >>  installed_rd, missing_rd =
> 
> get_installed_and_missing_repository_dependencies_for_new_install(trans, 
> repo_info_tuple )
> > Module tool_shed.util.common_install_util:190
> inget_installed_and_missing_repository_dependencies_for_new_install
> > >>  tool_shed, name, owner, changeset_revision,
> prior_installation_required
> =suc.parse_repository_dependency_tuple( rd_tup )
> > Module tool_shed.util.shed_util_common:1106 in
> parse_repository_dependency_tuple
> > >>  prior_installation_required =
> str( prior_installation_required )
> > UnboundLocalError: local variable
> 'prior_installation_required'
> > referenced before assignment
> >
> >
> > I got this error when I tried to install either of the three
> revisions
> > of the tool. Am I doing something wrong?
> >
> >
> >
> >
> > Any guidance is appreciated! Thanks in advance!
> >
> >
> > Cheers,
> > Mo Heydarian
> >
> > PhD candidate
> > The Johns Hopkins School of Medicine
> > Department of Biological Chemistry
> > 725 Wolfe Street
> > 402 Biophysics
> > Baltimore, MD 21205
> 
> 
> 
> 
> 
> 

[galaxy-dev] how to viz. gff file on fasta file from history in trackster?

[Eric Rasche]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

I'm at a bit of a loss here, I've found that when I have a GFF file, it
offers to be visualized, but I cannot figure out how to visualize on a
Fasta file in my history.

I've done the following

1. GFF3 output file -> trackster
2. New viz
3. Build not listed -> click to add build from a fasta file (my genome)
4. Back to new viz, reference genome selected as the one I created.

Now I'm faced with this error:

Error: The requested genome file
(/home/galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len) could not be
opened. Exiting!
sort: write failed: standard output: Broken pipe
sort: write error
Couldn't open /home/galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len , No
such file or directory

Am I *only* able to viz. gff files on UCSC chromosomes?

It seems a bit obtuse when I have GFF data sets related to fasta phage
genomes that I'm working with, all of which were uploaded/generated in
galaxy.

Is there any (preferrably easy) way to accomplish this?

Cheers,
Eric

- -- 
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
404-692-2048
e...@tamu.edu
rasche.e...@yandex.ru
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