Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility

[Dannon Baker]

Hey Eric,

We use sqlalchemy, and the detailed documentation is here:

http://docs.sqlalchemy.org/en/rel_0_7/core/engines.html#postgresql

That said, the basic format is:  dialect+driver://username:password@host
:port/database

So, you're going to be looking at something like: postgres://
glxe...@wigserv5.cshl.edu:5432/glxeric



On Fri, May 23, 2014 at 3:49 PM, Paniagua, Eric  wrote:

> Hi Dannon,
>
> There have been some developments, and I would like to update my question
> accordingly.
>
> I have set up PostgreSQL 9.1 on a separate box from our Galaxy server, and
> ferried the database contents over.  My question is this:
>
> What is the appropriate syntax to use for the parameter
> "database_connection" in universe_wsgi.ini to use a remote database server?
>  Specifically:
>
> Galaxy host: genomics.cshl.edu
> Database host: wigserv5.cshl.edu
> Database name: glxeric
> Database user/role: glxeric
> Database port: 5432 (postgresql default port)
> Database password: not required under the current configuration.
>
> Can someone please explain how to fill in the "database_connection"
> parameter appropriately?
>
> Many thanks,
> Eric
>
> 
> From: galaxy-user-boun...@lists.bx.psu.edu [
> galaxy-user-boun...@lists.bx.psu.edu] on behalf of Paniagua, Eric [
> epani...@cshl.edu]
> Sent: Thursday, May 22, 2014 1:38 PM
> To: Dannon Baker
> Cc: Galaxy ‎[galaxy-u...@bx.psu.edu]‎
> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
>
> Hi Dannon,
>
> I have attached a screenshot of the error as it appears in the Galaxy web
> site and a screenshot of the log.
>
> Please let me know if I can provide any more information.
>
> Also, please note that the version information I gave for PostgreSQL
> before was incorrect.  I am actually running PostgreSQL 8.1.22.
>
> Thanks for your assistance,
> Eric
>
> 
> From: galaxy-user-boun...@lists.bx.psu.edu [
> galaxy-user-boun...@lists.bx.psu.edu] on behalf of Paniagua, Eric [
> epani...@cshl.edu]
> Sent: Thursday, May 22, 2014 11:14 AM
> To: Dannon Baker
> Cc: Galaxy ‎[galaxy-u...@bx.psu.edu]‎
> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
>
> Hi Dannon,
>
> I am in a meeting right now.  I should be done at noon.  I'll send you
> more info then.  Thank you for your assistance!
>
> Best,
> Eric
>
>
>  Original message 
> From: Dannon Baker
> Date:2014/05/22 11:08 (GMT-05:00)
> To: "Paniagua, Eric"
> Cc: "Galaxy ‎[galaxy-u...@bx.psu.edu]‎"
> Subject: Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility
>
> Hey Eric,
>
> Looking into this.  Can you send the exact error/trace if available?
>
> -Dannon
>
>
> On Thu, May 22, 2014 at 10:17 AM, Paniagua, Eric  <mailto:epani...@cshl.edu>> wrote:
> Hi,
>
> I am running a Galaxy instance at Cold Spring Harbor Laboratory, and in
> the process of preparing an update I have encountered some problems.  When
> I try to create a new dataset (e.g. by running a tool), I receive an error
> message indicating a syntactic problem with backend database commands.
>  Specifically, the error mentions a read-only cursor and occurs when the
> system is trying to look up the history hid number for the new dataset, a
> value which (as far as I understand it) should be an autoincrementing
> primary key.
>
> My codebase is the 68a8b0397947 commit on the stable branch, plus some
> custom tool definitions, but no real modification to any core Galaxy code.
>  The database I am using is PostgreSQL 9.1.  I am using Python 2.6.4.  In
> the target (production) environment, we run with 3 web server processes and
> 3 job runner processes, but I am encountering this error in a
> single-Galaxy-process test instance.  The error is reported both in the
> logs (with a traceback originating in the bowels of SQLAlchemy) and via the
> web interface.
>
> I dug through the commit history and found a comit (e1bc855165bc) with the
> comment "Upgrade psycopg2 to 2.5.1 (statically linked to PostgreSQL
> 9.2.4)." on Sep 23, 2013.  I am wondering if this means I need to upgrade
> my database backend to PostgreSQL 2.4.x.  The wrinkle lies in the fact that
> I need to keep 2 parallel Galaxy instances running for an extended time
> period (~1 month).  The first is the current (not updated) local Galaxy
> instance, and the second is the new (updated) Galaxy instance, which
> naturally implies diverging databases.  Does this mean I will need to
> maintain parallel installations of PostgreSQL 9.1 and 

Re: [galaxy-user] Urgent Question about PostgreSQL Compatibility

[Dannon Baker]

Hey Eric,

Looking into this.  Can you send the exact error/trace if available?

-Dannon


On Thu, May 22, 2014 at 10:17 AM, Paniagua, Eric  wrote:

> Hi,
>
> I am running a Galaxy instance at Cold Spring Harbor Laboratory, and in
> the process of preparing an update I have encountered some problems.  When
> I try to create a new dataset (e.g. by running a tool), I receive an error
> message indicating a syntactic problem with backend database commands.
>  Specifically, the error mentions a read-only cursor and occurs when the
> system is trying to look up the history hid number for the new dataset, a
> value which (as far as I understand it) should be an autoincrementing
> primary key.
>
> My codebase is the 68a8b0397947 commit on the stable branch, plus some
> custom tool definitions, but no real modification to any core Galaxy code.
>  The database I am using is PostgreSQL 9.1.  I am using Python 2.6.4.  In
> the target (production) environment, we run with 3 web server processes and
> 3 job runner processes, but I am encountering this error in a
> single-Galaxy-process test instance.  The error is reported both in the
> logs (with a traceback originating in the bowels of SQLAlchemy) and via the
> web interface.
>
> I dug through the commit history and found a comit (e1bc855165bc) with the
> comment "Upgrade psycopg2 to 2.5.1 (statically linked to PostgreSQL
> 9.2.4)." on Sep 23, 2013.  I am wondering if this means I need to upgrade
> my database backend to PostgreSQL 2.4.x.  The wrinkle lies in the fact that
> I need to keep 2 parallel Galaxy instances running for an extended time
> period (~1 month).  The first is the current (not updated) local Galaxy
> instance, and the second is the new (updated) Galaxy instance, which
> naturally implies diverging databases.  Does this mean I will need to
> maintain parallel installations of PostgreSQL 9.1 and 9.2.x?  How would I
> go about setting up that configuration?
>
> Any assistance on debugging this error would be greatly appreciated.  Our
> initial goal was to roll out this update tomorrow afternoon, but that may
> need to be delayed because of this show-stopper.  If I can provide any
> further useful information, please let me know, and I will be happy to do
> so.
>
> Best,
> Eric Paniagua
>
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Re: [galaxy-user] Data Uploading through FTP

[Dannon Baker]

Scott,

1) Please create new threads when you have a new question, instead of
replying to unrelated threads.

2) Have you tried the things Jen mentioned before?  If so, please reply to
the list (in that thread), with what issues you're having.  Always "Reply
All" to keep the list on the thread so that we can actually help you.

-Dannon


On Fri, Mar 14, 2014 at 11:24 AM, Scott Tighe  wrote:

>
>  Hi Galaxy List
>>
>> If anybody has some insight as to how to upload data to the new Galaxy, I
>> sure would enjoy hearing the trick.
>>
>> Scott
>>
>> Scott Tighe
>> Senior Core Laboratory Research Staff
>> Advanced Genome Technologies Core
>> NextGen Sequencing/Flow Cytometry
>> University of Vermont and Vermont Cancer Center
>> 149 Beaumont ave
>> Health Science Research Facility 303/305
>> Burlington Vermont 05405
>> 802-656-2482 (AGTC)
>>
>> On 3/14/2014 10:25 AM, Jennifer Jackson wrote:
>>
>>> Hi Elvio,
>>>
>>> Peter is correct - you can manage any list membership through the
>>> mailman web pages.
>>>
>>> I found you only on this list and unsubscribed you. If you want to
>>> instead consider the galaxy-announce mailing list (low volume, general
>>> project updates), links for how to sign up are on this wiki:
>>> https://wiki.galaxyproject.org/MailingLists
>>>
>>> Best,
>>>
>>> Jen
>>> Galaxy team
>>>
>>> On 3/14/14 2:58 AM, Elvio Pederzolli wrote:
>>>
 Hi there can you please unsubscribe me from all Galaxy lists please

 Thank you

 Elvio Pederzolli

 Sent from my iPad
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>>>
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Re: [galaxy-user] Installing tool in galaxy on cloud

[Dannon Baker]

After adding yourself as an admin in Cloudman, your galaxy instance
restarted, correct?  If so, can you double check that the cloudman admin
interface indicates your exact email address that you've logged into galaxy
as?

-Dannon


On Mon, Feb 3, 2014 at 12:32 PM, Malik, Shivani wrote:

> Hi All,
> I want to use Tophat2 on amazon cloud. I could not find it in the regular
> tools unlike the public server. Am I using the right version?
>  I  tried installing it through admin on cloud .Though I was able to make
> myself admin through cloudman instance , I could not see any admin panel on
> Galaxy main page. What am I doing wrong?Any help is appreciated.
>
> Thanks.
> Shivani
>
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Re: [galaxy-user] Importing workflow from file fails in Galaxy instance on Amazon Cloud

[Dannon Baker]

Sébastien,

This seems to be a galaxy bug from a little while back.  To fix your cloud
instance, go to the cloud admin console and click "Update Galaxy", and the
problem should be resolved once galaxy updates and restarts.

-Dannon


On Fri, Jan 3, 2014 at 6:42 PM, Sébastien Vigneau <
sebastien.vign...@gmail.com> wrote:

> Hi,
>
> I can't import workflows from file on a freshly installed instance of
> Galaxy on Amazon Cloud. The error message is copied below. Do you have some
> idea on how to fix this?
>
> Thanks,
>
> Sébastien
>
>
> Internal Server Error
>> Galaxy was unable to sucessfully complete your request
>> URL:
>> http://ec2-50-19-79-199.compute-1.amazonaws.com/workflow/import_workflow
>> 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.webapps.galaxy.controllers.workflow:1127 in import_workflow
>> >>  workflow, missing_tool_tups = self._workflow_from_dict( trans, data,
>> source=src,add_to_menu=add_to_menu )
>> Module galaxy.webapps.galaxy.controllers.workflow:1823 in
>> _workflow_from_dict
>> >>  module = module_factory.from_dict( trans, step_dict, secure=False )
>> Module galaxy.workflow.modules:428 in from_dict
>> >>  return self.module_types[type].from_dict( trans, d, **kwargs )
>> Module galaxy.workflow.modules:222 in from_dict
>> >>  module.state.decode( d[ "tool_state" ], module.tool,
>> module.trans.app, secure=secure )
>> Module galaxy.tools:849 in decode
>> >>  self.inputs = params_from_strings( tool.inputs, values, app,
>> ignore_errors=True )
>> Module galaxy.tools.parameters:92 in params_from_strings
>> >>  value = json_fix( from_json_string( value ) )
>> Module simplejson:384 in loads
>> Module simplejson.decoder:402 in decode
>> TypeError: expected string or buffer
>
>
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Re: [galaxy-user] Grouping Histories into related Projects

[Dannon Baker]

The right approach here is probably to use history tags (at the top of a
history panel, click the tag icon just below the history name).  You could
tag several histories with a particular sample name, organism, etc.  While
you can *search* for histories by tags and get a list of, say, all "Mouse"
tagged histories, the current Saved Histories grid doesn't display tags in
a particularly useful fashion by default and this could probably be
improved.


On Fri, Nov 1, 2013 at 1:39 PM, Avery DeVries wrote:

> Hello,
>
> I was wondering if there way any way to group related histories into
> "Projects" (like a home directory and sub-directories).
>
> Currently, I have several annotations/analyses in separate histories
> related to the same dataset (i.e. one for gene annotation, one for ENCODE
> elements, etc) and as you can imagine, as I have several other datasets
> each with separate histories for each analysis I conduct, my Saved
> Histories page can get pretty convoluted.
>
> I would like to keep them in separate histories so I can easily find
> separate analyses, but I really wish there was a way to group them together
> so I could parse through my long list of histories quickly.
>
> Is this possible to do?  Thank you so much
>
> Avery
>
> *Avery DeVries*
> afric...@email.arizona.edu
>
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Re: [galaxy-user] 'Could not connect to server'

[Dannon Baker]

I apologize, saw right as I was sending that that I'd said galaxyproject.org.
 Main's ftp location is ftp://usegalaxy.org.


On Wed, Oct 30, 2013 at 4:05 PM, Dannon Baker wrote:

> Hi Alex,
>
> The new, permanent ftp address for the main Galaxy server is
> ftp://galaxyproject.org -- you should see this on the upload page as well.
>
> -Dannon
>
>
>
> On Wed, Oct 30, 2013 at 1:55 PM, Leontovich, Alexey A., Ph.D. <
> leontovich.ale...@mayo.edu> wrote:
>
>>  I successfully uploaded files to the main Galaxy server a month ago
>> using ftp.  However, any attempts to upload files today have failed.  I get
>> a 'Could not connect to server' error when trying to connect to
>> main.g2.bx.psu.edu uisng FileZilla.  Any suggestions?
>>
>> Thank you.
>> Alex
>>
>> ** **
>>
>> *Alexey Leontovich, Ph.D.* | Assistant Professor of Medical Informatics
>> | Biomedical Statistics and Informatics |Phone: 507-284-4850 | Fax:
>> 507-538-0850 | leontovich.ale...@mayo.edu
>> *Mayo Clinic* | 200 First Street SW | Rochester, MN 55905 |
>> mayoclinic.org <http://www.mayoclinic.org>
>>
>> ** **
>>
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>
>
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Re: [galaxy-user] 'Could not connect to server'

[Dannon Baker]

Hi Alex,

The new, permanent ftp address for the main Galaxy server is
ftp://galaxyproject.org -- you should see this on the upload page as well.

-Dannon



On Wed, Oct 30, 2013 at 1:55 PM, Leontovich, Alexey A., Ph.D. <
leontovich.ale...@mayo.edu> wrote:

>  I successfully uploaded files to the main Galaxy server a month ago
> using ftp.  However, any attempts to upload files today have failed.  I get
> a 'Could not connect to server' error when trying to connect to
> main.g2.bx.psu.edu uisng FileZilla.  Any suggestions?
>
> Thank you.
> Alex
>
> ** **
>
> *Alexey Leontovich, Ph.D.* | Assistant Professor of Medical Informatics |
> Biomedical Statistics and Informatics |Phone: 507-284-4850 | Fax:
> 507-538-0850 | leontovich.ale...@mayo.edu
> *Mayo Clinic* | 200 First Street SW | Rochester, MN 55905 | 
> mayoclinic.org
> 
>
> ** **
>
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Re: [galaxy-user] inconsistant error messages on disk quota?

[Dannon Baker]

Hey Francis,

There's a bug in the current release of cloudman that causes files fetched by 
galaxy (this doesn't affect direct http or ftp upload) to use the root volume 
as temporary storage, which has very little space.  This is fixed in the next 
release scheduled to coincide with the galaxy-dist release.Until that's 
available, I'd recommend using one of the other upload options.  If this isn't 
possible, let me know and I'll try to figure out another workaround.  Sorry for 
the trouble!

-Dannon

On Oct 24, 2013, at 8:45 AM, Francis Ouellette  wrote:

> 
> I'm on cloudman, trying to upload files, and I'm getting this error message:
> 
> "No space left on device" transferring a 1 GB file to my instance, but the 
> cloudman console says I have more than 5 GB left?
> 
> Is this a bad error message?
> 
> Is there some other file you want to see?
> 
> @bffo
> 
> 
>  
> 
> 
> 
> 
> 
> 
> -- 
> B.F. Francis Ouellette  http://oicr.on.ca/person/francis-ouellette
> 
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Re: [galaxy-user] inconsistant error messages on disk quota?

[Dannon Baker]

One quick additional comment -- you may want to ssh in to the instance and 
remove any large upload files that were created in /tmp by galaxy, or other 
things might also start failing.


On Oct 26, 2013, at 3:03 PM, Dannon Baker  wrote:

> Hey Francis,
> 
> There's a bug in the current release of cloudman that causes files fetched by 
> galaxy (this doesn't affect direct http or ftp upload) to use the root volume 
> as temporary storage, which has very little space.  This is fixed in the next 
> release scheduled to coincide with the galaxy-dist release.Until that's 
> available, I'd recommend using one of the other upload options.  If this 
> isn't possible, let me know and I'll try to figure out another workaround.  
> Sorry for the trouble!
> 
> -Dannon
> 
> On Oct 24, 2013, at 8:45 AM, Francis Ouellette  wrote:
> 
>> 
>> I'm on cloudman, trying to upload files, and I'm getting this error message:
>> 
>> "No space left on device" transferring a 1 GB file to my instance, but the 
>> cloudman console says I have more than 5 GB left?
>> 
>> Is this a bad error message?
>> 
>> Is there some other file you want to see?
>> 
>> @bffo
>> 
>> 
>>  
>> 
>> 
>> 
>> 
>> 
>> 
>> -- 
>> B.F. Francis Ouellette  http://oicr.on.ca/person/francis-ouellette   
>>  
>> 
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Re: [galaxy-user] Need your helps about Galaxy

[Dannon Baker]

Ahh, ok, so you're hitting a bug from a previous release, sorry about that.
 If you're able, updating cloudman itself will fix that (among other small
issues).

That file is also in /mnt/cm as 'paster.log' if you can SSH in to get it.


On Wed, Oct 9, 2013 at 5:18 PM, Lei Yan  wrote:

> Dear Dannon,
>
> When I click the four “Log” links for Galaxy, PostgreSQL, SGE, and Galaxy
> Reports on the Admin Console interface, all of they throw exceptions.
> Please see attachments.
> There is another way I can get the log files?
> Thanks.
>
>
> Lei Yan
> Center for Integrative and Translational Genomics
> The University of Tennessee Health Science Center
>
>
> On Wed, Oct 9, 2013 at 4:04 PM, Dannon Baker wrote:
>
>> Can you send me the more detailed full cloudman log from the admin
>> interface (it may be quite large).  This will help me see what may have
>> happened.
>>
>>
>> On Wed, Oct 9, 2013 at 3:56 PM, Lei Yan  wrote:
>>
>>> Hi all,
>>>
>>> I found some very strange problems on our cloud Galaxy (
>>> http://galaxyclass.genenetwork.org/) recently, EVEN I did nothing.
>>>
>>>- It shows galaxy and galaxyIndices have errors in CloudMan Admin
>>>Console.
>>>- This Galaxy had 3 nodes before, but right now only one node is
>>>there.
>>>- Galaxy front end still can be opened, but I don’t know it really
>>>works as before or not.
>>>
>>> I attached some screenshot and log files.
>>> Does anybody have any ideas for this? Thanks a lot.
>>>
>>>
>>> Lei Yan
>>> Center for Integrative and Translational Genomics
>>> The University of Tennessee Health Science Center
>>>
>>
>>
>
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Re: [galaxy-user] Need your helps about Galaxy

[Dannon Baker]

Can you send me the more detailed full cloudman log from the admin
interface (it may be quite large).  This will help me see what may have
happened.


On Wed, Oct 9, 2013 at 3:56 PM, Lei Yan  wrote:

> Hi all,
>
> I found some very strange problems on our cloud Galaxy (
> http://galaxyclass.genenetwork.org/) recently, EVEN I did nothing.
>
>- It shows galaxy and galaxyIndices have errors in CloudMan Admin
>Console.
>- This Galaxy had 3 nodes before, but right now only one node is there.
>- Galaxy front end still can be opened, but I don’t know it really
>works as before or not.
>
> I attached some screenshot and log files.
> Does anybody have any ideas for this? Thanks a lot.
>
>
> Lei Yan
> Center for Integrative and Translational Genomics
> The University of Tennessee Health Science Center
>
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Re: [galaxy-user] How to lauch bulit cluster on Cloudman?

[Dannon Baker]

That means that the galaxy instance for your cluster didn't start.  It
probably should have.  Can you send me (directly, without the list -- it
can contain sensitive info) the cloudman log from the admin panel?

-Dannon


On Tue, Oct 8, 2013 at 9:17 AM, Yan He  wrote:

> Dear all,
>
> ** **
>
> I just established Galaxy Cloudman on Amazon EC2. I created a cluster
> named “exon_capture” and uploaded a lot of data to it. After some analysis,
> I terminated the cluster. The second time I wanted to get access to the
> “exon_capture” cluster, I created a new instance under the “exon_capture”.
> However, under this instance, the “access galaxy” button is in grey and not
> active. I tried several time, but the button was always in grey. Does
> anyone know what’s wrong? Did I miss something? It may be a very simple
> question, but it bothers me a whole afternoon. Thanks a lot!
>
> ** **
>
> Yan
>
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Re: [galaxy-user] galaxy cloud: location of imported and converted fastq's

[Dannon Baker]

Hi PT,

What exactly do you mean by "Galaxy on the Cloud appears to expect that the
imported and converted fastq files are in the same S3 bucket where the
fastq.gz files were"?  Once imported from S3, you're correct in that
everything will be on the local EBS volume.

-Dannon


On Sun, Oct 6, 2013 at 4:43 AM, p Vedell  wrote:

> Hi,
>
> ** **
>
> I had fastq.gz files in an Amazon S3 bucket. I created a Galaxy on the
> Cloud instance using CloudMan. I used GetData and pasted in the url’s of
> the fastq.gz files into Galaxy on the Cloud. They were successfully
> imported into the session and converted to fastq’s, it seems. However, at
> the next step (fastq groomer), Galaxy on the Cloud appears to expect that
> the imported and converted fastq files are in the same S3 bucket where the
> fastq.gz files were. But, they are not there. I read somewhere in
> documentation or notes that the data is actually in /mnt/galaxyData folder.
> However, I am not sure how to point fastq groomer to this place in the web
> interface  or alternatively, I am not sure how to move the fastq’s back to
> the s3 bucket (w/o downloading and re-uploading which would be very
> time-consuming). Thanks for any help you can provide. 
>
> ** **
>
> PT
>
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Re: [galaxy-user] Need your helps about Galaxy

[Dannon Baker]

Sorry for not being able to take a look at this sooner, thanks for figuring
it out and posting back!  This one must have fallen through the cracks when
we updated all the paths with the last Cloudman release, I'll make a note
to fix it with our next minor update.

-Dannon


On Thu, Sep 26, 2013 at 12:05 PM, Lei Yan  wrote:

> Hi all,
>
> I think I have fixed this bug, and Galaxy GUI can execute MACS
> successfully on my cloud Galaxy.
> I did the following changes to fix it:
>
>- It looks like the latest version of cloud Galaxy uses MACS 1.3, so I
>changed the default:
>
> default -> /mnt/galaxy/tools/macs/1.3.7.1/
>
>- There are two path mistakes in the MACS environment variable file
>(/mnt/galaxy/tools/macs/1.3.7.1/env.sh), and "galaxyTools" should be
>"galaxy":
>
> < PATH=/mnt/galaxy/tools/macs/1.3.7.1/bin:$PATH
> < PYTHONPATH=/mnt/galaxy/tools/macs/
> 1.3.7.1/lib/python2.6/site-packages:$PYTHONPATH
> > PATH=/mnt/galaxyTools/tools/macs/1.3.7.1/bin:$PATH
> > PYTHONPATH=/mnt/galaxyTools/tools/macs/
> 1.3.7.1/lib/python2.6/site-packages:$PYTHONPATH
>
>
> Maybe this can help somebody.
>
>
> Lei Yan
> Center for Integrative and Translational Genomics
> UTHSC
>
>
> On Tue, Sep 24, 2013 at 2:55 PM, Lei Yan  wrote:
>
>> Hi all,
>>
>> http://galaxyclass.genenetwork.org/
>> This cloud Galaxy was built by Cloud Galaxy Launch (
>> https://main.g2.bx.psu.edu/cloudlaunch) yesterday.
>> I found two problems about MACS on it:
>>
>>- When I execute MACS on Galaxy GUI, I got a “not found” error.
>>Please see attachment (error1.png).
>>- If I login the Galaxy server by ssh, I found it looks like MACS was
>>already installed on it, please see attachment (error2.png). But if I run
>>MACS in a terminal, I got another error. Please see attachment 
>> (error3.png).
>>
>> Anybody has any idea for this? Thanks a lot.
>>
>>
>> Lei Yan
>> Center for Integrative and Translational Genomics
>> UTHSC
>>
>>
>> On Tue, Sep 24, 2013 at 2:24 PM, Jennifer Jackson  wrote:
>>
>>>  Hi Lawrence,
>>>
>>> What version of MACS are you running? The Galaxy wrapper in galaxy-dist
>>> supports v1.3. I am 99% certain that the latest Cloudman image is the same,
>>> but Dannon can correct me. The two Tool Shed repos for MACS support v1.4
>>> and v2.0.10. Making sure that the wrapper & binary are a match might be the
>>> first place to check - these can get easily confused, especially when
>>> binaries install with un-versioned symbolic links by default.
>>>
>>> If you are re-running a workflow/job that came from the public Main
>>> server, and running galaxy-dist/central, then you want to use the v1.3
>>> binary, unless purposefully upgrading both wrapper & binary. The workflow
>>> reproducibility tracking will alert you about a change in tool versions and
>>> permit you to select updated tools upon execution (once tool is configured)
>>> if from the *same exact wrapper/tool*, but not if a *different
>>> wrapper/tool/repo* - so will likely take a workflow edit to change out
>>> the tool in this case if upgrading to newer MACS version.
>>>
>>> I noticed that the tool form README link for the MACS v2.0.10 wrapper is
>>> incorrect, copy link & add an ".rst" to find doc. Fairly certain these are
>>> expected to be ".txt" - I'll ask our team if this is a Tool Shed or repo
>>> input issue if extension different.
>>>
>>> Full help for installing tools from the Tool Shed is here:
>>>
>>> http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_instance
>>>
>>> And current wrapper/binary versions in galaxy-dist/central are listed
>>> here:
>>> http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
>>> With help for managing those dependencies here:
>>> http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
>>>
>>> Hopefully this helps,
>>>
>>> Jen
>>> Galaxy team
>>>
>>>
>>> On 9/24/13 9:41 AM, Reiter, Larry T wrote:
>>>
>>> Thanks, James. I worked it out by downloading my data files and workflow. 
>>> For some reason MACS still doesn't work. Any ideas?
>>>
>>> Lawrence T Reiter, PhD
>>> UTHSC, Memphis, TN
>>>
>>>
>>>  --
>>> Jennifer Hillman-Jacksonhttp://galaxyproject.org
>>>
>>>
>>
>
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Re: [galaxy-user] Error "out of memory" when trying to retrieve output

[Dannon Baker]

Do you have debug enabled in your universe_wsgi.ini?  IIRC, this causes the
entire request to be loaded into memory (which is a bad thing when the
response is 20GB).


On Thu, Aug 29, 2013 at 3:50 PM, Delong, Zhou wrote:

>  Hello,
> I wanted to download the accepted junction .bam file from tophat output of
> my local instance and I get an "out of memory" error. When I examine the
> server via command line, I found that a python process used by galaxy
> occupied more than 80% of total memory (on the virtual machine with 10G of
> RAM).. I tried curl command to retrieve the datafile after rebooted the
> virtual machine, and python is activated again and used up all the memory.
> The bam is around 20G of size, but I never had this kind of problem with
> other tophat analyses before on my local instance although they are of the
> same size. The discription on the web mentioned some .dat files that I
> manage to find on the disk, but not the bam.
> Can anyone explain what python is doing and how can I solve this please?
> Thanks,
> Delong
>
>
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Re: [galaxy-user] cloudman console not responding add/remove nodes

[Dannon Baker]

On Sun, Aug 25, 2013 at 3:35 PM, Deniz Erezyilmaz wrote:

> When I try to add nodes from the galaxy console, they never register as
> "available" and the icons never switch from blue to yellow to green. The
> cluster status log shows that they have been added. However, when I try to
> use the "remove nodes" option, the cluster status log tells me:"no idle
> instances found", and I cannot remove the extra instances.
>

So they remain blue the whole time in the cluster status display?  You
should always be able to terminate extra nodes if you click "force removal
of non-idle nodes" at terminate, or if you click the node in the cluster
diagram and terminate the specific node from there.  Have you tried this
and found it not to work?

Are you able to share your cloudman log (directly with me is fine -- it can
contain information you wish to keep private)?

The amazon EC2 cloud is showing that the added instances are running, and I
> am being charged for them. I believe the nodes are not actually working
> because the program is running at a snail's pace.
>

Can you look at the SGE queue (via the cloud admin panel) and see 1) if the
nodes have been registered at all, and 2) if so, what the nodes are doing?
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Re: [galaxy-user] galaxy-user Digest, Vol 86, Issue 17

[Dannon Baker]

Hi Jun,

Thanks for the clarification.  Workflow step annotations would best suit
your needs, I think.  When you're in the editor, click on any step and on
the right side you'll see a field "Annotation / Notes" which will be
displayed when the workflow is viewed.  This can be used to clear up any
confusion about what the individual step does.

Good luck!

Dannon


On Wed, Aug 21, 2013 at 8:22 PM, Jun Fan  wrote:

> Hi Jen,
>
>Maybe I have not explained my question cleared which caused the
> confusion: I did not mean the name of dataset.  Actually I asked about the
> display of the tool in the graphic view from the default value (guess it is
> the name attribute in the tool element of the wrapper) to something else in
> the workflow editor. As my ultimate purpose is to share my workflow with
> someone else. If they see three steps with the same displayed name and do
> not have the related knowledge, they will get lost. To help myself to
> explain well, here is the illustration:
> >From
> --- ---
> ---
> | mzidLib:PostProcessing|   | mzidLib:PostProcessing|
> | mzidLib:PostProcessing|
> |-| |-|
> |-|
> | input file   |   -->| input file
> |
> -->| input file|
> |-|   |
> |-|   |
> |-|
> |output (mzid) |-   |output (mzid)
> |-  |output (mzid) |
> --- |-|
> |-|
> To
> -
> ---
> 
> | mzidLib:PostProcessing FDR|   | mzidLib:PostProcessing
> Threshold|  | mzidLib:PostProcessing ProteoGroup|
> |--|
> |--|
> |--|
> | input file   |   -->| input file
> |   >| input file  |
> |--|   |
> |--|   |
> |--|
> |output (mzid) |-   |output (mzid)
> |-  |output (mzid) |
> ---
> |--|
> |--|
>
> Best regards!
> Jun
>
> Date: Tue, 20 Aug 2013 11:34:47 -0700
> From: Jennifer Jackson 
> To: Jun Fan 
> Cc: galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] customize tool display in the workflow
> Message-ID: <5213b6c7.5030...@bx.psu.edu>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi Jun,
>
> You are very close - just click on the "create" button within the "Edit
> Step
> Actions" box and it will expand, where you can then enter the new custom
> name. It will look something like this:
>
>
>
> The other post you are referring to is a method to name the output dataset
> based on the input datasets name. You can certainly try this out and see if
> it is useful.
>
> Hope this helps,
>
> Jen
> Galaxy team
>
> On 8/20/13 9:34 AM, Jun Fan wrote:
> > Hi  Jennifer,
> >
> >Many thanks for your reply. Unfortunately I am not clever to
> > figure out how to using the existing workflow dataset renaming
> > functions. I only know how to rename a dataset within history. Could
> > you show me how to do this? I have attached a screen shot of my
> > workflow. You can see that I have only managed to add annotation/notes
> > to this step. Ideally I would like to have the step with the label of
> > "mzidLib:PostProcessing FDR"  in the graphic view. From other thread,
> > someone mentioned to use ${method} in the label, I failed to apply this
> trick.
> >
> > Best regards!
> > Jun
> >
> > Message: 3
> > Date: Mon, 19 Aug 2013 10:18:32 -0700
> > From: Jennifer Jackson 
> > To: Jun Fan 
> > Cc: galaxy-user@lists.bx.psu.edu
> > Subject: Re: [galaxy-user] customize tool display in the workflow
> > Message-ID: <52125368.1060...@bx.psu.edu>
> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> >
> > Hi Jun,
> >
> > I asked Dannon (our workflow lead developer) and he suggested just
> > using the existing workflow datastet renaming functions. These are in
> > the right panel when you click on a dataset within the workflow editor
> > (as you probably know).
> >
> > Inherited naming is not something that is currently being worked on,
> > but you can always start a Trello card and see if it gathers votes or
> > the attention of a contributor from the larger development commun

Re: [galaxy-user] problem with custom database build

[Dannon Baker]

Hi Ann,

My guess is that this is related to the issue you were having before.  I'm
taking a look now.

-Dannon


On Mon, Jun 10, 2013 at 7:31 PM, Ann Holtz-Morris, M.S. <
aholtzmor...@chori.org> wrote:

> Hi,
>
> I’m trying to create a new custom build . I keep getting *GURU
> MEDITATION: #aa96a62c69784be49b7864f6ef42ddc6  *I’ve been trying  1 or 2
> times a day for the last 3 days. Thanks
>
> Ann
>
> ** **
>
> ** **
>
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[galaxy-user] Fwd: galaxy on the cloud

[Dannon Baker]

Hi Alejandro,

It should show up if you search for the AMI ID, which is ami-da58aab3.
 That said, the easiest way to launch a galaxy cloud cluster if you're not
already familiar with EC2 is probably using usegalaxy.org/cloudlaunch.
 This interface will guide you through the launch process without any extra
input on your part other than providing your AWS keys.
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Re: [galaxy-user] receiving an email when a processing step finishes

[Dannon Baker]

Actually, you can do this in workflows out of the box in Galaxy (as long as
your instance is configured to send mail).

All you need to do is edit the workflow, select the step you want to be
notified following, and add a Step Action-> Email Notification.



On Fri, May 17, 2013 at 9:41 AM, Geert Vandeweyer <
geert.vandewey...@ua.ac.be> wrote:

>  Hi,
>
> Currently not. For local/cloud instances, you can install an extra tool
> for this from the toolshed:
>
> http://toolshed.g2.bx.psu.edu/view/geert-vandeweyer/sendmail
>
> best
> geert
>
>
> On 05/17/2013 03:01 PM, Nikolay N. wrote:
>
> Hi,
>
>  I am using the main galaxy instance and have submitted several
> processing steps that seem to have been scheduled for execution. Is there a
> way to get an email notification when such a processing step finishes?
>
>  many thanks,
> Nickyo
>
>
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>
>
> --
>
> Geert Vandeweyer, Ph.D.
> Department of Medical Genetics
> University of Antwerp
> Prins Boudewijnlaan 43
> 2650 Edegem
> Belgium
> Tel: +32 (0)3 275 97 56
> E-mail: 
> geert.vandewe...@ua.ac.behttp://ua.ac.be/cognitivegeneticshttp://www.linkedin.com/pub/geert-vandeweyer/26/457/726
>
>
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Re: [galaxy-user] Downloading files via FTP

[Dannon Baker]

No, currently HTTP is the only way to download files from Galaxy.

-Dannon


On Tue, May 7, 2013 at 4:22 AM, lilach noy  wrote:

> Is it possible? If so, how?
>
> Thank you,
> Lilach
>
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Re: [galaxy-user] fastq quality trimmer

[Dannon Baker]

Hi Tomaž,

The script depends on galaxy libraries, but could probably be set up
standalone if you made the appropriate libraries available -- the source is
distributed with galaxy, see
https://bitbucket.org/galaxy/galaxy-central/src/tip/tools/fastq/fastq_trimmer_by_quality.py?at=default

-Dannon



On Wed, Apr 17, 2013 at 7:30 AM, Tomaz Rijavec  wrote:

> Dear "Galaxy Team",
>
> I have a question regarding the fastq quality trimmer (by sliding window)
> tool. What is the script running behind it? Is it a modified version of the
> fastx_quality_trimmer found in the fastx tools package? Is there a
> standalone version of it one can set up locally and run it from the command
> line.
> Thanks for all the info you can provide.
>
> best regards,
> Tomaž
>
>
>
>
>
> --
> Lep pozdrav / Best Regards,
> dr. Tomaž Rijavec
> 
> Inštitut za fizikalno biologijo d.o.o. / Toplarniška ulica 19, 1000
> Ljubljana / T: 01 587 54 70 / www.ifb.si
> Institute of Physical Biology / Toplarniška ulica 19, SI-1000 Ljubljana,
> Slovenia / T: +3861 587 54 70 / www.ifb.si
>
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Re: [galaxy-user] Welcome to the "galaxy-user" mailing list (Digest mode)

[Dannon Baker]

Of course!  Any subscriber can post -- it looks like your message
"Post Galaxy-ChIP-seq analysis: UCSC Genome browser can't read the wig
file" went through correctly.

Thanks for your interest.

-Dannon

On Wed, Feb 20, 2013 at 11:36 AM, Bodour Al-Khamees
 wrote:
> Hello,
>
> I would like to ask few question. I wonder if I can post in this mailing
> list.
>
>
> Thank you very much!
> Bodour
>
>
> On Wed, Feb 20, 2013 at 11:28 AM, 
> wrote:
>>
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Re: [galaxy-user] Galaxy on one computer not showing latest runs in history

[Dannon Baker]

Dikla,

After refreshing the browser, the most up-to-date view of the history should 
definitely be available.  Are you positive you're looking at the same history 
in both places?  I would verify that there's nothing in "Saved Histories" that 
looks like what you're expecting.

-Dannon

On Feb 13, 2013, at 1:43 AM, Dikla Aharonovich  
wrote:

> Hi
> I am running galaxy and am working both from home and work. 
> Last night at home, my history had up to 35 items in it, that all ran.
> At work today, I can only see 30. This includes number 27 in my history, 
> which shows that it is still running, while I already saw the results for it 
> at home last night.
> I tried logging in and out, and pressing the refresh button.
> Please let me know what else may be causing this
> Many thanks,
> Dikla
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Re: [galaxy-user] gather results from multiple histories

[Dannon Baker]

Hey Mark,

Yep, sure can.  Just click on the gear in the history panel and go to "Copy 
Datasets", and copy those datasets you're interested in to th specific new 
history you want to use.

-Dannon

On Feb 1, 2013, at 10:15 AM, mark.r...@syngenta.com wrote:

> Hi All
>  
> Let’s say that I have results produced from a step in multiple different 
> histories and that I now want to gather these results into a new history so 
> that they can be joined.  Is there a way to do this without exporting results 
> to my desktop and then uploading?
>  
> Thanks
>  
> Mark
>  
> 
> 
> This message may contain confidential information. If you are not the 
> designated recipient, please notify the sender immediately, and delete the 
> original and any copies. Any use of the message by you is prohibited. 
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Re: [galaxy-user] [galaxy-dev] Workflows

[Dannon Baker]

Geert, this is great stuff!

One small correction -- the API is enabled by default as of revision 
7022:8376ad08ae41 (April 2012).

-Dannon


On Jan 16, 2013, at 1:17 AM, Geert Vandeweyer  wrote:

> Hi, 
> 
> I've put together some exempels for activating and using the api. You can 
> find them here: 
> 
> http://geertvandeweyer.zymichost.com/index.php?page=read&id=29
> 
> Best regards, 
> 
> Geert vandeweyer
> 
> Op 16-jan.-2013 om 02:52 heeft  het volgende 
> geschreven:
> 
>> Hi
>>Sorry if these questions are obvious but I just don’t know how to find 
>> the answers.
>>  
>> I’m trying to get one of the API examples to work in 
>> http://wiki.galaxyproject.org/Learn/API/Examples .
>>  
>> I’ve got my API key but how do I get/find the workflow id (f2db41e1fa331b3e 
>> in the examples). I’ve created workflow but don’t know how to access this 
>> key.
>>  
>> Also in the first example it states /api/workflows However I 
>> don’t have the “api/workflows” directory structure in my galaxy-dist, do I 
>> need to create this?
>>  
>> Thanks
>> Neil
>>  
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Re: [galaxy-user] [External] Re: galaxy cloudman login

[Dannon Baker]

On Jan 2, 2013, at 5:17 PM, "Sun, Wenping [USA]"  wrote:
> 1. how to retain my previous work?

If you were logged in when you were working previously, we just have to figure 
out who you were logged in as, and log back in.  You may also want to check 
"Saved Histories" to make sure you aren't unintentionally in a fresh history 
instead of the one you want.

> 2. I could not find "Mange User" under admin, either from cloudman and galaxy 
> web. Where is it?

This is from within the Galaxy interface, not cloudman.  Click "Admin" in the 
top masthead, and then on the left side you should see a bunch of options.  The 
first of these should be "Manage users".

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Re: [galaxy-user] galaxy cloudman login

[Dannon Baker]

To be clear, your admin user still works on this instance but another one does 
not?  If this is the case, can you log in as the admin user (and, if not, 
simply register a new user and make it an admin) and take a look at the user 
list in the admin panel?

To get to the user list when in Galaxy, just click "Admin" at the top and then 
"Manage Users".  Are there users listed?  If your user is listed but you're 
unable to log in, you can reset your password here.

-Dannon


On Dec 31, 2012, at 10:41 AM, "Sun, Wenping [USA]"  wrote:

> Hello,
>  
> I have galaxy cloudman running and had tried one time success to log in to 
> retain the previous data and history after re-launching followed by 1sttime 
> restart. Today I am re-launching again along with the correct size of ebs 
> volumes that I adjusted earlier. However, my login is not recognized at all 
> (“error:no such user….”). I tried several time of terminating and restarting 
> and it is still the same. My admin which is same as the login was able to 
> retained every time. What’s the issue with the log in??
>  
> It is taking time to repeat previous data/history. I need your help to 
> retrieve my login.
>  
> Thank you in advance,
> Kathryn
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Re: [galaxy-user] [External] Re: galaxy cluster nodes from the cloudlaunch site

[Dannon Baker]

In the main (non-admin) cloudman UI you'll see a little icon next to the volume 
size.  Click this and you'll have the opportunity to enter a new size.  Upon 
submitting this, galaxy will need to temporarily shut down, but it should be 
automatically restarted once the procedure is complete.  Note that resizing can 
take quite some time (hours, even) depending on the size of the EBS volume in 
question.


On Dec 27, 2012, at 10:09 AM, "Sun, Wenping [USA]"  wrote:

> Thanks for the information. Would you help providing further information on 
> expanding ebs volume via cloudman UI? 
> Thank you in advance,
> Kathryn
> 
> -Original Message-
> From: dannonba...@me.com [mailto:dannonba...@me.com] 
> Sent: Thursday, December 27, 2012 10:03 AM
> To: Sun, Wenping [USA]
> Cc: galaxy-u...@bx.psu.edu
> Subject: [External] Re: [galaxy-user] galaxy cluster nodes from the 
> cloudlaunch site
> 
> 
> The root size for the worker nodes doesn't matter.  The only thing relevant 
> to Galaxy here are the available compute units and memory.
> The only storage and working space used is actually attached to the master 
> node (the EBS volume you configure at initial launch) and shared over NFS 
> with the workers.  If you find yourself needing more space, you can expand 
> this volume through the cloudman UI if you want.
> 
> 
> 
> -Dannon
> 
> 
> 
> Sun, Wenping [USA] wrote:
> 
> 
> 
> .sanitized-message p.MsoNormal, .sanitized-message li.MsoNormal, 
> .sanitized-message div.MsoNormal { margin : 0in; margin-bottom :
> .0001pt; font-size : 11.0pt; font-family : "Calibri","sans-serif"; } 
> .sanitized-message a:link, .sanitized-message span.MsoHyperlink { color : 
> blue; text-decoration : underline; } .sanitized-message a:visited, 
> .sanitized-message span.MsoHyperlinkFollowed { color :
> purple; text-decoration : underline; } .sanitized-message
> span.EmailStyle17 { font-family : "Calibri","sans-serif"; color :
> windowtext; } .sanitized-message .MsoChpDefault { font-family :
> "Calibri","sans-serif"; } .sanitized-message div.WordSection1 { }
> 
> 
> Dear Galaxy users,
> 
> I created galaxy instance using galaxy ami the first time. When I re- launch 
> via cloudlaunch site the 2nd time, I have question on adding cluster nodes. 
> There are several pull-down options for the nodes type, no matter which type 
> I choose, they always generate nodes with only 15gb. Is there other option I 
> can have option to define the root space for the nodes?
> 
> Thank you,
> Kathryn
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Re: [galaxy-user] [External] Re: galaxy cloudman login and aws instance

[Dannon Baker]

On Dec 20, 2012, at 2:52 PM, "Sun, Wenping [USA]"  wrote:
> The problem is that if use usegalaxy.org/cloudlaunch to restart galaxy, it 
> will launch to main.g2.bx.psu.edu, where I have no control on the data 
> security and running queues. Meanwhile, the correspondingly initiated ec2 
> instance is brand new and has no previous work records to track with. 

This isn't quite correct, but I think I see the confusion.

When you launch an instance using usegalaxy.org/cloudlaunch it actually does 
start an instance in the cloud.  A link to your new instance should be 
presented to you on a page saying something like "While it may take a few 
moments to boot, you will be able to access the cloud control panel at ".  If you don't click on that link to your new instance but 
instead just click "Analyze Data" in the masthead of that page you're going to 
go back to usegalaxy.org, which is the same server as main.g2.bx.psu.edu.

So, for your use in the cloud you want to launch using 
usegalaxy.org/cloudlaunch, but make sure you're actually *using* the instance 
this starts for you, and *not* galaxyproject.org(main.g2.bx.psu.edu), even 
though we use that server to launch your personal cloud instance.
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Re: [galaxy-user] [External] Re: galaxy cloudman login and aws instance

[Dannon Baker]

On Dec 20, 2012, at 2:33 PM, "Sun, Wenping [USA]"  wrote:

> Thank you very much for the information.
> 
> For the last part of using ec2 instances at aws, is there an option that I 
> can control galaxy's operation at aws site? This way I can start/stop the 
> instance when I need. I am not willing to terminate the instance since 
> everything will be lost. 

We'd recommend you not ever stop/start through the aws console -- this is 
basically guaranteed to cause problems with your instance.  Always use the 
cloudman interface (on your ec2 instance -- http:///cloud) to 
terminate, and then use usegalaxy.org/cloudlaunch to restart it.

> Meantime, I am wondering the data structure on ec2 galaxy instance. Where is 
> the location for the data uploaded from the galaxy gui? If I ssh the Ubuntu, 
> where is the data directory for holding the work?

Everything will be in /mnt/galaxyData/files (which is symlinked to 
/mnt/galaxyTools/galaxy-central/database/files).  Note that the filenames will 
be by id (like files/000/dataset_001.dat is dataset id 1, etc), and not 
particularly accessible in this format without a little extra legwork.
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Re: [galaxy-user] [External] Re: galaxy cloudman login and aws instance

[Dannon Baker]

The ec2 instance is your personal instance that you have complete control over 
for customization, you don't have a personal quota, nobody else will be waiting 
in line to run jobs, etc.  

The server at main.g2.bx.psu.edu is our public galaxy instance that we provide 
and administer, but because it's a public service we do have quotas and 
sometimes processing queues, and so on.

Regarding data security, here's the relevant snippet from the public galaxy 
welcome page:

"""This is a free, public, internet accessible resource. Data transfer and data 
storage are not encrypted. If there are restrictions on the way your research 
data can be stored and used, please consult your local institutional review 
board or the project PI before uploading it to any public site, including this 
Galaxy server. If you have protected data, large data storage requirements, or 
short deadlines you are encouraged to setup your own local Galaxy instance or 
run Galaxy on the cloud."""

Lastly, for aws, you don't *have* to terminate the ec2 instance and start it 
back up when you want to use it, but remember that for every hour of use Amazon 
does bill you.  If you aren't running any jobs on the instance, it would make 
sense to terminate it and start it back up when you want it again.

On Dec 20, 2012, at 1:52 PM, "Sun, Wenping [USA]"  wrote:

> Thanks. 
> 
> When I use main.g2.bx.psu.edu to access the galaxy, I did see the ec2 
> instance initiated from my aws console. Why this happen and what this 
> instance doing?
> 
> Meantime, what is the data security on main.g2.bx.psu.edu? 
> 
> If I use aws instance for the data works, do I have to terminate the ec2 
> instances/cluster and then launch the instance every time? 
> 
> Thank you,
> Kathryn
> 
> -Original Message-
> From: Dannon Baker [mailto:dannonba...@me.com] 
> Sent: Thursday, December 20, 2012 1:43 PM
> To: Sun, Wenping [USA]
> Cc: galaxy-u...@bx.psu.edu
> Subject: Re: [External] Re: [galaxy-user] galaxy cloudman login and aws 
> instance
> 
> Ahh, ok.  If you want to work exclusively on main and don't have the need for 
> a cloud instance, just terminate (and permanently delete, if desired) cloud 
> instances through the cloudman interface and keep using main.g2.bx.psu.edu.
> 
> -Dannon
> 
> 
> On Dec 20, 2012, at 1:41 PM, "Sun, Wenping [USA]"  wrote:
> 
>> Thanks and my question is--
>> 
>> How to shutting down the cloud if working on main.g2.bx.psu.edu?
>> 
>> Thanks,
>> Kathryn
>> 
>> -Original Message-
>> From: Dannon Baker [mailto:dannonba...@me.com]
>> Sent: Thursday, December 20, 2012 1:38 PM
>> To: Sun, Wenping [USA]
>> Cc: galaxy-u...@bx.psu.edu
>> Subject: [External] Re: [galaxy-user] galaxy cloudman login and aws 
>> instance
>> 
>> It looks like you've worked on both the public galaxy site we provide 
>> (main.g2.bx.psu.edu) and your own cloud instance.  Data on the public 
>> instance won't be automatically migrated to the cloud instance and vice 
>> versa.
>> 
>> All work done on the cloud site will remain there and persist after 
>> termination and restart of that cloud cluster.  Work on main.g2.bx.psu.edu 
>> is completely separate and will remain there.
>> 
>> -Dannon
>> 
>> 
>> On Dec 20, 2012, at 12:44 PM, "Sun, Wenping [USA]"  
>> wrote:
>> 
>>> Dear galaxy members,
>>> 
>>> I have question on galaxy running on cloud with the issue of authorization 
>>> matter.
>>> 
>>> I have launched aws galaxy cloudman instances to work with, shutting 
>>> down the cluster afterwards. Then the 2nd time here are the steps 
>>> that I did-
>>> 
>>> 1.   Launch the galaxy at cloudlaunch site
>>> 2.   Register and then log in
>>> 3.   Worked with data uploading and processing (the login information 
>>> can see from pull-down menu), as well as the data history
>>> 
>>> 
>>> 
>>> 4.   Go to aws console to check, find the instance is running
>>> 5.   Copy the dns site followed by /cloud to check the cluster nodes, 
>>> click "access galaxy" button there
>>> 6.   On the galaxy window choose user login
>>> 7.   And here is the window I have - I cannot login and no history data 
>>> there.
>>> 
>>> 
>>> 
>>> 
>>> My question:
>>> it seems that the two galaxy access is not the same. I rather to use the 
>>> site from cloudlaunch site if it is preferred. However, I still have to go 
>>>

Re: [galaxy-user] [External] Re: galaxy cloudman login and aws instance

[Dannon Baker]

Ahh, ok.  If you want to work exclusively on main and don't have the need for a 
cloud instance, just terminate (and permanently delete, if desired) cloud 
instances through the cloudman interface and keep using main.g2.bx.psu.edu.

-Dannon


On Dec 20, 2012, at 1:41 PM, "Sun, Wenping [USA]"  wrote:

> Thanks and my question is--
> 
> How to shutting down the cloud if working on main.g2.bx.psu.edu?
> 
> Thanks,
> Kathryn
> 
> -----Original Message-
> From: Dannon Baker [mailto:dannonba...@me.com] 
> Sent: Thursday, December 20, 2012 1:38 PM
> To: Sun, Wenping [USA]
> Cc: galaxy-u...@bx.psu.edu
> Subject: [External] Re: [galaxy-user] galaxy cloudman login and aws instance
> 
> It looks like you've worked on both the public galaxy site we provide 
> (main.g2.bx.psu.edu) and your own cloud instance.  Data on the public 
> instance won't be automatically migrated to the cloud instance and vice versa.
> 
> All work done on the cloud site will remain there and persist after 
> termination and restart of that cloud cluster.  Work on main.g2.bx.psu.edu is 
> completely separate and will remain there.
> 
> -Dannon
> 
> 
> On Dec 20, 2012, at 12:44 PM, "Sun, Wenping [USA]"  
> wrote:
> 
>> Dear galaxy members,
>> 
>> I have question on galaxy running on cloud with the issue of authorization 
>> matter.
>> 
>> I have launched aws galaxy cloudman instances to work with, shutting 
>> down the cluster afterwards. Then the 2nd time here are the steps that 
>> I did-
>> 
>> 1.   Launch the galaxy at cloudlaunch site
>> 2.   Register and then log in
>> 3.   Worked with data uploading and processing (the login information 
>> can see from pull-down menu), as well as the data history
>> 
>> 
>> 
>> 4.   Go to aws console to check, find the instance is running
>> 5.   Copy the dns site followed by /cloud to check the cluster nodes, 
>> click "access galaxy" button there
>> 6.   On the galaxy window choose user login
>> 7.   And here is the window I have - I cannot login and no history data 
>> there.
>> 
>> 
>> 
>> 
>> My question:
>> it seems that the two galaxy access is not the same. I rather to use the 
>> site from cloudlaunch site if it is preferred. However, I still have to go 
>> to the instance DNS site for shutting down the instance/cluster to avoid aws 
>> unnecessary charge. And, if I need to add cluster nodes, I still need to go 
>> to the DNS site.
>> 
>> What is the appropriate procedure I need to follow to retain the data 
>> history and log in between two accesses, especially while shutting down and 
>> restart?
>> 
>> I really appreciate your inputs and helps!
>> Kind regards,
>> Kathryn
>> ___
>> The Galaxy User list should be used for the discussion of Galaxy 
>> analysis and other features on the public server at usegalaxy.org.  
>> Please keep all replies on the list by using "reply all" in your mail 
>> client.  For discussion of local Galaxy instances and the Galaxy 
>> source code, please use the Galaxy Development list:
>> 
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>> 
>> To manage your subscriptions to this and other Galaxy lists, please 
>> use the interface at:
>> 
>> http://lists.bx.psu.edu/
> 

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Re: [galaxy-user] galaxy cloudman login and aws instance

[Dannon Baker]

It looks like you've worked on both the public galaxy site we provide 
(main.g2.bx.psu.edu) and your own cloud instance.  Data on the public instance 
won't be automatically migrated to the cloud instance and vice versa.

All work done on the cloud site will remain there and persist after termination 
and restart of that cloud cluster.  Work on main.g2.bx.psu.edu is completely 
separate and will remain there.

-Dannon


On Dec 20, 2012, at 12:44 PM, "Sun, Wenping [USA]"  wrote:

> Dear galaxy members,
>  
> I have question on galaxy running on cloud with the issue of authorization 
> matter.
>  
> I have launched aws galaxy cloudman instances to work with, shutting down the 
> cluster afterwards. Then the 2nd time here are the steps that I did—
>  
> 1.   Launch the galaxy at cloudlaunch site
> 2.   Register and then log in
> 3.   Worked with data uploading and processing (the login information can 
> see from pull-down menu), as well as the data history
>  
> 
>  
> 4.   Go to aws console to check, find the instance is running
> 5.   Copy the dns site followed by /cloud to check the cluster nodes, 
> click “access galaxy” button there
> 6.   On the galaxy window choose user login
> 7.   And here is the window I have – I cannot login and no history data 
> there.
>  
> 
>  
>  
> My question:
> it seems that the two galaxy access is not the same. I rather to use the site 
> from cloudlaunch site if it is preferred. However, I still have to go to the 
> instance DNS site for shutting down the instance/cluster to avoid aws 
> unnecessary charge. And, if I need to add cluster nodes, I still need to go 
> to the DNS site.
>  
> What is the appropriate procedure I need to follow to retain the data history 
> and log in between two accesses, especially while shutting down and restart?
>  
> I really appreciate your inputs and helps!
> Kind regards,
> Kathryn
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
> 
>  http://lists.bx.psu.edu/listinfo/galaxy-dev
> 
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
> 
>  http://lists.bx.psu.edu/


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Re: [galaxy-user] [External] Re: question on galaxy reference genome window

[Dannon Baker]

On Dec 19, 2012, at 11:09 AM, "Sun, Wenping [USA]"  wrote:
> I also have the preconfigured cloud instance set up recently. However, when I 
> stopped the instances (master and cluster nodes) from aws, I couldn't get the 
> galaxy web running again (the instance running however the DNS not able to 
> access). What is the right steps to stop the instances and restart it next 
> time?

The cloud deployment isn't designed to be stopped/started through the AWS 
console -- that'll definitely cause problems.  Instead, just terminate the 
instance through the cloudman interface and when you want to use the cluster 
again simply use the same clustername and start a new instance.  The old data 
will be automatically mounted (the cluster details are saved in S3 and the data 
is all on an EBS volume that's persisted in your account) and you'll be right 
back where you left off.
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Re: [galaxy-user] question on galaxy reference genome window

[Dannon Baker]

Kathryn,

Are you using the galaxy cloud configuration provided by the team, or have you 
installed your own galaxy on a cloud instance?

It sounds like the latter, in which case you'll need to configure reference as 
detailed here: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup.  You 
may also want to experiment with using the preconfigured cloud instances, see 
this page for more information on those: http://wiki.galaxyproject.org/CloudMan

-Dannon

On Dec 18, 2012, at 2:21 PM, "Sun, Wenping [USA]"  wrote:

> Dear Galaxy members,
>  
> I am new to galaxy and just installed galaxy on aws cloud. I am testing how 
> it works and have the following question below:
>  
> 1.   I tried to test bowtie2 with the dataset I uploaded, however, the 
> window for reference genome is very narrow and nothing from pull-down menu 
> can be selected. When I omit that option to execute bowtie2, galaxy give 
> error message for requesting reference genome. I am using hg19, should I 
> upload myself? If so, how?
> 2.   Same error happen for me to run fastqc --- the reference genome 
> selection window is way too narrow and nothing can be selected
>  
> Thank you very much for your inputs and helps!
> Kind regards,
> Kathryn
>  
> ___
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> please use the interface at:
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Re: [galaxy-user] Galaxy server configuration - what is [server:main]?

[Dannon Baker]

That's just the section demarcation stating that everything following (until 
the next such bracketed line) is a property of the 'server:main' section -- 
there should be no need to change that, though you can certainly change any of 
the properties within the section as needed.

-Dannon


On Nov 16, 2012, at 8:59 AM, greg  wrote:

> I see this setting at the top of universe_wsgi.ini:
> 
> # Configuration of the internal HTTP server.
> 
> [server:main]
> 
> I'm confused what that's for.  Do I need to change it?
> 
> Thanks,
> 
> Greg
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Re: [galaxy-user] Teaching GALAXY

[Dannon Baker]

Lei -

It looks like you have two worker nodes, but both are currently listed as 
non-idle, yet have low load.  My guess is that something has gone wrong with 
the SGE configuration causing jobs to simply wait in the queue.  If you look at 
the contents of qconf and qstat on the admin page, does it look like there are 
jobs backed up and/or worker nodes processing the queue?  Depending on how 
comfortable you are working with SGE, it might be easiest to just click 
"restart" for SGE in the admin panel and see if everything goes back to normal.

-Dannon


On Nov 8, 2012, at 12:43 PM, Lei Yan  wrote:

> Dear Dannon,
> 
> My name is Lei Yan, and I am a systems administrator at UTHSC.
> I installed a Cloud Galaxy on the Amazon EC2 about two months ago, and most 
> functions work well at that time.
> http://galaxycloud.genenetwork.org/
> But from the day before yesterday, jobs were hung up always. In my opinion, I 
> didn’t find any reasons, because all look correct from Galaxy Admin page (see 
> attachments please).
> Would you please help us to check it? I can give you the administrator 
> password if you need.
> Thanks so much.
> 
> 
> Lei Yan
> leiyan2...@gmail.com
> UTHSC
> 
> 
> 
> On Wed, Nov 7, 2012 at 4:07 PM, Larry Reiter  wrote:
> Dannon,
> 
> Maybe you can, but not through me.  I'm just a lowly user and biologist.  You 
> would have to contact the guy who did the installation and runs the server: 
> Lei Yan (leiyan2...@gmail.com)
> 
> I would think he would be receptive to some help, so you should mail him.
> 
> LTR
> 
> On 11/7/12 4:05 PM, Dannon Baker wrote:
>> Main will complete the jobs eventually, though obviously that's not 
>> particularly useful in the context of your class today.  How is your cloud 
>> instance set up?  Cloud or local instances should be the best and most 
>> reliable option for teaching with and I'd definitely like to figure out why 
>> yours failed.
>> 
>> -Dannon
>> 
>> 
>> On Nov 7, 2012, at 3:57 PM, Larry Reiter 
>> 
>>  wrote:
>> 
>> 
>>> Dannon,
>>> 
>>> Thanks for getting back to me.  Both the local cloud install and the main 
>>> server are frozen.  Well, not exactly frozen.  I can still rename or delete 
>>> jobs, etc.  I can even switch histories and such, but I can't get it to run 
>>> even simple jobs - like taking a demo file and running Fastq Groomer.  I 
>>> realize the load is high today on the main server, but we were able to get 
>>> jobs to run right up until we tried to MAP using Bowtie for Illumina.  At 
>>> that point, all members of the class - and me - could not go any further 
>>> (i.e. jobs are grey and never start to run).  Class ended almost three 
>>> hours ago.
>>> 
>>> Does this help?
>>> 
>>> LTR
>>> 
>>> On 11/7/12 2:52 PM, Dannon Baker wrote:
>>> 
>>>> Can you describe more about what is broken with your cloud install? 
>>>> 
>>>> Regarding main - the server has been under heavy load today and, while it 
>>>> shouldn't remain frozen, might be slow to dispatch and, depending on the 
>>>> type, execute) jobs.
>>>> 
>>>> -Dannon
>>>> 
>>>> On Nov 7, 2012, at 1:12 PM, Larry Reiter 
>>>> 
>>>> 
>>>> 
>>>>  wrote:
>>>> 
>>>> 
>>>> 
>>>>> Tried to teach a class today on ChipSeq analysis, but the local Cloud 
>>>>> install is broken and then the Penn server froze on us.  Is there 
>>>>> something I should know?
>>>>> 
>>>>> LTR
>>>>> 
>>>>> -- 
>>>>> Lawrence T. Reiter, Ph.D.
>>>>> Associate Professor, Department of Neurology
>>>>> 855 Monroe Ave., Link 415
>>>>> Memphis, TN 38163
>>>>> 
>>>>> 
>>>>> 901-448-2635
>>>>>  (Office)
>>>>> 
>>>>> 901-448-7440
>>>>>  (FAX)
>>>>> 
>>>>> 901-448-7443
>>>>>  (Lab)
>>>>> e-mail: 
>>>>> 
>>>>> lrei...@uthsc.edu
>>>>> 
>>>>> 
>>>>> 
>>>>> Reiter Faculty Page
>>>>> Reiter Citation Index
>>>>> Tooth Study
>>>>> ___
>>>>> The Galaxy User list should be used for the discussion of
>>>>> Galaxy analysis and other fe

Re: [galaxy-user] tophat

[Dannon Baker]

It isn't normal, but this can happen during periods of extremely high load like 
we're currently experiencing.  If you leave your jobs in the queue, they'll 
execute as soon as possible - don't cancel or restart your jobs as this will 
only move them to the back of the queue and delay completion.

-Dannon

On Nov 8, 2012, at 5:13 AM, "Vevis, Christis"  
wrote:

> Hi all,
>  
> I am trying to perform tophat for illumina from the main server of galaxy and 
> is in queue for 24 hours…is that normal??
>  
> Regards
>  
> Kristis Vevis, PhD Student
> Cell Biology
> UCL Institute of Ophthalmology
> 11-43 Bath Street
> London
> EC1V 9EL, UK
> 020 7608 4067
>  
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> 
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> please use the interface at:
> 
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Re: [galaxy-user] Teaching GALAXY

[Dannon Baker]

NGS jobs are experiencing significant delays at this time due to load -- we're 
looking into it.  Regarding the local install I'd have to recommend pinging the 
administrator on site there -- they should be able to help out.

-Dannon

On Nov 8, 2012, at 10:44 AM, Larry Reiter  wrote:

> It looks like both the main server and our local install are frozen.  Nothing 
> has run since we started yesterday at about 11:30am.  Anybody know why?
> 
> LTR
> 
> On 11/7/12 4:05 PM, Dannon Baker wrote:
>> Main will complete the jobs eventually, though obviously that's not 
>> particularly useful in the context of your class today.  How is your cloud 
>> instance set up?  Cloud or local instances should be the best and most 
>> reliable option for teaching with and I'd definitely like to figure out why 
>> yours failed.
>> 
>> -Dannon
>> 
>> 
>> On Nov 7, 2012, at 3:57 PM, Larry Reiter 
>> 
>>  wrote:
>> 
>> 
>>> Dannon,
>>> 
>>> Thanks for getting back to me.  Both the local cloud install and the main 
>>> server are frozen.  Well, not exactly frozen.  I can still rename or delete 
>>> jobs, etc.  I can even switch histories and such, but I can't get it to run 
>>> even simple jobs - like taking a demo file and running Fastq Groomer.  I 
>>> realize the load is high today on the main server, but we were able to get 
>>> jobs to run right up until we tried to MAP using Bowtie for Illumina.  At 
>>> that point, all members of the class - and me - could not go any further 
>>> (i.e. jobs are grey and never start to run).  Class ended almost three 
>>> hours ago.
>>> 
>>> Does this help?
>>> 
>>> LTR
>>> 
>>> On 11/7/12 2:52 PM, Dannon Baker wrote:
>>> 
>>>> Can you describe more about what is broken with your cloud install? 
>>>> 
>>>> Regarding main - the server has been under heavy load today and, while it 
>>>> shouldn't remain frozen, might be slow to dispatch and, depending on the 
>>>> type, execute) jobs.
>>>> 
>>>> -Dannon
>>>> 
>>>> On Nov 7, 2012, at 1:12 PM, Larry Reiter 
>>>> 
>>>> 
>>>> 
>>>>  wrote:
>>>> 
>>>> 
>>>> 
>>>>> Tried to teach a class today on ChipSeq analysis, but the local Cloud 
>>>>> install is broken and then the Penn server froze on us.  Is there 
>>>>> something I should know?
>>>>> 
>>>>> LTR
>>>>> 
>>>>> -- 
>>>>> Lawrence T. Reiter, Ph.D.
>>>>> Associate Professor, Department of Neurology
>>>>> 855 Monroe Ave., Link 415
>>>>> Memphis, TN 38163
>>>>> 
>>>>> 901-448-2635 (Office)
>>>>> 901-448-7440 (FAX)
>>>>> 901-448-7443 (Lab)
>>>>> e-mail: 
>>>>> 
>>>>> lrei...@uthsc.edu
>>>>> 
>>>>> 
>>>>> 
>>>>> Reiter Faculty Page
>>>>> Reiter Citation Index
>>>>> Tooth Study
>>>>> ___
>>>>> The Galaxy User list should be used for the discussion of
>>>>> Galaxy analysis and other features on the public server
>>>>> at usegalaxy.org.  Please keep all replies on the list by
>>>>> using "reply all" in your mail client.  For discussion of
>>>>> local Galaxy instances and the Galaxy source code, please
>>>>> use the Galaxy Development list:
>>>>> 
>>>>>  
>>>>> 
>>>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>>>> 
>>>>> 
>>>>> 
>>>>> To manage your subscriptions to this and other Galaxy lists,
>>>>> please use the interface at:
>>>>> 
>>>>>  
>>>>> 
>>>>> http://lists.bx.psu.edu/
>>> 
>>> -- 
>>> Lawrence T. Reiter, Ph.D.
>>> Associate Professor, Department of Neurology
>>> 855 Monroe Ave., Link 415
>>> Memphis, TN 38163
>>> 
>>> 901-448-2635 (Office)
>>> 901-448-7440 (FAX)
>>> 901-448-7443 (Lab)
>>> e-mail: 
>>> lrei...@uthsc.edu
>>> 
>>> 
>>> Reiter Faculty Page
>>> Reiter Citation Index
>>> Tooth Study
>>> 
> 
> 
> -- 
> Lawrence T. Reiter, Ph.D.
> Associate Professor, Department of Neurology
> 855 Monroe Ave., Link 415
> Memphis, TN 38163
> 
> 901-448-2635 (Office)
> 901-448-1160 (FAX)
> 901-448-7443 (Lab)
> e-mail: lrei...@uthsc.edu
> 
> Reiter Faculty Page
> Reiter Citation Index

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Re: [galaxy-user] Teaching GALAXY

[Dannon Baker]

Main will complete the jobs eventually, though obviously that's not 
particularly useful in the context of your class today.  How is your cloud 
instance set up?  Cloud or local instances should be the best and most reliable 
option for teaching with and I'd definitely like to figure out why yours failed.

-Dannon


On Nov 7, 2012, at 3:57 PM, Larry Reiter  wrote:

> Dannon,
> 
> Thanks for getting back to me.  Both the local cloud install and the main 
> server are frozen.  Well, not exactly frozen.  I can still rename or delete 
> jobs, etc.  I can even switch histories and such, but I can't get it to run 
> even simple jobs - like taking a demo file and running Fastq Groomer.  I 
> realize the load is high today on the main server, but we were able to get 
> jobs to run right up until we tried to MAP using Bowtie for Illumina.  At 
> that point, all members of the class - and me - could not go any further 
> (i.e. jobs are grey and never start to run).  Class ended almost three hours 
> ago.
> 
> Does this help?
> 
> LTR
> 
> On 11/7/12 2:52 PM, Dannon Baker wrote:
>> Can you describe more about what is broken with your cloud install? 
>> 
>> Regarding main - the server has been under heavy load today and, while it 
>> shouldn't remain frozen, might be slow to dispatch and, depending on the 
>> type, execute) jobs.
>> 
>> -Dannon
>> 
>> On Nov 7, 2012, at 1:12 PM, Larry Reiter 
>> 
>>  wrote:
>> 
>> 
>>> Tried to teach a class today on ChipSeq analysis, but the local Cloud 
>>> install is broken and then the Penn server froze on us.  Is there something 
>>> I should know?
>>> 
>>> LTR
>>> 
>>> -- 
>>> Lawrence T. Reiter, Ph.D.
>>> Associate Professor, Department of Neurology
>>> 855 Monroe Ave., Link 415
>>> Memphis, TN 38163
>>> 
>>> 901-448-2635 (Office)
>>> 901-448-7440 (FAX)
>>> 901-448-7443 (Lab)
>>> e-mail: 
>>> lrei...@uthsc.edu
>>> 
>>> 
>>> Reiter Faculty Page
>>> Reiter Citation Index
>>> Tooth Study
>>> ___
>>> The Galaxy User list should be used for the discussion of
>>> Galaxy analysis and other features on the public server
>>> at usegalaxy.org.  Please keep all replies on the list by
>>> using "reply all" in your mail client.  For discussion of
>>> local Galaxy instances and the Galaxy source code, please
>>> use the Galaxy Development list:
>>> 
>>>  
>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>> 
>>> 
>>> To manage your subscriptions to this and other Galaxy lists,
>>> please use the interface at:
>>> 
>>>  
>>> http://lists.bx.psu.edu/
> 
> 
> -- 
> Lawrence T. Reiter, Ph.D.
> Associate Professor, Department of Neurology
> 855 Monroe Ave., Link 415
> Memphis, TN 38163
> 
> 901-448-2635 (Office)
> 901-448-7440 (FAX)
> 901-448-7443 (Lab)
> e-mail: lrei...@uthsc.edu
> 
> Reiter Faculty Page
> Reiter Citation Index
> Tooth Study

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Re: [galaxy-user] Teaching GALAXY

[Dannon Baker]

Can you describe more about what is broken with your cloud install? 

Regarding main - the server has been under heavy load today and, while it 
shouldn't remain frozen, might be slow to dispatch and, depending on the type, 
execute) jobs.

-Dannon

On Nov 7, 2012, at 1:12 PM, Larry Reiter  wrote:

> Tried to teach a class today on ChipSeq analysis, but the local Cloud install 
> is broken and then the Penn server froze on us.  Is there something I should 
> know?
> 
> LTR
> 
> -- 
> Lawrence T. Reiter, Ph.D.
> Associate Professor, Department of Neurology
> 855 Monroe Ave., Link 415
> Memphis, TN 38163
> 
> 901-448-2635 (Office)
> 901-448-7440 (FAX)
> 901-448-7443 (Lab)
> e-mail: lrei...@uthsc.edu
> 
> Reiter Faculty Page
> Reiter Citation Index
> Tooth Study
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
> 
>  http://lists.bx.psu.edu/listinfo/galaxy-dev
> 
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
> 
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Re: [galaxy-user] Batch jobs...

[Dannon Baker]

Connect the Input Dataset workflow step to the dataset input of the step you'd like to run multiple inputs across, like below.  With that example workflow, I can select a batch of inputs that will *all* be mapped with BWA.On Oct 30, 2012, at 9:04 PM, neil.burd...@csiro.au wrote:Thanks Dannon,   I can see them now but how do I use them now? As I now have 3 steps:Input File (as before)Input Dataset (new)Atlas list (as before)I select the "Input file" in step 1, and atlases in step 3 (as before) and I can select multiple files for the Input Dataset (but how does that tie into step  1 and 3 as its not connected on the workflow diagram? Neil-Original Message-----From: Dannon Baker [mailto:dannonbaker@me.com] Sent: Wednesday, 31 October 2012 10:54 AMTo: Burdett, Neil (ICT Centre, Herston - RBWH)Cc: bjoern.gruen...@pharmazie.uni-freiburg.de; galaxy-user@lists.bx.psu.eduSubject: Re: [galaxy-user] Batch jobs...Ahh, I see what's going on.  Galaxy relies on the "Input Dataset" step for this feature.  If you use these in your workflow, Galaxy will be able to perform the batch execution.  Find them in the workflow editor under "Workflow control" -> inputs.-DannonOn Oct 30, 2012, at 8:46 PM, neil.burd...@csiro.au wrote:Do i need to modify a setting in universe_wsgi.ini or somewhere then ? As I attach screenshots of what I've got (I have a recent subversion checkout)...ThanksNeil___
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Re: [galaxy-user] Batch jobs...

[Dannon Baker]

Ahh, I see what's going on.  Galaxy relies on the "Input Dataset" step for this 
feature.  If you use these in your workflow, Galaxy will be able to perform the 
batch execution.  Find them in the workflow editor under "Workflow control" -> 
inputs.

-Dannon


On Oct 30, 2012, at 8:46 PM, neil.burd...@csiro.au wrote:

> Do i need to modify a setting in universe_wsgi.ini or somewhere then ? As I 
> attach screenshots of what I've got (I have a recent subversion checkout)...
>  
> Thanks
> Neil
>  
>  
> 
>  
>  
>  
> 

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Re: [galaxy-user] Batch jobs...

[Dannon Baker]

They were introduced and described in this news brief (with screenshots!): 
http://wiki.g2.bx.psu.edu/DevNewsBriefs/2011_05_20

Hope this helps,

Dannon


On Oct 30, 2012, at 7:33 PM, neil.burd...@csiro.au wrote:

> Thanks Bjorn,
> But I can't seem to locate the symbol/icon (looks like papers). 
> Is there any documentation where it is located on the screen?
> 
> Thanks
> Neil
> 
> -Original Message-
> From: Björn Grüning [mailto:bjoern.gruen...@pharmazie.uni-freiburg.de] 
> Sent: Friday, 26 October 2012 9:47 PM
> To: Burdett, Neil (ICT Centre, Herston - RBWH)
> Cc: galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] Batch jobs...
> 
> Hi Neil,
> 
> if you run your workflow, there is small little symbol/icon (looks like 
> papers). If you click these ... you can select multiple input files at once. 
> Also you can probably use the Galaxy API for your task [1].
> 
> Happy research!
> Bjoern
> 
> [1] http://wiki.g2.bx.psu.edu/Learn/API
> 
>> Hi,
>>   I've created a workflow that works well. The workflow accepts 2 input 
>> files. After uploading all my input files (there is a lot). How can I batch 
>> the process, because I don't want to select files manually and run each job 
>> manually. Is there a way to batch this action?
>> 
>> Thanks
>> Neil
>> ___
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>> analysis and other features on the public server at usegalaxy.org.  
>> Please keep all replies on the list by using "reply all" in your mail 
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>> 
>> To manage your subscriptions to this and other Galaxy lists, please 
>> use the interface at:
>> 
>>  http://lists.bx.psu.edu/
> 
> --
> Björn Grüning
> Albert-Ludwigs-Universität Freiburg
> Institute of Pharmaceutical Sciences
> Pharmaceutical Bioinformatics
> Hermann-Herder-Strasse 9
> D-79104 Freiburg i. Br.
> 
> Tel.:  +49 761 203-4872
> Fax.:  +49 761 203-97769
> E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
> Web: http://www.pharmaceutical-bioinformatics.org/
> 
> Tel.:  +49 761 203-4872
> Fax.:  +49 761 203-97769
> E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
> Web: http://www.pharmaceutical-bioinformatics.org/
> 
> 
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Re: [galaxy-user] Galaxy not showing my reference genome in Drop down for BowTie

[Dannon Baker]

Looking at your screenshot, you have "Use a built-in index" selected.  If you 
change this to "Use one from the history", do you see your fasta file listed?

-Dannon

On Oct 10, 2012, at 9:02 AM, greg  wrote:

> Thanks Jen.  But it looks like the datatype was already set to fasta.
> I tried setting it again and saving but it didn't seem to help.
> 
> Is there anything else I can try?
> 
> thanks,
> 
> Greg
> 
> On Tue, Oct 9, 2012 at 9:10 PM, Jennifer Jackson  wrote:
>> Hi Greg,
>> 
>> Nice pic, it helps! My guess is that the datatype is not assigned as
>> "fasta". To do this, click on the pencil icon for the custom reference
>> genome dataset (#1) to bring up the Edit Attributes forms in the center
>> panel. Then click on the "Datatype" tab and change this to be "fasta" and
>> save.
>> 
>> Full help in our wiki with Custom genomes starts here:
>> http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome
>> 
>> Please let us know if you need more help,
>> 
>> Jen
>> Galaxy team
>> 
>> 
>> 
>> 
>> On 10/9/12 11:08 AM, greg wrote:
>>> 
>>> Hi guys,
>>> 
>>> As shown in the attached screenshot I uploaded a fasta file.  And I
>>> want to use it as my reference genome for running bow tie but it
>>> doesn't appear in the dropdown on the bow tie tool.
>>> 
>>> I'm sure I'm missing something obvious.
>>> 
>>> Thanks,
>>> 
>>> Greg
>>> 
>>> 
>>> 
>>> ___
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>> 
>> 
>> --
>> Jennifer Jackson
>> http://galaxyproject.org
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Re: [galaxy-user] Cloudman share string not working

[Dannon Baker]

Yes, entering the string on the instance's initial configuration dialog will 
always be an option.

-Dannon

On Sep 18, 2012, at 1:20 PM, greg  wrote:

> Thanks Dannon.
> 
> I'm actually writing some documentation that I won't be able to update
> again for a few months.
> 
> Will the old method (entering the share string on the initial
> configuration dialog) be around for a while?
> 
> If so I'll just tell users to do that.
> 
> Thanks,
> 
> Greg
> 
> On Tue, Sep 18, 2012 at 9:51 AM, Dannon Baker  wrote:
>> My hunch is that there's a race condition during boot that I haven't had a 
>> chance to track down and fix yet.  I've actually disabled the share_string 
>> launch parameter using Galaxy's built-in cloudlaunch until this has been 
>> fixed.  You can definitely still use the share string, but start the 
>> instance without specifying it via your launcher (cloudlaunch, 
>> biocloudcentral, or manually in user data) and enter it in the initial 
>> configuration dialog for the instance instead.
>> 
>> -Dannon
>> 
>> On Sep 18, 2012, at 9:44 AM, greg  wrote:
>> 
>>> Hi guys,
>>> 
>>> I entered my share string
>>> "cm-808d863548acae7c2328c39a90f52e29/shared/2012-09-17--19-47" on this
>>> page "https://biocloudcentral.herokuapp.com/launch"; in the field
>>> labeled "Shared cluster string" and click the button to create my
>>> instance.  But then when I log into Cloudman the "Initial Cluster
>>> configuration" dialog is still appearing.
>>> 
>>> I ran the same thing yesterday with an older share string and
>>> everything worked fine.
>>> 
>>> Any ideas what could be going on?  I'm pretty stuck.
>>> 
>>> Thanks,
>>> 
>>> Greg
>>> 
>>> 
>>> This is all I see in the cluster status log (I entered my share string
>>> again on the dialog, the disk status says 0 / 0 and applications and
>>> data lights are yellow, and don't seem to progress):
>>> 
>>> 13:34:46 - Master starting
>>> 13:34:50 - Retrieved file
>>> 'shared/2012-09-17--19-47/shared_instance_file_list.txt' from bucket
>>> 'cm-808d863548acae7c2328c39a90f52e29' to
>>> 'shared_instance_file_list.txt'.
>>> 13:41:29 - Retrieved file
>>> 'shared/2012-09-17--19-47/shared_instance_file_list.txt' from bucket
>>> 'cm-808d863548acae7c2328c39a90f52e29' to
>>> 'shared_instance_file_list.txt'.
>>> 13:41:30 - Retrieved file 'persistent_data.yaml' from bucket
>>> 'cm-c8c215c4c67525d91b3a2598f9e370f7' to 'shared_p_d.yaml'.
>>> 13:41:31 - Created a data volume 'vol-7f2cc105' of size 5GB from
>>> shared cluster's snapshot 'snap-cfa775ba'
>>> 13:41:31 - Saved file 'persistent_data.yaml' to bucket
>>> 'cm-c8c215c4c67525d91b3a2598f9e370f7'
>>> 13:41:31 - Retrieved file 'persistent_data.yaml' from bucket
>>> 'cm-c8c215c4c67525d91b3a2598f9e370f7' to 'pd.yaml'.
>>> ___
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>> 

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Re: [galaxy-user] Cloudman share string not working

[Dannon Baker]

My hunch is that there's a race condition during boot that I haven't had a 
chance to track down and fix yet.  I've actually disabled the share_string 
launch parameter using Galaxy's built-in cloudlaunch until this has been fixed. 
 You can definitely still use the share string, but start the instance without 
specifying it via your launcher (cloudlaunch, biocloudcentral, or manually in 
user data) and enter it in the initial configuration dialog for the instance 
instead.

-Dannon

On Sep 18, 2012, at 9:44 AM, greg  wrote:

> Hi guys,
> 
> I entered my share string
> "cm-808d863548acae7c2328c39a90f52e29/shared/2012-09-17--19-47" on this
> page "https://biocloudcentral.herokuapp.com/launch"; in the field
> labeled "Shared cluster string" and click the button to create my
> instance.  But then when I log into Cloudman the "Initial Cluster
> configuration" dialog is still appearing.
> 
> I ran the same thing yesterday with an older share string and
> everything worked fine.
> 
> Any ideas what could be going on?  I'm pretty stuck.
> 
> Thanks,
> 
> Greg
> 
> 
> This is all I see in the cluster status log (I entered my share string
> again on the dialog, the disk status says 0 / 0 and applications and
> data lights are yellow, and don't seem to progress):
> 
> 13:34:46 - Master starting
> 13:34:50 - Retrieved file
> 'shared/2012-09-17--19-47/shared_instance_file_list.txt' from bucket
> 'cm-808d863548acae7c2328c39a90f52e29' to
> 'shared_instance_file_list.txt'.
> 13:41:29 - Retrieved file
> 'shared/2012-09-17--19-47/shared_instance_file_list.txt' from bucket
> 'cm-808d863548acae7c2328c39a90f52e29' to
> 'shared_instance_file_list.txt'.
> 13:41:30 - Retrieved file 'persistent_data.yaml' from bucket
> 'cm-c8c215c4c67525d91b3a2598f9e370f7' to 'shared_p_d.yaml'.
> 13:41:31 - Created a data volume 'vol-7f2cc105' of size 5GB from
> shared cluster's snapshot 'snap-cfa775ba'
> 13:41:31 - Saved file 'persistent_data.yaml' to bucket
> 'cm-c8c215c4c67525d91b3a2598f9e370f7'
> 13:41:31 - Retrieved file 'persistent_data.yaml' from bucket
> 'cm-c8c215c4c67525d91b3a2598f9e370f7' to 'pd.yaml'.
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Re: [galaxy-user] Attempting to use parallelism in BWA

[Dannon Baker]

Hi Kevin,

I'm not able to reproduce this with python 2.7.  Can you confirm that galaxy is 
indeed using the installed python 2.7 and not, perhaps, 2.4?  The structure of 
python's try/except/finally clause changed with python 2.5 and if you were 
unintentionally running 2.4 that would explain this error.

And lastly, regarding the parallelization of BWA, there's nothing else you need 
to do; setting use_tasked_jobs = True should handle it.

-Dannon


On Jul 17, 2012, at 12:27 PM, Kevin C. Dorff wrote:

> Hi,
> 
> I am using Python 2.7. I am running with an hg checked out, up to date 
> version of "https://bitbucket.org/galaxy/galaxy-dist/";.
> 
> I am very new to Galaxy. I have an instance setup and running locally. I am 
> able to perform routine actions such as uploading files, processing with 
> Picard, and aligning with BWA. I have been able to make the jobs execute out 
> our SGE cluster.
> 
> In order to better utilize my cluster, I attempted to enable parallelism of 
> the tasks that support it (such as BWA) by configuring the universe_wsgi.ini 
> file with the parameter
> 
>use_tasked_jobs = True
> 
> When I do this and attempt execute a BWA alignment on a 4.1Gb fastq file, I 
> am given the error
> 
> Result 256 from mv 
> /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_1/dataset_21.dat
>  
> /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/files/000/dataset_21.dat
> /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_0:
> Traceback (most recent call last):
>   File "./scripts/extract_dataset_part.py", line 25, in ?
> import galaxy.model.mapping #need to load this before we unpickle, in 
> order to setup properties assigned by the mappers
>   File 
> "/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/model/__init__.py",
>  line 13, in ?
> import galaxy.datatypes.registry
>   File 
> "/pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/datatypes/registry.py",
>  line 146
> finally:
>   ^
> SyntaxError: invalid syntax
> The alignment failed.
> 
> If you need the complete error message, contact me and I can supply you with 
> it. It's too large to paste in-line and attachments aren't allowed.
> 
> Is there more I need to do to enable parallel jobs (splitting of input, 
> align, then merge)? 
> 
> Any suggestions are greatly appreciated.
> 
> Kevin
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Re: [galaxy-user] Galaxy in AWS AMI

[Dannon Baker]

>From the log, it looks like your cluster is trying to restart from an existing 
>instance and failing.  This happens (by design) when you use the same cluster 
>name.  Can you send me the galaxy log to see where the failure might be 
>happening?  This is available at:

http:///cloud/root/service_log?service_name=Galaxy&show=all

Additionally, when you go directly to your instance (remove /cloud from the 
url, so it's just http:///), what do you see?

-Dannon


On Jun 13, 2012, at 5:47 PM, Lilach Friedman wrote:

> Hi,
> Can somebody please help me?
> I'm trying for hours to connect to Galaxy on Amazon EC2. I did everything 
> according the instructions, but did not succeed.
> The "Access Galaxy" button in the instance remains grey out.
> I copied the screen print and the log to the attached file.
> Can anyone help me please?
> 
> and another questions: I want to use it to analyze MiSeq results (to align to 
> the human genome). 100 Gb EBS and a large machine are enough? too much?
> 
> Many thanks,
>Lilach.
>  log.docx>___
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Re: [galaxy-user] How to transfer files between two galaxy instances

[Dannon Baker]

The data is not a part of the workflow -- what you want is a history export.

>From the history you want to export, in the history menu, select "Export to 
>File".  This step may take a while depending on the size of your history.  
>Navigate to the link to make sure it's done packaging the history.  If it 
>isn't, you'll see "Still exporting history ; please check back 
>soon".  If it is, a download will automatically start.  You can save this, or 
>just cancel the download (if it's large).

Once the data is ready (the link works), on the destination Galaxy instance, 
select "Import from File" in the history menu.  Put in your link.

This should migrate the entire history.

On May 29, 2012, at 12:08 PM, shamsher jagat wrote:

> Ok. Perhaps I am not understanding the process- I am not making any head way 
> in transfering the data from one Galaxy instance to other. I have uploaded 
> some files in Rutsch lab galaxy instance and have url 
> http://galaxy.tuebingen.mpg.de/workflow/for_direct_import?id=9b305a114b324ccf
>  
> Nothing is happening. Is it possible that some one from Galaxy team can 
> enlist steps of - how to transfer files (data) from one galaxy instance to 
> other please, considering me as a beginer. Thanks. Sorry for pushing this 
> question.
>  
> Vasu
> On Fri, May 25, 2012 at 11:33 AM, Dannon Baker  wrote:
> Hi,
> 
> Just wanted to add a few clarifications here.  It definitely *is* currently 
> possible to transfer a workflow from one instance to another instance that 
> does not have (some or all) of the tools for a particular workflow.
> 
> The error you're running into "No JSON object" means that you likely have the 
> wrong link to your workflow.  The one you want is accessible via the workflow 
> context menu -> Download or Export -> URL for importing into another galaxy.  
> Or, you could just download the raw file if you want and upload that as you 
> figured out.  The format of the correct URL should look like this, note the 
> "for_direct_import" in the string:
> 
> https://main.g2.bx.psu.edu/workflow/for_direct_import?id=53b7bf0869d3e7ee
> 
> As a correction to what was previously said, I would not recommend stripping 
> out tools from an existing workflow prior to export.  When you upload the 
> workflow to a new instance, if tools aren't available you will see something 
> like the following when you edit the workflow, which specifies that the tool 
> is not found:
> 
> 
> 
> And at this point the unrecognized tools can be installed if it's your galaxy 
> server, or if you wish, removed from the workflow via the editor.  This must 
> be done before the workflow will be usable.
> 
> Lastly, workflows don't contain any data, just the organization and 
> parameters of steps for a process.  What it sounds like you're looking for 
> (to get your data there as well) is a history export, which is available 
> through the menu at the top of your history as "Export to File".
> 
> -Dannon
> 
> 
> On May 24, 2012, at 4:06 PM, shamsher jagat wrote:
> 
>> Thanks Jen for the update. I tried following:
>> Go to Ratsch Galaxy instance > workflow> make work flow accessible via link
>> Go to galaxy Penn server
>> Workflow> import workflow URL> galaxy UR
>>  
>> error is
>>  The data content does not appear to be a Galaxy workflow.
>> Exception: No JSON object could be decoded: line 1 column 0 (char 0)
>>  
>> I also downloaded the file from Ratsch serever saved on computer and  use 
>> option of Choose file under import galaxy flow it importe dthe file afetr a 
>> while and when I opened workflow there was no data only steps of the 
>> workflow were there.
>>  
>> Do you have any suggestion wheer I am doing something wrong.
>>  
>> Thanks
> 
> 

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Re: [galaxy-user] How to transfer files between two galaxy instances

[Dannon Baker]

Hi,Just wanted to add a few clarifications here.  It definitely *is* currently possible to transfer a workflow from one instance to another instance that does not have (some or all) of the tools for a particular workflow.The error you're running into "No JSON object" means that you likely have the wrong link to your workflow.  The one you want is accessible via the workflow context menu -> Download or Export -> URL for importing into another galaxy.  Or, you could just download the raw file if you want and upload that as you figured out.  The format of the correct URL should look like this, note the "for_direct_import" in the string:https://main.g2.bx.psu.edu/workflow/for_direct_import?id=53b7bf0869d3e7eeAs a correction to what was previously said, I would not recommend stripping out tools from an existing workflow prior to export.  When you upload the workflow to a new instance, if tools aren't available you will see something like the following when you edit the workflow, which specifies that the tool is not found:And at this point the unrecognized tools can be installed if it's your galaxy server, or if you wish, removed from the workflow via the editor.  This must be done before the workflow will be usable.Lastly, workflows don't contain any data, just the organization and parameters of steps for a process.  What it sounds like you're looking for (to get your data there as well) is a history export, which is available through the menu at the top of your history as "Export to File".-DannonOn May 24, 2012, at 4:06 PM, shamsher jagat wrote:Thanks Jen for the update. I tried following:Go to Ratsch Galaxy instance > workflow> make work flow accessible via linkGo to galaxy Penn serverWorkflow> import workflow URL> galaxy UR error is The data content does not appear to be a Galaxy workflow.Exception: No JSON object could be decoded: line 1 column 0 (char 0) I also downloaded the file from Ratsch serever saved on computer and  use option of Choose file under import galaxy flow it importe dthe file afetr a while and when I opened workflow there was no data only steps of the workflow were there. Do you have any suggestion wheer I am doing something wrong. Thanks___
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Re: [galaxy-user] cuff... errors

[Dannon Baker]

There was a temporary cluster issue, but it looks like jobs are running again.  
Try resubmitting your jobs now, and they should succeed.

-Dannon

On May 1, 2012, at 8:30 PM, Jeremy Coate wrote:

> Hi all,
> FYI, I've gotten the same error recently when trying to run Bowtie (using 
> Galaxy Main).
> Jeremy
> 
> On Tue, May 1, 2012 at 4:37 PM, Richard Mark White  wrote:
> Hi,
> Ive been trying to run cufflinks/cuffdiff but keep getting this error: Job 
> output not returned by PBS: the output datasets were deleted while the job 
> was running, the job was manually dequeued or there was a cluster error.
> 
> is there a system issue or something with my data?
> 
> r
> 
> 
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Re: [galaxy-user] "Server Error"on Main when viewing or downloading FastQC results

[Dannon Baker]

Thanks for reporting this, I see the error and we'll have a fix out shortly.

-Dannon

On Apr 18, 2012, at 9:50 AM, Davis, Wade wrote:

> I've run FastQC successfully on several different files, but I can not 
> download them or view them.  In either. case I receive the following message 
> in my browser (Firefox):
> Server Error
> An error occurred. See the error logs for more information. (Turn debug on to 
> display exception reports here)
> 
> If I go into a history and try to view other FastQC reports that I have 
> viewed before, I get the same error. So I don't think this is a data format 
> or tools issue.
> 
> I searched the archives, and the server error message has been reported 
> before, and was fixed but no details were given.
> 
> Thanks for your help.
> 
> Wade
> 
> 
> 
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Re: [galaxy-user] Screencasts on screencast.g2.bx.psu.edu ?

[Dannon Baker]

Hi Peter,

You should be automatically redirected from screencast.g2.bx.psu.edu to 
http://wiki.g2.bx.psu.edu/Learn/Screencasts, which is the wiki page with a 
listing of all available screencasts.  What browser are you using?

-Dannon


On Apr 18, 2012, at 8:12 AM, Peter van Heusden wrote:

> Hi there
> 
> I'm trying to download the screencasts referenced in the Galaxy ENCODE
> paper (Blankenberg et al 2007). They appear to be on
> screencast.g2.bx.psu.edu, but while that domain resolves, it doesn't
> respond to HTTP requests. Does anyone know where they are currently
> available?
> 
> Thanks,
> Peter
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Re: [galaxy-user] Cloudman - Problem starting shared cluster

[Dannon Baker]

The first thing to check would be to verify that that the bucket and contents 
exist in your account.  Use the AWS console to log in, go to the S3 tab, and 
look for the bucket 'cm-31bf91279e41769ff78af22c1a276ece' and verify the 
/shared/2012-01-12--18-03 folder structure exists.

-Dannon

On Apr 2, 2012, at 12:40 PM, mailing list wrote:

> Hi guys, I'm still stuck on this :-(.
> 
> Are there any log files I could look at to get more details?  I'm
> definitely willing to dive in an get to the bottom of this issue.  Can
> anyone recommend a starting point?
> 
> Thanks again,
> 
> Greg
> 
> On Mon, Apr 2, 2012 at 9:01 AM, mailing list  wrote:
>> Hi guys,
>> 
>> After launching Cloudman on the Initial Cluster Configuration dialog I
>> selected the "Share-an-Instance Cluster" option and put in this share
>> string:
>> cm-31bf91279e41769ff78af22c1a276ece/shared/2012-01-12--18-03
>> 
>> But after that I see this message in the log:
>> 
>> 12:52:19 - Problem copying shared cluster configuration files. Cannot
>> continue with shared cluster initialization.
>> 
>> And nothing else happens after that.  The "applications" status stays
>> yellow, and disk status says "0/0".
>> 
>> Here is some more information about the run:
>> 
>> That sharestring is from a share I made in January.  It worked when I
>> last tested it in January.
>> I launched via the BioCloudCentral wep app.
>> 
>> Other run information:
>> Instance ID i-8523cee2
>> Image ID (AMI)  ami-500cd139
>> Security group  CloudMan
>> Key paircloudman_key_pair
>> Placement (zone)us-east-1b
>> 
>> Let me know what other information would be helpful.
>> 
>> Thanks,
>> 
>> Greg
> 
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Re: [galaxy-user] Problems starting Galaxy Cloudman

[Dannon Baker]

Greg,

The problem here is that the galaxy update failed to merge a change to run.sh 
because of minor customizations it has.  We'll have a long term fix out for 
this soon, but for now what you can do is ssh in to your instance and update 
run.sh yourself prior to restarting galaxy.  All you need to do is add 
'migrated_tools_conf.xml.sample' to the SAMPLES in 
/mnt/galaxyTools/galaxy-central/run.sh, execute `sh run.sh --run-daemon` (or 
restart galaxy again from the admin page) and you should be good to go.

That new AMI you're seeing is not owned by the Galaxy Team, and we don't 
actually know who made it.  Keep using the same galaxy-cloudman-2011-03-22 for 
now (and we'll always have the most up-to-date AMI listed at 
usegalaxy.org/cloud).  Because of Cloudman's modular volume design almost 
nothing resides on the AMI itself, so we can (and do) update the tools and 
index volumes without having to touch it.  So while the AMI reflects a date of 
almost a year old, the galaxy tools volume (and thus the actual Galaxy instance 
you're running) has been updated much more recently.

One last note- if you're updating and copying your tools in every time, you may 
want to try using the 'Persist changes' functionality available in the Cloudman 
admin panel.  Once you've set your instance up how you want, if you click 
'Persist changes to galaxyTools', it'll create a custom snapshot of your tools 
volume that will be used from that point forward with this instance.

Let me know if you have any more issues,

-Dannon

On Mar 9, 2012, at 2:53 AM, Greg Edwards wrote:

> Hi,
> 
> I'm trying to restart my Galaxy Cloudman service, using the same approach 
> that has been successful over the last couple of months ..
> 
>  - launch AMI 861460482541/galaxy-cloudman-2011-03-22 as m1.large
>  - update from Cloudman console
>  - copy in my tools etc etc
>  - restart
>  - away we go, all works
> 
> However today the update fails, the log says ...
> 
> /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
>  RuntimeWarning: __builtin__.file size changed, may indicate binary 
> incompatibility
>   from csamtools import *
> python path is: 
> /mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, 
> /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
>  /mnt/galaxyTools/galaxy-central/eggs/boto-2.2.2-py2.6.egg, 
> /mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg, 
> /mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs4.egg,
>  
> /mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
>  
> /mnt/galaxyTools/galaxy-central/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
>  /mnt/galaxyTools/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg, 
> /mnt/galaxyTools/galaxy-central/eggs/pexpect-2.4-py2.6.egg, 
> /mnt/galaxyTools/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, 
> /mnt/galaxyTools/galaxy-central/eggs/Babel-0.9.4-py2.6.egg, 
> /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
>  /mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg, /mnt/g!
 alaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
 /mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, 
/mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.3.3-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/eggs/PasteScript-1.7.3-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/eggs/Paste-1.6-py2.6.egg, 
/mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/, 
/usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk, 
/usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload
> Traceback (most recent call last):
>   File "/mnt/galaxyTools/galaxy-central/lib/galaxy/web/buildapp.py", line 82, 
> in app_factory
> app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/mnt/galaxyTools/galaxy-central/lib/galaxy/app.py", line 24, in 
> __init__
> self.config.check()
>   File "/mnt/galaxyTools/galaxy-central/lib/galaxy/config.py", line 243, in 
> check
> tree = parse_xml( config_filename )
>   File "/mnt/galaxyTools/galaxy-central/lib/galaxy/util/__init__.py", line 
> 105, in parse_xml
> tree = ElementTree.parse(fname)
>   File 
> "/mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/elementtree/ElementTree.py",
>  line 859, in parse
> tree.parse(source, parser)
>   File 
> "/mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg/e

Re: [galaxy-user] error uploading from ftp site

[Dannon Baker]

This should be fixed as of yesterday afternoon.  Are you still having issues?

-Dannon

On Mar 1, 2012, at 11:28 AM, Keith E. Giles wrote:

> All of a sudden I can not upload any files from the FTP server.  The files 
> upload into my ftp directory fine, but when I try to upload them into galaxy, 
> I get the following error:
> 
> "Error executing tool: normalize() argument 2 must be unicode, not str"
> 
> any ideas?
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Re: [galaxy-user] Megablast question

[Dannon Baker]

Noa has the right idea, but if you're asking for how to split a dataset into 
two non-overlapping halves you'll want to use "Select First" and "Select Last", 
instead of random lines.  Get an accurate line count from your file using the 
"Line/Word/Character count" tool and then split it right in the middle using 
select first/last.

-Dannon

On Feb 16, 2012, at 2:35 PM, Noa Sher wrote:

> Hi Scott
> I  never used megablast so what i am writing is true of just any fasta file 
> (so if there is anything quirky in megablast that i dont know about, 
> apologies!):
>   • Take your fasta file and convert to tabular (under "fasta 
> manipulation" - this will make it go to one line per record).
>   • Then randomly choose whatever number of reads you want using "select 
> random lines from a file" under the text maniupulation tab.
>   • Then convert the tabular file back to fasta. (under the fasta 
> manipulation tab)
> noa
> On 16/02/2012 19:31, Scott Tighe wrote:
>> Hi all
>> 
>> When using Galaxy megablast, is there a simple way to reduce my FASTA files 
>> from 23 million reads to 1/2 that size and submit to megablast separately?
>> 
>> Thanks
>> -- 
>> Scott Tighe
>> Advanced Genome Technology Lab
>> Vermont Cancer Center at the University of Vermont
>> 149 Beaumont Avenue
>> Health Science Research Bd RM 305
>> Burlington Vermont USA 05405
>> lab  802-656-AGTC (2482)
>> cell 802-999-
>> 
>> 
>> 
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Re: [galaxy-user] Problem launching Cloudman console

[Dannon Baker]

Arjun,

My first guess would be a javascript error preventing the configuration dialog. 
 What version of IE are you using?  And, do you see any errors noted in IE  
(look for a page warning icon, maybe in the bottom right)?   If so, what are 
they?

And, while it isn't a solution, to get you going again in the short term do you 
have access to another browser?

-Dannon


On Feb 15, 2012, at 8:48 PM, Arjun Vadapalli wrote:

> When I start the EC2 instance using the public image of 
> 861460482541/galaxy-cloudman-2010-03-22, I do not see the EC2 cluster 
> configuration dialog.  I followed all the instructions listed under 
> http://wiki.g2.bx.psu.edu/Admin/Cloud. What I get directly is a cloudman 
> console page which has 0 bytes allocated and inoperative buttons. As per the 
> description in the help page, the Access Galaxy button is supposed to be 
> greyed out but as can be seen in the screen capture I have attached the 
> button is not greyed out. When I click on it the message says that a Cloudman 
> instance is not running. I have attached a screenshot of console page.  I am 
> using Internet Explorer as my web browser. I would appreciate any help in 
> understanding what I am doing wrong.
> Thanks
> Arjun
>  
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Re: [galaxy-user] Production environment

[Dannon Baker]

On Feb 10, 2012, at 3:28 AM, David Castillo wrote:

>   • I haven't been able to 'Edit' Workflows like in the public server, I 
> have been able to create them, but once I try to edit them it just attempts 
> to load the 'Workflow Editor' but it never does. How can I solve this? Do I 
> have to configure something before attempting to do this?

This should work out of the box without any extra configuration.  Do you see 
any errors(failure to load a resource, javascript errors, etc) when you attempt 
to load the editor?  My hunch is that galaxy.workflow_editor.canvas.js isn't 
being found, perhaps due to a proxy configuration being not quite right.  Is 
this galaxy instance set up behind apache or nginx?

-Dannon
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Re: [galaxy-user] The size of the history

[Dannon Baker]

Jiwen,

After purging datasets, the history size update has a bit of a delay.  Let us 
know if you find that after a while it hasn't recalculated to what you expect 
the value to be.

-Dannon


On Feb 1, 2012, at 4:21 PM, 杨继文 wrote:

> Hi all,
> First I would like to thank you for your fast replies to my questions.
> As you know, at top right corner of Galaxy window, there are records of the 
> history size and how many percentage of memory space has been used. I found 
> that the number in the records only increases, but doesn't decrease after I 
> delete files permanently.
> DId I miss something? How to let the record show the real size of the 
> histories?
> Thanks in advance.
> Greetings,
> Jiwen
> 
> 
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Re: [galaxy-user] A simple operation didn't work out

[Dannon Baker]

Hi Jiwen,

The way the filter expression evaluates, you need to specify that you're 
matching on the string '19', and not the numerical value 19.  Everything should 
work if you rerun with the filter condition:
c1=='19'

Thanks!

Dannon



On Feb 1, 2012, at 9:56 AM, 杨继文 wrote:

>  Hi All,
> I got a bit disappointed when I failed in the following operation which seems 
> to be simple.
> 
> I uploaded mouse annotation/reference gene sets (GTF format) to Galaxy. The 
> file is located at ftp://ftp.ensembl.org/pub/release-65/gtf/mus_musculus/.
>  
> As far as I know, GTF file is tab delimited, thus I used "Filter and Sort" 
> --"filter" With following condition:C1 == 19 .
> column 1 is where chromosomes are located. I want to pick up all lines which 
> belong to chromosome19.
> However, I only got an empty file. 
> 
> I know this is not a bit issue to discuss here. But I still  hope  you can 
> help me figure out what 's wrong.
> Thanks
> Jiwen
> 
> 
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Re: [galaxy-user] Server Error when running workflow

[Dannon Baker]

Stephen,

I'll take a look, could you share one of the offending workflows (and perhaps 
the history involved?) with me?

-Dannon

On Jan 31, 2012, at 2:06 PM, Stephen Eacker wrote:

> Hello,
>   I'm using Galaxy main to run some workflows.  I'm running into a 
> "Server Error An error occurred. See the error logs for more information. 
> (Turn debug on to display exception reports here)" when running my workflow.  
> I've seen that a number of others in the Q&A archives have had similar 
> problems that were resolved by patches.
> 
> Steve
> 
> Stephen Eacker, Ph.D.
> Postdoctoral Fellow
> Dawson Lab
> Institute for Cell Engineering
> Johns Hopkins Medical Institute
> (443) 287-5605
> seack...@jhmi.edu
> 
> 
> 
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Re: [galaxy-user] Problem uploading files gt 1 Mbyte to Galaxy Cloud

[Dannon Baker]

Great, glad it worked for you!

And, once we release a new AMI, it'll be fixed retroactively.  That is, you'll 
be able to use your existing cloud setup with the new AMI and it should just 
work.

-Dannon


On Jan 23, 2012, at 5:35 AM, Greg Edwards wrote:

> Dannon,
> 
> Cool, that seems to have worked. I set 
> 
> server {
> listen   80;
> client_max_body_size 500m;
> 
> in  /opt/galaxy/pkg/nginx/conf/nginx.conf
> 
> and issued   sudo kill -HUP `cat /opt/galaxy/pkg/nginx/logs/nginx.pid`
> 
> and it's uploading my test files of 2mb to 25mb ok.
> 
> I think it will be easier to do that in my Cloud setup than instruct my (not 
> very computer keen) wet-lab Proteomist clients how to use a subsidiary FTP 
> package, easy though that is. But I'll try the FTP approach too for 
> compariosn.
> 
> Thanks,
> Greg E
> 
> 
> On Mon, Jan 23, 2012 at 8:58 PM, Dannon Baker  wrote:
> It's the other nginx.conf at /opt/galaxy/pkg/nginx/conf/nginx.conf, I don't 
> think that one you found is used.  And it isn't explicitly set at all 
> currently, so the default 1m gets applied.
> 
> And, to reload with the modified config, I think this should do the trick (as 
> the ubuntu user)-
> 
> sudo kill -HUP `cat /opt/galaxy/pkg/nginx/logs/nginx.pid`
> 
> -Dannon
> 
> 
> On Jan 23, 2012, at 4:43 AM, Greg Edwards wrote:
> 
> > Hi Dannon,
> >
> > I found nginx.conf at  /opt/galaxy/pkg/nginx_upload_module-2.0.12/nginx.conf
> >
> > It contains ..
> >
> >  client_max_body_size 100m;
> >
> > That looks like 100 Megabyte ?? but seems to result in 1 Megabyte. Can I 
> > set it to 1m, or 1g ?
> >
> > Can't see how to restart nginx yet.
> >
> > Thanks,
> > Greg E
> >
> >
> >
> >
> >
> > On Mon, Jan 23, 2012 at 8:18 PM, Dannon Baker  wrote:
> > Hi Greg,
> >
> > This is a problem with the default client_max_body_size option in nginx 
> > being set far too small in the nginx.conf on the cloud AMI.  It'll be fixed 
> > with our next AMI update, but to fix it you have to edit the nginx.conf on 
> > your cloud node to change the client_max_body_size to something more 
> > appropriate for Galaxy uploads and then restart the nginx process.
> >
> > You'd have to do it for every instance, unfortunately, since that section 
> > of the filesystem is not persisted after shutdown.  As a workaround the URL 
> > upload will work correctly with any size file if you're able to host the 
> > file you want to upload somewhere local, or you could use FTP upload and 
> > that should also function correctly.
> >
> > -Dannon
> >
> >
> > On Jan 23, 2012, at 4:09 AM, Greg Edwards wrote:
> >
> > > Hi,
> > >
> > > I'm building a Galaxy Cloud implementation, and running into a problem 
> > > uploading data files > 1 Mbyte, or 1,048,576 bytes.
> > >
> > > I've started Galaxy Cloudman and a single server, all according to to the 
> > > Wiki. I can upload fasta format files < 1048756 bytes, and general CSV 
> > > format peptide files, and indeed junk data files built with variants of " 
> > > jot -r -c 103 a z | rs -g 0 100 >junk ".
> > >
> > > If I upload files (via the built-in Get Data / Upload Files From Your 
> > > Computer) that are > than approx 2^20 bytes, the upload just hangs in the 
> > > History and never completes.
> > >
> > > These files upload fine to a local Galaxy server, and to Galaxy Main. On 
> > > the Galaxy local server, they run fine with my custom proteomics code. 
> > > Ditto on the Cloud galaxy server when the (smaller than 1 Mbtye) files 
> > > successfully upoad.
> > >
> > > I can't see anthing useful in the logs, but I'm not sure which logs I 
> > > should be looking at. I'm just looking at tyhe logs presented on the 
> > > Cloudman admin page.
> > >
> > > 
> > >
> > > My environment is Mac, OS X 10.6.8. My data files are terminated with /n, 
> > > but the problem manifests the same with Windows style /r/n files.
> > >
> > > I'll leave it at that in the hope this is a ridiculously simple probelm 
> > > and needs no more description ! If not, please let me know the logs I 
> > > should look at and whatever else I should check.
> > >
> > > Many thanks,
> > > Greg E
> > >
> > > --
> > > Greg Edwards,
> > > Port Jac

Re: [galaxy-user] Problem uploading files gt 1 Mbyte to Galaxy Cloud

[Dannon Baker]

It's the other nginx.conf at /opt/galaxy/pkg/nginx/conf/nginx.conf, I don't 
think that one you found is used.  And it isn't explicitly set at all 
currently, so the default 1m gets applied.

And, to reload with the modified config, I think this should do the trick (as 
the ubuntu user)-

sudo kill -HUP `cat /opt/galaxy/pkg/nginx/logs/nginx.pid`

-Dannon


On Jan 23, 2012, at 4:43 AM, Greg Edwards wrote:

> Hi Dannon,
> 
> I found nginx.conf at  /opt/galaxy/pkg/nginx_upload_module-2.0.12/nginx.conf
> 
> It contains ..
> 
>  client_max_body_size 100m;
> 
> That looks like 100 Megabyte ?? but seems to result in 1 Megabyte. Can I set 
> it to 1m, or 1g ?
> 
> Can't see how to restart nginx yet.
> 
> Thanks,
> Greg E
> 
> 
> 
> 
> 
> On Mon, Jan 23, 2012 at 8:18 PM, Dannon Baker  wrote:
> Hi Greg,
> 
> This is a problem with the default client_max_body_size option in nginx being 
> set far too small in the nginx.conf on the cloud AMI.  It'll be fixed with 
> our next AMI update, but to fix it you have to edit the nginx.conf on your 
> cloud node to change the client_max_body_size to something more appropriate 
> for Galaxy uploads and then restart the nginx process.
> 
> You'd have to do it for every instance, unfortunately, since that section of 
> the filesystem is not persisted after shutdown.  As a workaround the URL 
> upload will work correctly with any size file if you're able to host the file 
> you want to upload somewhere local, or you could use FTP upload and that 
> should also function correctly.
> 
> -Dannon
> 
> 
> On Jan 23, 2012, at 4:09 AM, Greg Edwards wrote:
> 
> > Hi,
> >
> > I'm building a Galaxy Cloud implementation, and running into a problem 
> > uploading data files > 1 Mbyte, or 1,048,576 bytes.
> >
> > I've started Galaxy Cloudman and a single server, all according to to the 
> > Wiki. I can upload fasta format files < 1048756 bytes, and general CSV 
> > format peptide files, and indeed junk data files built with variants of " 
> > jot -r -c 103 a z | rs -g 0 100 >junk ".
> >
> > If I upload files (via the built-in Get Data / Upload Files From Your 
> > Computer) that are > than approx 2^20 bytes, the upload just hangs in the 
> > History and never completes.
> >
> > These files upload fine to a local Galaxy server, and to Galaxy Main. On 
> > the Galaxy local server, they run fine with my custom proteomics code. 
> > Ditto on the Cloud galaxy server when the (smaller than 1 Mbtye) files 
> > successfully upoad.
> >
> > I can't see anthing useful in the logs, but I'm not sure which logs I 
> > should be looking at. I'm just looking at tyhe logs presented on the 
> > Cloudman admin page.
> >
> > 
> >
> > My environment is Mac, OS X 10.6.8. My data files are terminated with /n, 
> > but the problem manifests the same with Windows style /r/n files.
> >
> > I'll leave it at that in the hope this is a ridiculously simple probelm and 
> > needs no more description ! If not, please let me know the logs I should 
> > look at and whatever else I should check.
> >
> > Many thanks,
> > Greg E
> >
> > --
> > Greg Edwards,
> > Port Jackson Bioinformatics
> > gedwar...@gmail.com
> >
> > ___
> > The Galaxy User list should be used for the discussion of
> > Galaxy analysis and other features on the public server
> > at usegalaxy.org.  Please keep all replies on the list by
> > using "reply all" in your mail client.  For discussion of
> > local Galaxy instances and the Galaxy source code, please
> > use the Galaxy Development list:
> >
> >  http://lists.bx.psu.edu/listinfo/galaxy-dev
> >
> > To manage your subscriptions to this and other Galaxy lists,
> > please use the interface at:
> >
> >  http://lists.bx.psu.edu/
> 
> 
> 
> 
> -- 
> Greg Edwards,
> Port Jackson Bioinformatics
> gedwar...@gmail.com
> 

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Re: [galaxy-user] Problem uploading files gt 1 Mbyte to Galaxy Cloud

[Dannon Baker]

Hi Greg,

This is a problem with the default client_max_body_size option in nginx being 
set far too small in the nginx.conf on the cloud AMI.  It'll be fixed with our 
next AMI update, but to fix it you have to edit the nginx.conf on your cloud 
node to change the client_max_body_size to something more appropriate for 
Galaxy uploads and then restart the nginx process.

You'd have to do it for every instance, unfortunately, since that section of 
the filesystem is not persisted after shutdown.  As a workaround the URL upload 
will work correctly with any size file if you're able to host the file you want 
to upload somewhere local, or you could use FTP upload and that should also 
function correctly.

-Dannon


On Jan 23, 2012, at 4:09 AM, Greg Edwards wrote:

> Hi,
> 
> I'm building a Galaxy Cloud implementation, and running into a problem 
> uploading data files > 1 Mbyte, or 1,048,576 bytes.
> 
> I've started Galaxy Cloudman and a single server, all according to to the 
> Wiki. I can upload fasta format files < 1048756 bytes, and general CSV format 
> peptide files, and indeed junk data files built with variants of " jot -r -c 
> 103 a z | rs -g 0 100 >junk ".
> 
> If I upload files (via the built-in Get Data / Upload Files From Your 
> Computer) that are > than approx 2^20 bytes, the upload just hangs in the 
> History and never completes.
> 
> These files upload fine to a local Galaxy server, and to Galaxy Main. On the 
> Galaxy local server, they run fine with my custom proteomics code. Ditto on 
> the Cloud galaxy server when the (smaller than 1 Mbtye) files successfully 
> upoad.
> 
> I can't see anthing useful in the logs, but I'm not sure which logs I should 
> be looking at. I'm just looking at tyhe logs presented on the Cloudman admin 
> page.
> 
> 
> 
> My environment is Mac, OS X 10.6.8. My data files are terminated with /n, but 
> the problem manifests the same with Windows style /r/n files.
> 
> I'll leave it at that in the hope this is a ridiculously simple probelm and 
> needs no more description ! If not, please let me know the logs I should look 
> at and whatever else I should check.
> 
> Many thanks,
> Greg E
> 
> -- 
> Greg Edwards,
> Port Jackson Bioinformatics
> gedwar...@gmail.com
> 
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
> 
>  http://lists.bx.psu.edu/listinfo/galaxy-dev
> 
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
> 
>  http://lists.bx.psu.edu/

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Re: [galaxy-user] Should I hg update a Galaxy Cloud ?

[Dannon Baker]

Galaxy is actually stored separately from the AMI, but the revision you'll get by default right now is:changeset:   5757:963e73d40e24date:        Wed Jun 29 13:27:01 2011 -0400You can use hg directly to update galaxy, or you can use this component of the admin panel to do it:Just click update galaxy, and it will update all the way to tip for you.  You also have the option of specifying a particular revision, if you'd like.And lastly, yes, you will want to persist these changes to have them available the next time you run your cluster.-DannonOn Jan 12, 2012, at 3:46 PM, Greg Edwards wrote:Hi,Still experimenting with Galaxy and Cloudman on AWS EC2.The latest galaxy AMI is described as 861460482541/galaxy-cloudman-2011-03-22.How up to date is that Galaxy rev ? Should I use hg to update it before running, or saving as a customised Cloud AMI ?Thanks. -- Greg Edwards,Port Jackson Bioinformatics Consulting.gedwar...@gmail.com___The Galaxy User list should be used for the discussion ofGalaxy analysis and other features on the public serverat usegalaxy.org.  Please keep all replies on the list byusing "reply all" in your mail client.  For discussion oflocal Galaxy instances and the Galaxy source code, pleaseuse the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-devTo manage your subscriptions to this and other Galaxy lists,please use the interface at: http://lists.bx.psu.edu/___
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Re: [galaxy-user] CloudMan - Startup Options - Galaxy Cluster vs Data Cluster

[Dannon Baker]

Yes, galaxyData is the only persistent volume you have in your data only 
cluster, so everything should go there.  SCP should work for getting data 
there, unless the file is already hosted somewhere in which case wget is 
probably a better choice.

And yes, FTP is configured specifically for Galaxy uploads and is unavailable 
in the case of a non-galaxy cluster.  The usernames used for logging in, etc, 
come straight from the Galaxy database.

On Jan 12, 2012, at 12:56 PM, mailing list wrote:

> Hi guys,
> 
> Another related question.  So if I need a large data set for my
> program to run on, should that also be stored in GalaxyData?  What is
> the best way to get the data on there?
> 
> I saw something about FTP but it seemed kind of confusing.  Also I
> chose the data cluster option so I don't think I have an instance of
> Galaxy running.  Is that what would do the FTP?
> 
> Thanks again,
> 
> Greg

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Re: [galaxy-user] Login error + admin rights

[Dannon Baker]

Sarah,

See the universe_wsgi.ini in your galaxy directory for configuration settings.  
Specifically, the admin_users section:

# Administrative users - set this to a comma-separated list of valid Galaxy
# users (email addresses).  These users will have access to the Admin section
# of the server, and will have access to create users, groups, roles,
# libraries, and more.  For more information, see:
# http://wiki.g2.bx.psu.edu/Admin/Interface
#admin_users = None

And change 

#admin_users = None

To something like:

admin_users = sarah.ma...@toulouse.inra.fr

And then restart your local galaxy.

For a lot more information on running your own galaxy server, see the wiki page 
at:

http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server

Lastly, regarding your accounts-- I don't see either email address registered.  
Which galaxy server are you referring to here?

Thanks for using Galaxy!

Dannon

On Jan 11, 2012, at 6:19 AM, sarah Maman wrote:

> Dear,
> 
> Galaxy is installed on our own instance and I would like to administrer 
> Galaxy.
> I would like to know how could I register myself to access on admin's 
> interface ?
> 
> Moreover, I have 2 accounts :
> 1 - sarah.ma...@toulouse.inra.fr
> 2 - sarah.ma...@inra.toulouse.fr
> The second one (sarah.ma...@inra.toulouse.fr) is a mistake. Could you please 
> delete the second one ?
> 
> 
> Thank you in advance,
> Sarah MAMAN
> 
> -- 
> Sarah Maman
> INRA - LGC - SIGENAE
> Chemin de Borde-Rouge - Auzeville - BP 52627
> 31326 Castanet-Tolosan cedex - FRANCE
> Tel:   +33(0)5.61.28.57.08
> Tax:   +33(0)5.61.28.57.53
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Re: [galaxy-user] Data upload

[Dannon Baker]

Ateeq,

The preferred method for uploading large files (that aren't already hosted 
somewhere) is FTP.  See the instructions here: 
http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP

We don't generally provide specific analysis pipelines, rather the tools for 
composing them, though you're welcome to look through the shared workflows, 
histories, and pages (See "Shared Data" in Galaxy) for examples and perhaps 
someone else will chime in with their experiences analyzing bacterial 
transcriptomes.

Lastly, try not to piggyback on unrelated threads (as in your other email).  It 
makes tracking email replies more difficult.

-Dannon

On Jan 9, 2012, at 10:30 AM, Ateequr Rehman wrote:

> Dear galaxy Users
> 
> I am very very new to galaxy, will be highly obliged if some one could help 
> me to find the way to analyse bacterial tramnscriptome. in the first step 
> itself , i am having trouble to upload files...
> 
> Does any one knows how to generate URL to upload data, my fastq files are 
> about 3 gb each, 
> 
> Is there any specific pipeline to analyse bacterial transcriptome
> 
> Thanking all of you
> 
> Ateeq
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Re: [galaxy-user] CloudMan - Persist changes to file system is not a hyperlink / clickable

[Dannon Baker]

For sharing a cluster (of any kind) just click the sharing icon () next to the cluster name and the dialog that pops up will walk you through the next steps.-DannonOn Jan 11, 2012, at 7:27 AM, mailing list wrote:So how do I get a share string for /mnt/galaxyData?Thanks again,GregOn Tue, Jan 10, 2012 at 4:16 PM, Dannon Baker <dannonba...@me.com> wrote:Sorry, I should have specified before -- /mnt/galaxyData is automatically persisted, as it is assumed (and used behind the scenes in the case of a Galaxy Cluster) that this is where data will be kept.  It's only /mnt/galaxyTools or /mnt/galaxyIndices that need individual flagging for persistence.So, /mnt/galaxyData *is* safe to use for your own customizations and will be persisted automatically with no additional steps required on your part.-DannonOn Jan 10, 2012, at 4:02 PM, mailing list wrote:I'm following the instructions here:http://wiki.g2.bx.psu.edu/Admin/Cloud/Customize%20Galaxy%20CloudI ssh'd in and just made this change:cd /mnt/galaxyDatasudo git clone git://github.com/JaneliaSciComp/msg.gitNow I want to persist it, but as my subject line says, I don't seem tohave the option in the admin.Thanks,Greg___The Galaxy User list should be used for the discussion ofGalaxy analysis and other features on the public serverat usegalaxy.org.  Please keep all replies on the list byusing "reply all" in your mail client.  For discussion oflocal Galaxy instances and the Galaxy source code, pleaseuse the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-devTo manage your subscriptions to this and other Galaxy lists,please use the interface at: http://lists.bx.psu.edu/___
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Re: [galaxy-user] CloudMan - Persist changes to file system is not a hyperlink / clickable

[Dannon Baker]

Sorry, I should have specified before -- /mnt/galaxyData is automatically 
persisted, as it is assumed (and used behind the scenes in the case of a Galaxy 
Cluster) that this is where data will be kept.  It's only /mnt/galaxyTools or 
/mnt/galaxyIndices that need individual flagging for persistence.

So, /mnt/galaxyData *is* safe to use for your own customizations and will be 
persisted automatically with no additional steps required on your part.

-Dannon

On Jan 10, 2012, at 4:02 PM, mailing list wrote:

> I'm following the instructions here:
> http://wiki.g2.bx.psu.edu/Admin/Cloud/Customize%20Galaxy%20Cloud
> 
> I ssh'd in and just made this change:
> 
> cd /mnt/galaxyData
> sudo git clone git://github.com/JaneliaSciComp/msg.git
> 
> Now I want to persist it, but as my subject line says, I don't seem to
> have the option in the admin.
> 
> Thanks,
> 
> Greg
> ___
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Re: [galaxy-user] CloudMan Launch Page - Hanging

[Dannon Baker]

In your AWS management console delete the s3 bucket containing the cluster 
information.  In the s3 viewer, the .clusterName file reflects the name of the 
cluster.

You'll probably also want to delete the EBS data volume associated with that 
cluster, though electing to keep this won't prevent starting a new cluster.  
These volume id's are in the persistent_data.yaml file in the primary bucket 
(that you're deleting).

And then to avoid this in the future, when you want to permanently kill a 
cluster select the deletion option at cluster termination to remove the bucket 
and volumes permanently.

-Dannon

On Jan 10, 2012, at 3:18 PM, mailing list wrote:

> Yes, I did use the same name.  I thought once I terminated everything
> would be gone.
> 
> So how do I make a "clean start"?
> 
> Thanks,
> 
> Greg
> 
> On Tue, Jan 10, 2012 at 3:08 PM, Dannon Baker  wrote:
>> It looks like you're trying to restart an existing cluster (same cluster 
>> name) that previously had galaxy included.  Is this the case?  If so, you'll 
>> need to start it in the same availability zone as the existing volumes.
>> 
>> 
>> On Jan 10, 2012, at 3:03 PM, mailing list wrote:
>> 
>>> The page seems to be loading now but I think I'm getting some weird
>>> behavior on my started instance.
>>> 
>>> None of the services except SGE started up, and I see this under
>>> cluster status log on the main page:
>>> 
>>>* 19:57:11 - Retrieved file 'persistent_data.yaml' from bucket
>>> 'cm-31bf91*22c1a276ece' to 'pd.yaml'.
>>>* 19:57:11 - Master starting
>>>* 19:57:11 - Completed initial cluster configuration.
>>>* 19:57:27 - PostgreSQL data directory
>>> '/mnt/galaxyData/pgsql/data' does not exist (yet?)
>>>* 19:57:27 - Prerequisites OK; starting service 'SGE'
>>>* 19:57:32 - Configuring SGE...
>>>* 19:57:41 - Successfully setup SGE; configuring SGE
>>>* 19:58:16 - Attaching volume 'vol-35*58' to instance
>>> 'i-ee7e298c' as device '/dev/sdg3' failed. Exception:
>>> EC2ResponseError: 400 Bad Request InvalidVolume.ZoneMismatchThe volume
>>> 'vol-35d4f058' is not in the same availability zone as instance
>>> 'i-ee*def-3ce4-4c41-8909-15e0*6e15
>>>* 19:59:16 - Cannot detach volume 'vol-35d4f058' in state 'available'
>>>* 20:00:17 - Cannot detach volume 'vol-35d4f058' in state 'available'
>>> # 20:01:19 - STATUS CHECK: File system named 'galaxyData' is not
>>> mounted. Error code 0
>>> # 20:01:19 - Cannot start service 'Postgres' because prerequisites are
>>> not yet satisfied.
>>> # 20:01:19 - Cannot start service 'Galaxy' because prerequisites are
>>> not yet satisfied.
>>> # 20:01:19 - Saved file 'persistent_data.yaml' to bucket
>>> 'cm-31bf9*9ff78a*a276ece'
>>> # 20:01:19 - Trouble comparing local (/mnt/cm/post_start_script) and
>>> remote (post_start_script) file modified times: [Errno 2] No such file
>>> or directory: '/mnt/cm/post_start_script'
>>> # 20:01:24 - STATUS CHECK: File system named 'galaxyData' is not
>>> mounted. Error code 0
>>> # 20:01:24 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
>>> does not exist (yet?)
>>> # 20:01:41 - STATUS CHECK: File system named 'galaxyData' is not
>>> mounted. Error code 0
>>> # 20:01:41 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
>>> does not exist (yet?)
>>> # 20:01:57 - STATUS CHECK: File system named 'galaxyData' is not
>>> mounted. Error code 0
>>> # 20:01:57 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
>>> does not exist (yet?)
>>> # 20:02:14 - STATUS CHECK: File system named 'galaxyData' is not
>>> mounted. Error code 0
>>> # 20:02:14 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
>>> does not exist (yet?)
>>> 
>>> 
>>> (I masked some of the numbers in case they're sensitive)
>>> 
>>> 
>>> 
>>> On Tue, Jan 10, 2012 at 2:15 PM, mailing list  wrote:
>>>> Hi guys,
>>>> 
>>>> Is the launch page down today?
>>>> 
>>>> https://biocloudcentral.herokuapp.com/launch
>>>> 
>>>> It seems to just hang for

Re: [galaxy-user] CloudMan Launch Page - Hanging

[Dannon Baker]

It looks like you're trying to restart an existing cluster (same cluster name) 
that previously had galaxy included.  Is this the case?  If so, you'll need to 
start it in the same availability zone as the existing volumes.


On Jan 10, 2012, at 3:03 PM, mailing list wrote:

> The page seems to be loading now but I think I'm getting some weird
> behavior on my started instance.
> 
> None of the services except SGE started up, and I see this under
> cluster status log on the main page:
> 
>* 19:57:11 - Retrieved file 'persistent_data.yaml' from bucket
> 'cm-31bf91*22c1a276ece' to 'pd.yaml'.
>* 19:57:11 - Master starting
>* 19:57:11 - Completed initial cluster configuration.
>* 19:57:27 - PostgreSQL data directory
> '/mnt/galaxyData/pgsql/data' does not exist (yet?)
>* 19:57:27 - Prerequisites OK; starting service 'SGE'
>* 19:57:32 - Configuring SGE...
>* 19:57:41 - Successfully setup SGE; configuring SGE
>* 19:58:16 - Attaching volume 'vol-35*58' to instance
> 'i-ee7e298c' as device '/dev/sdg3' failed. Exception:
> EC2ResponseError: 400 Bad Request InvalidVolume.ZoneMismatchThe volume
> 'vol-35d4f058' is not in the same availability zone as instance
> 'i-ee*def-3ce4-4c41-8909-15e0*6e15
>* 19:59:16 - Cannot detach volume 'vol-35d4f058' in state 'available'
>* 20:00:17 - Cannot detach volume 'vol-35d4f058' in state 'available'
> # 20:01:19 - STATUS CHECK: File system named 'galaxyData' is not
> mounted. Error code 0
> # 20:01:19 - Cannot start service 'Postgres' because prerequisites are
> not yet satisfied.
> # 20:01:19 - Cannot start service 'Galaxy' because prerequisites are
> not yet satisfied.
> # 20:01:19 - Saved file 'persistent_data.yaml' to bucket
> 'cm-31bf9*9ff78a*a276ece'
> # 20:01:19 - Trouble comparing local (/mnt/cm/post_start_script) and
> remote (post_start_script) file modified times: [Errno 2] No such file
> or directory: '/mnt/cm/post_start_script'
> # 20:01:24 - STATUS CHECK: File system named 'galaxyData' is not
> mounted. Error code 0
> # 20:01:24 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
> does not exist (yet?)
> # 20:01:41 - STATUS CHECK: File system named 'galaxyData' is not
> mounted. Error code 0
> # 20:01:41 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
> does not exist (yet?)
> # 20:01:57 - STATUS CHECK: File system named 'galaxyData' is not
> mounted. Error code 0
> # 20:01:57 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
> does not exist (yet?)
> # 20:02:14 - STATUS CHECK: File system named 'galaxyData' is not
> mounted. Error code 0
> # 20:02:14 - PostgreSQL data directory '/mnt/galaxyData/pgsql/data'
> does not exist (yet?)
> 
> 
> (I masked some of the numbers in case they're sensitive)
> 
> 
> 
> On Tue, Jan 10, 2012 at 2:15 PM, mailing list  wrote:
>> Hi guys,
>> 
>> Is the launch page down today?
>> 
>> https://biocloudcentral.herokuapp.com/launch
>> 
>> It seems to just hang for me and not load.
>> 
>> Let me know if there's anything I can do
>> 
>> Thanks
>> 
>> Greg
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Re: [galaxy-user] CloudMan - Startup Options - Galaxy Cluster vs Data Cluster

[Dannon Baker]

Correct to the first point.

The space available to /mnt/galaxyTools is not configurable through the 
interface, though you could manually resize a volume if you did need more room. 
 /mnt/galaxyData is the volume referred to in the dialogs you're seeing.

-Dannon

On Jan 10, 2012, at 2:53 PM, mailing list wrote:

> Thanks.  So if I just want to run my own program that uses SGE, it
> sounds like I shouldn't need a Galaxy instance.  Is that right?
> 
> Does the storage space parameter control how much space is at 
> /mnt/galaxyTools?
> 
> -Greg
> 
> On Tue, Jan 10, 2012 at 2:50 PM, Dannon Baker  wrote:
>> Data Cluster only configures a persistent data volume and SGE.  Galaxy 
>> Cluster includes a running Galaxy instance in addition to the persistent 
>> data volume and SGE configuration components from the Data Cluster option.  
>> The Galaxy Cluster option is what most users will probably want to choose.
>> 
>> How much space is absolutely dependent on your needs.  Keep in mind that you 
>> can increase size later if necessary via the admin UI.  The maximum volume 
>> size (per an amazon limit to EBS volume size) is currently 1TB.
>> 
>> -Dannon
>> 
>> 
>> On Jan 10, 2012, at 2:42 PM, mailing list wrote:
>> 
>>> Hi guys,
>>> 
>>> When I first go to my cloudman page at /cloud I get a
>>> dialog asking for some settings.
>>> 
>>> What does the Galaxy Cluster choice do?  What does the Data Cluster
>>> choice do?  Why can't I choose both?  How much space should I
>>> allocate?
>>> 
>>> Thanks,
>>> 
>>> Greg
>>> 
>>> Text of dialog:
>>> 
>>> Galaxy Cluster: Galaxy application, available tools, reference
>>> datasets, SGE job manager, and a data volume. Specify the initial
>>> storage size (in Gigabytes):
>>> GBOK
>>> 
>>> Share-an-Instance Cluster: derive your cluster form someone else's
>>> cluster. Specify the provided cluster share-string (for example,
>>> cm-0011923649e9271f17c4f83ba6846db0/shared/2011-08-19--21-00):
>>> Cluster share-string
>>> 
>>> Data Cluster: a persistent data volume and SGE. Specify the initial
>>> storage size (in Gigabytes):
>>> GB
>>> 
>>> Test Cluster: SGE only. No persistent storage is created.
>>> ___
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>>> use the Galaxy Development list:
>>> 
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>>> 
>>> To manage your subscriptions to this and other Galaxy lists,
>>> please use the interface at:
>>> 
>>>  http://lists.bx.psu.edu/
>> 

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Re: [galaxy-user] CloudMan - Startup Options - Galaxy Cluster vs Data Cluster

[Dannon Baker]

Data Cluster only configures a persistent data volume and SGE.  Galaxy Cluster 
includes a running Galaxy instance in addition to the persistent data volume 
and SGE configuration components from the Data Cluster option.  The Galaxy 
Cluster option is what most users will probably want to choose.

How much space is absolutely dependent on your needs.  Keep in mind that you 
can increase size later if necessary via the admin UI.  The maximum volume size 
(per an amazon limit to EBS volume size) is currently 1TB.

-Dannon


On Jan 10, 2012, at 2:42 PM, mailing list wrote:

> Hi guys,
> 
> When I first go to my cloudman page at /cloud I get a
> dialog asking for some settings.
> 
> What does the Galaxy Cluster choice do?  What does the Data Cluster
> choice do?  Why can't I choose both?  How much space should I
> allocate?
> 
> Thanks,
> 
> Greg
> 
> Text of dialog:
> 
> Galaxy Cluster: Galaxy application, available tools, reference
> datasets, SGE job manager, and a data volume. Specify the initial
> storage size (in Gigabytes):
> GBOK
> 
> Share-an-Instance Cluster: derive your cluster form someone else's
> cluster. Specify the provided cluster share-string (for example,
> cm-0011923649e9271f17c4f83ba6846db0/shared/2011-08-19--21-00):
> Cluster share-string
> 
> Data Cluster: a persistent data volume and SGE. Specify the initial
> storage size (in Gigabytes):
> GB
> 
> Test Cluster: SGE only. No persistent storage is created.
> ___
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> 
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> please use the interface at:
> 
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Re: [galaxy-user] CloudMan - Galaxy - How does sharing work?

[Dannon Baker]

Yes on both counts.  Snapshots do cost money, and /mnt/galaxyTools is the right 
place to install new lib and programs.

-Dannon


On Jan 9, 2012, at 10:16 AM, mailing list wrote:

> Thanks.  It seems to me that http://aws.amazon.com/ebs/ says snapshots
> do carry a small charge.  I might be reading it wrong though.
> 
> Also if I'm installing new libraries and programs, would those go in
> /mnt/galaxyTools?
> 
> Thanks again,
> 
> Greg
> 
> On Mon, Jan 9, 2012 at 10:00 AM, Dannon Baker  wrote:
>> Greg-
>> 
>> When you make changes to the EBS volumes of a galaxy cloudman instance and 
>> choose 'persist' from the admin panel, an EBS snapshot is taken.  The next 
>> time you start an instance up, instead of creating the EBS volume from the 
>> base snapshot that we distribute, it is created from your own customized 
>> snapshot.
>> 
>> The share string is actually a handle to a cloudman s3 bucket.  That bucket 
>> contains all of the configuration information for your cluster and 
>> customizations.  You can look at your own buckets to see the information 
>> saved, if you'd like.  When the share-an-instance configuration steps happen 
>> and snapshots are taken, privileges are set to allow others to access those 
>> snapshots.
>> 
>> Since the customizations you make to galaxy are stored as an EBS snapshot, 
>> this does carry an extra cost.  See more information about EBS snapshots at 
>> http://aws.amazon.com/ebs/.
>> 
>> And, lastly, if you're *really* interested in the nuts and bolts of how it 
>> happens, see the source here: 
>> https://bitbucket.org/galaxy/cloudman/src/tip/cm/util/master.py#cl-859
>> 
>> -Dannon
>> 
>> 
>> 
>> On Jan 9, 2012, at 9:26 AM, mailing list wrote:
>> 
>>> I was wondering how the sharestring feature works?
>>> 
>>> Enis mention it a little bit here:
>>> http://biostar.stackexchange.com/questions/15467/galaxy-cloudman-best-way-to-customize-and-share-cloudman/15481#15481
>>> 
>>> So as I understand it, I do my customizations and persist them, and
>>> then I get a sharestring so others can load my customizations.
>>> 
>>> How does this work behind the scenes?
>>> 
>>> Also where are my customizations stored?  Am I charged by Amazon for
>>> storing them?  How do others have permissions to pull them from my
>>> Amazon account?
>>> 
>>> (I'm new to all of this, sorry if my questions are obvious)
>>> 
>>> -Greg
>>> ___
>>> The Galaxy User list should be used for the discussion of
>>> Galaxy analysis and other features on the public server
>>> at usegalaxy.org.  Please keep all replies on the list by
>>> using "reply all" in your mail client.  For discussion of
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>>> 
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>>> 
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>>> please use the interface at:
>>> 
>>>  http://lists.bx.psu.edu/
>> 

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Re: [galaxy-user] CloudMan - Galaxy - How does sharing work?

[Dannon Baker]

Greg-

When you make changes to the EBS volumes of a galaxy cloudman instance and 
choose 'persist' from the admin panel, an EBS snapshot is taken.  The next time 
you start an instance up, instead of creating the EBS volume from the base 
snapshot that we distribute, it is created from your own customized snapshot.

The share string is actually a handle to a cloudman s3 bucket.  That bucket 
contains all of the configuration information for your cluster and 
customizations.  You can look at your own buckets to see the information saved, 
if you'd like.  When the share-an-instance configuration steps happen and 
snapshots are taken, privileges are set to allow others to access those 
snapshots.

Since the customizations you make to galaxy are stored as an EBS snapshot, this 
does carry an extra cost.  See more information about EBS snapshots at 
http://aws.amazon.com/ebs/.

And, lastly, if you're *really* interested in the nuts and bolts of how it 
happens, see the source here: 
https://bitbucket.org/galaxy/cloudman/src/tip/cm/util/master.py#cl-859

-Dannon



On Jan 9, 2012, at 9:26 AM, mailing list wrote:

> I was wondering how the sharestring feature works?
> 
> Enis mention it a little bit here:
> http://biostar.stackexchange.com/questions/15467/galaxy-cloudman-best-way-to-customize-and-share-cloudman/15481#15481
> 
> So as I understand it, I do my customizations and persist them, and
> then I get a sharestring so others can load my customizations.
> 
> How does this work behind the scenes?
> 
> Also where are my customizations stored?  Am I charged by Amazon for
> storing them?  How do others have permissions to pull them from my
> Amazon account?
> 
> (I'm new to all of this, sorry if my questions are obvious)
> 
> -Greg
> ___
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Re: [galaxy-user] How to add a tool to Cloud Galaxy

[Dannon Baker]

Hi Greg,

In order to install custom tools you'll need to SSH into a running instance, 
install your tool and make any modifications to Galaxy you need in order to use 
it, and then use the "Persist changes to file system" option in the Cloudman 
administration panel.  By default, Cloudman discards and simply recreates from 
snapshot the galaxyTools and galaxyData volumes when an instance is relaunched, 
but this persistence command will make a snapshot specific to your instance 
that will be used going forward.

Here's a wiki link for more info: 
http://wiki.g2.bx.psu.edu/Admin/Cloud/Customize%20Galaxy%20Cloud

Let me know if you have any other questions, and good luck!

-Dannon



On Jan 6, 2012, at 7:28 PM, Greg Edwards wrote:

> Hi Folks,
> 
> I could use some help on adding a tool to the cloud version of Galaxy. The 
> Cloud startup process creates, among other things, 
> /mnt/galaxyTools/galaxy-central which has tools_conf.xml, and subdir tools 
> etc. This seems not accessible before starting the cloud. I assume I need to 
> add my tool into the structure as per a local Galaxy instance, and then get 
> Galaxy to restart, or re-read it's config ? Would appreciate some advice 
> there.
> 
> Just as background .. I have got a custom proteomics Perl script running ok 
> under a local version of Galaxy on Mac. Added in to tools_conf.xml, tools 
> etc. Made several mods to the Perl to stop any writing to stderr except for 
> fatal show-stopper errors, everyone seems to hit that one, and other small 
> things to make it play better with Galaxy. Also quite familiar with AWS EC2, 
> have been using that for a while.
> 
> I have Galaxy Cloudman running well, start/stop extra servers etc. Using the 
> free t1.micro AMI for now, slowish but ok for testing. Or a Spot Instance of 
> m1.large when I'm impatient.
> 
> I couldn't find the answer in a search of Galaxy archives, apologies if it's 
> there, or obvious in some other way.
> 
> Thanks!
> 
> -- 
> Greg Edwards,
> Port Jackson Bioinformatics Consulting.
> gedwar...@gmail.com
> 
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Re: [galaxy-user] Workflows & Multiple datasets

[Dannon Baker]

Ahh, I should have specified, that changeset is in the galaxy-central 
repository and has not been moved to galaxy-dist yet.  I think we're testing a 
few more things, but this should happen in the near future, at which point you 
could simply update from galaxy-dist as usual, or you could pull directly from 
galaxy-central right now if you'd like.

-Dannon

On Dec 19, 2011, at 12:50 PM, Adhemar wrote:

> Dannon, 
> Thanks for the immediate reply. 
> I just retrieved the latest code from the repository and it's not working
> 
> $ hg summary
> parent: 6298:b258de1e6cea tip
> 
> 
> I also tried 'hg pull -u -r 6368:de03f821784b' but it says: 
> 
> pulling from https://bitbucket.org/galaxy/galaxy-dist
> abort: unknown revision '6368:de03f821784b'!
> 
> 
> How or when can I update to the release you mentioned?
> Thanks,
> -Adhemar
> 
> 
> 2011/12/19 Dannon Baker 
> Adhemar,
> 
> This was a bug that has been fixed as of changeset 6368:de03f821784b, which 
> should be available on main.g2.bx.psu.edu in the near future.  If you're 
> running a local instance, you'll find this resolved as soon as you update to 
> that changeset or higher.
> 
> Unfortunately, there isn't a fast way to copy datasets into a data library 
> from multiple histories at once.  I think you might find it faster to use the 
> standard "Copy Datasets" functionality in the history Options menu to move 
> everything you'd like into a single new history, and from there move it into 
> a library.  This Copy Datasets action allows you to select an individual 
> history to copy from, instead of manually changing to the history first, so 
> it should save you some time to do it that way.
> 
> -Dannon
> 
> 
> On Dec 19, 2011, at 12:12 PM, Adhemar wrote:
> 
> > Hi,
> > I was searching for how to run a workflow for multiple input files and I 
> > was very happy to find it's already implemented as mentioned here: 
> > http://wiki.g2.bx.psu.edu/News%20Briefs/2011_05_20
> >
> > The problem is that it's not working for me. When I select two files, for 
> > example, it runs the workflow only in the first file. Even if I check 'Send 
> > results to a new history', it only creates a new history called 'test 1' 
> > and not the others. Is my instance somehow misconfigured or it's happening 
> > to others as well?
> >
> > I'm also looking for a way to add datasets to a library from different 
> > histories. Do I really need to open each history one by one and use 'Import 
> > datasets from your current library'?
> >
> > Thank you,
> > Adhemar
> >
> >
> >
> > ___
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> > Galaxy analysis and other features on the public server
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> >
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> >
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> > please use the interface at:
> >
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> 
> 

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Re: [galaxy-user] Workflows & Multiple datasets

[Dannon Baker]

Adhemar,

This was a bug that has been fixed as of changeset 6368:de03f821784b, which 
should be available on main.g2.bx.psu.edu in the near future.  If you're 
running a local instance, you'll find this resolved as soon as you update to 
that changeset or higher.

Unfortunately, there isn't a fast way to copy datasets into a data library from 
multiple histories at once.  I think you might find it faster to use the 
standard "Copy Datasets" functionality in the history Options menu to move 
everything you'd like into a single new history, and from there move it into a 
library.  This Copy Datasets action allows you to select an individual history 
to copy from, instead of manually changing to the history first, so it should 
save you some time to do it that way.

-Dannon


On Dec 19, 2011, at 12:12 PM, Adhemar wrote:

> Hi, 
> I was searching for how to run a workflow for multiple input files and I was 
> very happy to find it's already implemented as mentioned here: 
> http://wiki.g2.bx.psu.edu/News%20Briefs/2011_05_20 
> 
> The problem is that it's not working for me. When I select two files, for 
> example, it runs the workflow only in the first file. Even if I check 'Send 
> results to a new history', it only creates a new history called 'test 1' and 
> not the others. Is my instance somehow misconfigured or it's happening to 
> others as well? 
> 
> I'm also looking for a way to add datasets to a library from different 
> histories. Do I really need to open each history one by one and use 'Import 
> datasets from your current library'?
> 
> Thank you,
> Adhemar
> 
> 
> 
> ___
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> Galaxy analysis and other features on the public server
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> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
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> 
>  http://lists.bx.psu.edu/listinfo/galaxy-dev
> 
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> please use the interface at:
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Re: [galaxy-user] Cucumber genome

[Dannon Baker]

Changlong,

Lastz (and many other tools) allow you to select a reference from your history 
instead of picking one of Galaxy's built-in references.  To do this, upload 
your reference and then when you run Lastz select "in your history" for the 
reference location, and pick your uploaded file as the reference dataset.

-Dannon


On Dec 9, 2011, at 4:44 AM, changlong wen wrote:

> Hi,
> 
> In the NGS mapping option with "lastz" I cannot find the Cucumber genome.
> Could you please make this reference genome available? 
> Or we have the reference sequence. How to add them in in the local server?
> Many thanks.
> 
> Have a good day.
> 
> Best regards
> changlong
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Re: [galaxy-user] [galaxy-dev] Urgent help needed

[Dannon Baker]

I don't know anything about the tool or parameters in question , but it looks 
like the expected output filename is well formatted enough that you can derive 
it from the input filename and parameters.

You could write a small python wrapper to grant you full control over 
manipulating output files and finding/renaming them as you like, or, you could 
maybe try something like (and I have not tried this at all myself and have no 
idea what your parameters mean)  
from_work_dir="${input1}reads_l_${parameter1}_${parameter2}_CNTGS_DIST0_EM20.txt"

Good luck-

Dannon

On Dec 5, 2011, at 3:52 PM, Toqa Manasrah wrote:

> Thank you so much Dannon.
> I appreciate your help but I need some more clarification.
> 
> in the tool I am integrating (which is java classes) if the input parameters 
> are
> 
> ./main.bash  eps0.3_40reads.fa  population10_ref.fa 15 6 120
> 
> Then teh output is in eps0.3_40reads_I_6_15_CNTGS_DIST0_EM20.txt
> 
> As u notice the output file name is not specified in teh command line, and 
> actually I dont have the source files to go over this naming restriction.
> 
> how I can use from_work_dir attribute to tell galaxy this the file to display?
> 
> note: there are 11 output files and I am interested in this one only 
> ..._CNTGS_DIST0_EM20.txt
> 
> 
> any other method to overcome such problem  
> 
> I have presentation tomorrwo. hope things will work fine.
> 
> Thank you,
> 
> From: Dannon Baker [dannonba...@me.com]
> Sent: Monday, December 05, 2011 2:41 PM
> To: Toqa Manasrah
> Subject: Re: [galaxy-dev]  Urgent help needed
> 
> Sure.  See the link in my previous email 
> (http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) and look for 
> the  section for an explanation of the attributes available to you.  
> For an example of a tool that uses the from_work_dir element, see the 
> cufflinks, cuff compare, top hat, or trinity wrappers in your galaxy install.
> 
> -Dannon
> 
> 
> On Dec 5, 2011, at 2:25 PM, Toqa Manasrah wrote:
> 
>> Thank you Dannon,
>> I mean the first choice. no way to specify the output name in tool and it 
>> has many putputs but I am intereseted in one only.
>> 
>> Actually I dont know to use this attribute from_work_dir and I cant find 
>> help. can u help plz?
>> 
>> 
>> From: Dannon Baker [dannonba...@me.com]
>> Sent: Monday, December 05, 2011 1:54 PM
>> To: Toqa Manasrah
>> Cc: galaxy-...@bx.psu.edu dev; Jennifer Jackson; galaxy-user
>> Subject: Re: [galaxy-dev]  Urgent help needed
>> 
>> Toqa,
>> 
>> Just to make sure I've understood your question: the problem is that a tool 
>> that you're trying to wrap doesn't provide a way to specify a particular 
>> output filename?  Take a look at the from_work_dir attribute of a  
>> element.
>> 
>> Or are you asking how to define outputs in general?  For that, see the wiki 
>> at 
>> http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coutputs.3E_tag_set
>> 
>> Lastly, for new questions please start new email threads, instead of 
>> replying to old ones.  This makes it much easier for us to track our 
>> responses and make sure people get appropriate help.
>> 
>> -Dannon
>> 
>> 
>> On Dec 5, 2011, at 1:26 PM, Toqa Manasrah wrote:
>> 
>>> Hi Everybody,
>>> I am running a tool which is not defining the output file name as parameter.
>>> the tool is running and I can see the output file in the history directory 
>>> but not in the history frame.
>>> 
>>> how could I solve the problem? I should see and download the output file 
>>> from the history but I see an error message instead. the error message not 
>>> a real error but rather galaxy cannot figure out which file to display?
>>> 
>>> your help is appreciated,
>>> 
>>> 
>>> 
>>> From: Jennifer Jackson [j...@bx.psu.edu]
>>> Sent: Tuesday, November 08, 2011 8:22 AM
>>> To: Toqa Manasrah
>>> Cc: Galaxy Dev
>>> Subject: Re: [galaxy-dev] Installing Galaxy on local server
>>> 
>>> Hello Tuqa,
>>> 
>>> Galaxy will not stop by itself. That said, you will want to monitor the
>>> instance and any associated cluster, just as you would any other
>>> important processes.
>>> 
>>> Please send all follow-up with a cc to the mailing list ("reply-all").
>>> The development community is a great resource for administrative advice
>>> and they 

Re: [galaxy-user] [galaxy-dev] Urgent help needed

[Dannon Baker]

Toqa,

Just to make sure I've understood your question: the problem is that a tool 
that you're trying to wrap doesn't provide a way to specify a particular output 
filename?  Take a look at the from_work_dir attribute of a  element.

Or are you asking how to define outputs in general?  For that, see the wiki at 
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Coutputs.3E_tag_set

Lastly, for new questions please start new email threads, instead of replying 
to old ones.  This makes it much easier for us to track our responses and make 
sure people get appropriate help.

-Dannon


On Dec 5, 2011, at 1:26 PM, Toqa Manasrah wrote:

> Hi Everybody,
> I am running a tool which is not defining the output file name as parameter.
> the tool is running and I can see the output file in the history directory 
> but not in the history frame.
> 
> how could I solve the problem? I should see and download the output file from 
> the history but I see an error message instead. the error message not a real 
> error but rather galaxy cannot figure out which file to display?
> 
> your help is appreciated,
> 
> 
> 
> From: Jennifer Jackson [j...@bx.psu.edu]
> Sent: Tuesday, November 08, 2011 8:22 AM
> To: Toqa Manasrah
> Cc: Galaxy Dev
> Subject: Re: [galaxy-dev] Installing Galaxy on local server
> 
> Hello Tuqa,
> 
> Galaxy will not stop by itself. That said, you will want to monitor the
> instance and any associated cluster, just as you would any other
> important processes.
> 
> Please send all follow-up with a cc to the mailing list ("reply-all").
> The development community is a great resource for administrative advice
> and they may have more to add to this reply, i.e. how stable they have
> found Galaxy to be under various conditions.
> 
> Best,
> 
> Jen
> Galaxy team
> 
> On 11/8/11 4:01 AM, Toqa Manasrah wrote:
>> Thank you so much,
>> 
>> I did the installation and I ran it under my server.
>> I have one thing concerning about now. if u can help plz.
>> 
>> how to run Galaxy in such way that the html interface will continuously 
>> working and available for all users visiting the page?
>> 
>> i mean how to guarantee that the "sh run.sh" will keep running without any 
>> interrupt?
>> 
>> Thank you,
>> Tuqa
>> 
>> 
>> From: Jennifer Jackson [j...@bx.psu.edu]
>> Sent: Thursday, November 03, 2011 6:47 PM
>> To: Toqa Manasrah
>> Cc: galaxy-...@bx.psu.edu
>> Subject: Re: [galaxy-dev] Installing Galaxy on local server
>> 
>> Hello Toqa,
>> 
>>  From your description, this sounds like a local installation for the
>> Galaxy instance itself. Then you can add on a cluster (local or cloud)
>> as needed.
>> 
>> Help is under "Deploy Galaxy" at http://wiki.g2.bx.psu.edu/
>> Also see the "Tool Shed" at http://wiki.g2.bx.psu.edu/Tool%20Shed
>> 
>> Hopefully the documentation is helpful,
>> 
>> Best,
>> 
>> Jen
>> Galaxy team
>> 
>> On 11/3/11 9:40 AM, Toqa Manasrah wrote:
>>> Hello,
>>> 
>>> I am a graduate student at GSU. I am looking for installing GALAXY on
>>> our local server http://alla.cs.gsu.edu/~software. as a result I like my
>>> server homepage start with the GALAXY interface, like this one:
>>> http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some
>>> software tolls that we developed in ourdepartment. my primary question
>>> is which option Ihave to choose: Local or cloud?
>>> 
>>> looking forward for your help and directions.
>>> 
>>> Thank you.
>>> 
>>> Tuqa
>>> 
>>> 
>>> 
>>> ___
>>> 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/
>> 
>> --
>> Jennifer Jackson
>> http://usegalaxy.org
>> http://galaxyproject.org/wiki/Support
>> 
> 
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/wiki/Support
> 
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Re: [galaxy-user] my data files are missing from drop down menus

[Dannon Baker]

Maya,

Many tools require that fastq files specify that they are of sanger quality 
score.  Specifically, "Map with BWA for Illumina", etc.  If you click the 
pencil icon ("Edit Attributes") on your uploaded dataset and change the data 
type from 'fastq' to 'fastqsanger', you should be able to run your tools.

Thanks, and let me know if you have any other issues.

Dannon

On Nov 10, 2011, at 5:20 PM, Maya Kasowski wrote:

> Hello,
> 
> I uploaded a couple fastq files to Galaxy (Illumina GA2X sequencer).
> The files uploaded successfully and are green in the history section.
> However, neither file is visible in the drop down menus for any of the
> tools. I'd appreciate your help with this.
> 
> Thank you,
> Maya
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Re: [galaxy-user] SNPeff tool?

[Dannon Baker]

Hi Laura,

While the SNPeff developers have made Galaxy wrappers available, this is not a 
tool we currently have installed for use on the Galaxy server at 
main.g2.bx.psu.edu.  Off the top of my head, I don't know of any other public 
Galaxy servers that offer this tool, but if you have access to a local or cloud 
galaxy server you could use the provided wrapper to install the tool for use 
there.

Thanks!

-Dannon



On Nov 8, 2011, at 6:40 AM, Laura Elizabeth Spoor wrote:

> Hi,
> 
> I use the Galaxy server and was wondering how to use SNPeff tool? I have seen 
> that it can be integrating with Galaxy on their website 
> (http://snpeff.sourceforge.net/images/snpEff_galaxy.png) but cannot see it on 
> the server? Is it something that can be run on the server?
> 
> Best Wishes,
> 
> Laura
> 
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 
> 
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Re: [galaxy-user] Amazon AMI

[Dannon Baker]

I see in your screenshot that the security group is only listed as "default".  
Have you created the required security group as described in 
http://wiki.g2.bx.psu.edu/Admin/Cloud ?  If so, make sure you select that 
security group when you launch the instance, and my guess is that it'll solve 
your problem.

Thanks for trying Galaxy on the Cloud!

-Dannon


On Oct 28, 2011, at 10:51 PM, Daniel Muehlschlegel wrote:

> Hi,
> 
> I installed the Amazon Galaxy CloudMan today but am not able to load any of 
> the Galaxy AMIs. The AMI on the user galaxy webpage does not exist, but 3 
> AMIs do. I tried the 2 most current ones and they don't load:
> <710521EE-C6B4-43AB-B082-4461EAC78B9E.png>
> 
> 
> It looks like everything is fine on the Amazon side:
> 
> <0A021174-E68A-468C-A4DE-A60B9D854F70.png> 
> 
> 
> 
> Thanks for your help,
> 
> Danny
> <710521EE-C6B4-43AB-B082-4461EAC78B9E.png><0A021174-E68A-468C-A4DE-A60B9D854F70.png>___
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Re: [galaxy-user] Map with Bowtie for Illumina (version 1.1.2)

[Dannon Baker]

Hi Marc,

Yes, if you change "Bowtie settings to use" from common to full, you'll see the 
entire parameter list, including "Number of mismatches for SOAP-like alignment 
policy (-v):"

-Dannon

On Oct 27, 2011, at 8:40 AM, KNIGHT M.R. wrote:

> Hi, is it possible to run Map with Bowtie for Illumina (version 1.1.2) in –v 
> alignment mode/ If so, what settings do I need to enter? Many thanks, Marc.
>  
>  
> ***
> Professor Marc R. Knight,
> Director,
> Durham Centre for Crop Improvement Technology,
> School of Biological and Biomedical Sciences,
> Durham University,
> South Road,
> Durham DH1 3LE.
> Tel: +44 191 33 41224
> Fax: +44 191 33 41201
> Website: http://www.dur.ac.uk/dccit/
> ***
>  
>  
>  
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Re: [galaxy-user] Issue about uploading data

[Dannon Baker]

Nandan,

Have you tried using our FTP upload process?  This is much more robust than the 
standard upload, especially for large files.  See 
http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP

-Dannon

On Oct 20, 2011, at 7:05 PM, Nandan Deshpande wrote:

> Hi,
> 
> My user id is "deshpandenandan1...@gmail.com". I have been trying to upload 2 
> files each around 650 MB in size but the upload is in process for last 15 hrs 
> .. I had a similar problem in uploading data to Galaxy few months back and 
> had to give up using the tool. Can u suggest me a way out?
> 
> cheers,
> 
> Nandan
>  
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Re: [galaxy-user] Zoom function on workflow editor?

[Dannon Baker]

Arthur,

There is no zoom for the main editor window, though you can use(and resize) the 
little mini view in the bottom right corner to move around the workflow 
quickly.  You could also use the browser-level zoom (in Chrome and Firefox, at 
least) to see much more at a time.

-Dannon



On Oct 20, 2011, at 10:26 AM, Arthur Goldberg wrote:

> Hi 
> 
> Galaxy's cool!
> Is there a zoom function on the workflow editor? (I know about hiding nodes 
> from the tutorial.)
> 
> Thanks
> Arthur
> 
> -- 
> Senior Research Scientist
> Computational Biology
> Memorial Sloan-Kettering Cancer Center
> cBio Cancer Genomics Portal
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Re: [galaxy-user] Subscribing to Job Status Events

[Dannon Baker]

Oren,

Exactly what you're asking for doesn't currently exist, though depending on 
what you're building you could definitely use the API to monitor this sort of 
thing.  The histories controller provides the state of job, along with lots of 
other useful information.  For example, using the encoded id of a job and the 
provided (in your /galaxy/scripts/api directory) display.py script, you can 
make a request something like:

python ./display.py  
http://localhost:8080/api/histories//contents/

And you'll get a reply that includes the detailed state information of this 
particular dataset, something like what I've copied below.  In this, you can 
see that I'm currently uploading the file, for example.

Member Information
--
misc_blurb: None
name: sample.fasta
data_type: None
deleted: False
state: upload
download_url: /datasets/a799d38679e985db/display?to_ext=None
visible: True
genome_build: ?
model_class: HistoryDatasetAssociation
file_size: 0
metadata_data_lines: None
id: a799d38679e985db
misc_info: None
metadata_dbkey: ?


Let me know if you have more questions, or if this is sufficient to get you 
started.  Thanks!

-Dannon


On Oct 6, 2011, at 4:11 PM, Oren Livne wrote:

> Dear All,
> 
> Does Galaxy provide a way for a client app to subscribe to job status change 
> notifications? Best would be a web service that lists the currently running 
> jobs (for the current user / all users) and their status.
> 
> Thank you so much,
> Oren
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Re: [galaxy-user] Adding new tools in Galaxy

[Dannon Baker]

Makais, 

Any type of command line tool, whether script or a binary executable, can be 
used by Galaxy as long as it's properly installed on the system and accessible 
to the Galaxy user.

See 
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ccommand.3E_tag_set
 for more details on how you might call a compiled executable.

Thanks for using Galaxy,

-Dannon

On Oct 6, 2011, at 7:44 AM, Makis Ladoukakis wrote:

> Dear Galaxy developers,
> 
> Currently I am adding new tools to my galaxy instance as scripts written in 
> Perl language. I was wandering if there is a way to add tools either as .bin 
> or .exe format or if only scripts are supported. I couldn't find anything 
> about it in the wiki or in the FAQ. 
> 
> Thank you,
> Makis Ladoukakis
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Re: [galaxy-user] Adding new tools in Galaxy

[Dannon Baker]

Makais, 

Any type of command line tool, whether script or a binary executable, can be 
used by Galaxy as long as it's properly installed on the system and accessible 
to the Galaxy user.

See 
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Ccommand.3E_tag_set
 for more details on how you might call a compiled executable.

Thanks for using Galaxy,

-Dannon

On Oct 6, 2011, at 7:44 AM, Makis Ladoukakis wrote:

> Dear Galaxy developers,
> 
> Currently I am adding new tools to my galaxy instance as scripts written in 
> Perl language. I was wandering if there is a way to add tools either as .bin 
> or .exe format or if only scripts are supported. I couldn't find anything 
> about it in the wiki or in the FAQ. 
> 
> Thank you,
> Makis Ladoukakis
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Re: [galaxy-user] line estimation for pileup generation

[Dannon Baker]

===> Please use "Reply All" when responding to this email! <===

Sure, no problem.  Those estimates are indeed way off, ideally they're 
within about 10% of the actual count.  Would you mind sharing the 
history with me at this email address so that I might take a look and 
figure out where the estimation went wrong?  Thanks!


-Dannon

On 08/25/2011 06:33 PM, Austin Paul wrote:

Hi Dannon,

Thanks for telling me about that count tool.  I had not used it 
before.  So, it seems the line estimates in the history windows are a 
bit screwy.  One pileup file I mentioned estimated ~4,000,000 lines 
and the count tool showed 988,000.  And the other pileup file I 
mentioned estimated ~200,000 and the count tool showed 6,382,447.  The 
lines totals on the cut files were off as well, but the count tool 
showed consistent numbers between the pileup files and the cut files, 
so I feel better.  Thanks again.


Austin

On Thu, Aug 25, 2011 at 3:19 PM, Dannon Baker <mailto:dannonba...@me.com>> wrote:


As a first step, please confirm an exact line count for the files.
 See the "Line/Word/Character count" tool in the Text Manipulation
section to do this.  If the estimate is significantly off, please
share the history with me and I'll take a look to see what
happened with those particular datasets.

Thanks!

-Dannon

On Aug 25, 2011, at 6:08 PM, Austin Paul wrote:

> ===> Please use "Reply All" when responding to this email! <===
>
> Hello,
>
> I am curious if the line estimation shown in the history window
for pileup generation is at all accurate.  I am using the pileup
files to generate expression data from bwa mapping for looking at
differential expression, but I am having some trouble
understanding the line estimates.  For example, for one pileup
file, when I cut the reference id column and the number of hits
column (columns 1 and 4), the number of lines in the cut file is
about 25% that of the pileup file, and for another file it will be
5000%.   How can the number of lines grow 50x when I am just
cutting columns from the file?  Shouldnt the line estimate be the
same?
>
> Thanks,
> Austin
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Re: [galaxy-user] line estimation for pileup generation

[Dannon Baker]

 ===> Please use "Reply All" when responding to this email! <===

As a first step, please confirm an exact line count for the files.  See the 
"Line/Word/Character count" tool in the Text Manipulation section to do this.  
If the estimate is significantly off, please share the history with me and I'll 
take a look to see what happened with those particular datasets.

Thanks!

-Dannon

On Aug 25, 2011, at 6:08 PM, Austin Paul wrote:

> ===> Please use "Reply All" when responding to this email! <===
> 
> Hello,
> 
> I am curious if the line estimation shown in the history window for pileup 
> generation is at all accurate.  I am using the pileup files to generate 
> expression data from bwa mapping for looking at differential expression, but 
> I am having some trouble understanding the line estimates.  For example, for 
> one pileup file, when I cut the reference id column and the number of hits 
> column (columns 1 and 4), the number of lines in the cut file is about 25% 
> that of the pileup file, and for another file it will be 5000%.   How can the 
> number of lines grow 50x when I am just cutting columns from the file?  
> Shouldnt the line estimate be the same? 
> 
> Thanks,
> Austin
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Re: [galaxy-user] renaming dataset in workflow

[Dannon Baker]

While this is not currently possible, we have recently discussed exposing extra 
fields for use in both parameters and rename actions.  If you're interested, 
I've created a bitbucket enhancement request 
(https://bitbucket.org/galaxy/galaxy-central/issue/623/expose-more-fields-to-rename-action-and)
 that you can follow to track the progress of this feature.

Thanks for the suggestion!

-Dannon

On Jul 29, 2011, at 1:35 PM, Belinda M. Giardine wrote:

> Is it possible when renaming a dataset in a workflow to have it fill in the 
> dataset number like the default labels?
> 
> For example the default label may be "Filter on data 17".  What if I want it 
> to be "High coverage on data 17"?  Could I put some special variable in the 
> text to tell Galaxy to fill in the data number?  If it isn't possible please 
> consider this as a feature request.
> 
> Thanks,
> Belinda
> 
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Re: [galaxy-user] Workflow API

[Dannon Baker]

> My question is how I can modify the script to accept multiple inputs (i.e. 
> how do I define which files in the input folder I want to be each input) and 
> if there's a way to specify runtime parameters. For instance, the workflow I 
> want to execute has a filter step on a tabular input item as one of the later 
> steps which needs to be defined at runtime. How would I specify this in the 
> 'watch_folder.py' parameters? or is this not possible yet?

For accepting multiple inputs, I'm assuming you'd differentiate your input 
files by a particular naming scheme, or location.  Using the 
example_watch_folder.py as an example, you'd need to identify and upload both 
files (the portion creating the libset variable, you'd want to create multiple 
here) and finally modify the portion where the 'ds_map' is created.  That 
dictionary is a mapping of step id's (Input Dataset steps) to the uploaded 
library id's from libset.

As far as specifying other runtime parameters, support for this is planned but 
currently it isn't possible and the workflow needs to be fully predefined 
outside of the input datasets.

Hope this helps.  Thanks for using Galaxy, apologies for the delayed response,

Dannon
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Re: [galaxy-user] can I merge histories?

[Dannon Baker]

Yes, you can copy datasets from one history to another.  In the history panel, 
click "Options", and then "Copy Datasets" to do so.

-Dannon

On Jun 14, 2011, at 12:36 PM, Robert Curtis Hendrickson wrote:

> Folks,
>  
> Is there some way I can merge histories?
>  
> I ran a workflow on 3 different samples in one history, each time putting 
> them in a different history with the same name. However, Galaxy created 3 new 
> histories, each with the same name! But I need the data in the same history 
> to compare and contrast it.
>  
> Thanks,
> Curtis
>  
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> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
> 
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