[galaxy-dev] Support Question

[Jennifer Jackson]

Hi Tomas,

I am going to move your question over to the galaxy-...@bx.psu.edu 
mailing list, which give it better exposure to the development 
community. This is where you will also want to post questions about 
local installs going forward. Someone here may have advice about this 
tool - but really your best bet is with the tool/wrapper author.


I checked the Galaxy Main Tool Shed, and the repository there for this 
tool shows it is inactive/never downloaded in the current tool shed 
version. So, this was not your source or you obtained it some time ago 
(~ 2 yrs). Still, if this was your source/version, log into the Tool 
Shed, click on "Repository Actions", and contact the repo owner:

http://toolshed.g2.bx.psu.edu/view/petr-novak/repeatrxplorer
http://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Contacting_the_owner_of_a_repository

This is another link to the tool author for the Main Tool Shed wrapper 
and the primary tool itself, and perhaps for the wrapper version you are 
working with as well (from some other source, but you will have to check):

http://repeatexplorer.umbr.cas.cz/static/html/help/manual.html

Good luck!

Jen
Galaxy team

On 2/28/13 12:34 AM, Thomas Muench wrote:

Hi,

i have installed RepeatExplorer on our local galaxy instance, but with every 
try, i see only this error message and i don't know why? All installation steps 
of RepeatExplorer was correctly.

Thank you for your help

Thomas Münch
leibniz-institute for plant genetics and crop plant research
Gatersleben, Germany


Traceback (most recent call last):
   File "/opt/galaxy/lib/galaxy/jobs/runners/local.py", line 56, in run_job
 job_wrapper.prepare()
   File "/opt/galaxy/lib/galaxy/jobs/__init__.py", line 368, in prepare
 self.command_line = self.tool.build_command_line( param_dict )
   File "/opt/galaxy/lib/galaxy/tools/__init__.py", line 1524, in 
build_command_line
 command_line = fill_template( self.command, context=param_dict )
   File "/opt/galaxy/lib/galaxy/util/template.py", line 9, in fill_template
 return str( Template( source=template_text, searchList=[context] ) )
   File 
"/opt/galaxy/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py",
 line 1004, in __str__
 return getattr(self, mainMethName)()
   File "cheetah_DynamicallyCompiledCheetahTemplate_1362033265_04_79640.py", 
line 92, in respond
NotFound: cannot find '__root_dir__'


failure preparing job

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http://galaxyproject.org
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Re: [galaxy-dev] Tools and Data

[Enis Afgan]

Correct; certain NSG tools require additional configuration for their
indices (http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup)


On Tue, Mar 5, 2013 at 1:07 PM, shenwiyn  wrote:

> **
> Hi,
> I've installed Galaxy in local as what Rafael does.I want to make sure
> that the basic functions work successfully just depending on the
> necessary tools in Tool 
> dependencies 
> manual,and
> the NGS tools not only depend on the necessary tools but also some another
> needed data(such as indexes,and so on).
>
> thakks
>  --
>  shenwy
>
>
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Re: [galaxy-dev] Search software on public Galaxy servers

[Jeremy Goecks]

The tools API, incomplete as it is, could be used to automatically generate a 
list of tools for a single instance.

J.

On Mar 4, 2013, at 5:37 AM, Hans-Rudolf Hotz wrote:

> 
> 
> On 03/03/2013 05:18 PM, Dave Clements wrote:
>> Hi Bernardo,
>> 
>> I'm intrigued by this idea.  It might be possible to build a Google
>> custom search, similar to the Tools tab of the usegalaxy search
>> (http://galaxyproject.org/search/usegalaxy/).  That's would not be an
>> ideal solution, but it would be quick to implement.
>> 
> 
> or adding a new page to listing all the tools (similar to the "Tool versions" 
> page you get from the report tools). And this page can easily be called and 
> parsed from a central location.
> 
> This kind of reminds me to the "good old days" when we checked the list of 
> databases available from all the public SRS servers:
> 
> http://bioblog.instem.com/download/srs-parser-and-software-downloads/public-srs-installations/
> 
> where the info is all taken from pages like:
> 
> http://www.dkfz.de/menu/cgi-bin/srs7.1.3.1/wgetz?-page+databanks
> http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+databanks
> 
> 
> Such a page listing all the tools would also be nice for the users. Not 
> everybody likes search boxes. Some people prefer reading lists.
> 
> 
> Hans-Rudolf
> 
> 
> 
> 
> 
>> Let me take a look at this in a week or two (traveling this week) and
>> see if searching ~28 sites is tractable/possible with a free Google
>> custom search.
>> 
>> Thanks,
>> 
>> Dave C
>> 
>> 
>> On Thu, Feb 28, 2013 at 8:02 AM, Bernardo Bello > > wrote:
>> 
>>Hi community,
>> 
>>Due to the increasing Galaxy public servers PublicGalaxyServers
>> it would be very
>>useful to have a search tool in order to look for software
>>ready-to-use in the public servers.
>> 
>>Since I know this is not available. Will it be feasible?
>> 
>>Here is the Trello Card https://trello.com/c/FdF5h17c
>> 
>>Regards,
>> 
>>Bernardo
>> 
>> 
>> 
>>--
>> 
>>*Bernardo Bello Ortí*
>> 
>>PhD student
>> 
>>CReSA-IRTA
>> 
>>Campus de Bellaterra-Universitat Autònoma de Barcelona
>> 
>>Edifici CReSA
>> 
>>08193  Bellaterra (Barcelona, Spain)
>> 
>>Tel.: 647 42 52 63 *www.cresa.es  *
>> 
>>*
>>*
>> 
>> 
>> 
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>> 
>> 
>> 
>> 
>> --
>> http://galaxyproject.org/
>> http://getgalaxy.org/
>> http://usegalaxy.org/
>> http://wiki.galaxyproject.org/
>> 
>> 
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[galaxy-dev] Tools and Data

[shenwiyn]

Hi,
I've installed Galaxy in local as what Rafael does.I want to make sure that the 
basic functions work successfully just depending on the necessary tools in Tool 
dependencies manual,and the NGS tools not only depend on the necessary tools 
but also some another needed data(such as indexes,and so on).

thakks



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Re: [galaxy-dev] Composite datatype output for Cuffdiff

[Alex.Khassapov]

Hi Dannon,

I understand that instead of having one dataset with multiple files you are 
planning to use existing datasets and combine them in a 'collection'.  My 
concerns are:
1. Our data consists of 200-8000 files, can you imagine how many datasets we'll 
end up with? It will be a mess.
2. All these files in a  dataset belong to each other and it doesn't make much 
sense to keep them separately.
3. For performance reasons, all these files are located in a single directory 
which makes it easier to iterate over.
4. From my point of view, it makes perfect sense to have a concept of a 
"dataset" with multiple files, you have already a dataset_xxx_files folder 
anyway, and it's not a big change comparing to the new concept of "collection"
5. We are already using the "m:xxx" type datasets (thanks John) in our project, 
I guess you don't even have a timeframe for implementing the "collection" 
concept? I'm sure that for many projects using multi file datasets is a 
requirement now, not in 'years' time.
6. "Collection" is also a good idea and I guess they both can exist together, 
but only in the future, given current users an opportunity to use Galaxy for 
their needs. Otherwise we simply have to look at other frameworks which already 
support multi file datasets.

-Alex

From: Dannon Baker [mailto:dannon.ba...@gmail.com]
Sent: Tuesday, 5 March 2013 1:09 AM
To: Khassapov, Alex (CSIRO IM&T, Clayton)
Cc: chil...@msi.umn.edu; galaxy-...@bx.psu.edu; NeCTAR Cloud Imaging Project 
Team
Subject: Re: [galaxy-dev] Composite datatype output for Cuffdiff

Alex,

To reiterate what Jeremy has already said on the mailing list, this is 
definitely something we want, and need, for Galaxy.  While this particular 
implementation has a lot of good parts, creating these collections as 
first-class composite datasets isn't ideal and we'd be stuck supporting them 
going forward, forever.

There's a clear plan for implementing this in Trello 
(https://trello.com/c/325AXIEr), most of which is straightforward to implement. 
 The 'hard' part is really going to be implementing an ideal UI for dealing 
with these collections, something which we could do in phases.

What exactly are your concerns with the implementation as set out in the Trello 
card?

-Dannon


On Mon, Mar 4, 2013 at 1:32 AM, 
mailto:alex.khassa...@csiro.au>> wrote:
Yeah John,

This is sad, I don't understand why it is such a problem? If it's already 
implemented and used in real projects like ours - then it is needed for the 
community.  I don't think we have other options for our requirements, your 
multiple file datasets implementation was a real saviour for us.

-Alex

-Original Message-
From: jmchil...@gmail.com 
[mailto:jmchil...@gmail.com] On Behalf Of John 
Chilton
Sent: Monday, 4 March 2013 4:42 PM
To: Khassapov, Alex (CSIRO IM&T, Clayton)
Cc: mailto:galaxy-...@bx.psu.edu>>
Subject: Re: [galaxy-dev] Composite datatype output for Cuffdiff

Hi Alex,

  Thanks for the comments. The galaxy team has made it clear here and to me 
privately that this will NOT be included in the Galaxy main code base. I hope 
and am I confident that they will make grouping datasets work, hopefully even 
to thousands of files.

  I do not believe the two ideas are mutually exclusive and I will be 
maintaining a fork of galaxy-central with these additions, I will set this up 
this week hopefully. I will do my best to respond to support requests and make 
multiple file datasets and composite types in general as robust as possible, 
keep up with Galaxy updates, etc
Obviously, it is risky to let a code base drift so far from galaxy main's 
however and you, me, and others who might want to use them will have to 
carefully weigh the risks when determining if multiple file datasets are worth 
the headache.

  Thanks for all your help and inputs. I am sorry this did not turn out 
differently, I feel I have really failed here.

-John


On Sun, Mar 3, 2013 at 10:08 PM,  
mailto:alex.khassa...@csiro.au>> wrote:
> Hi John,
>
> Are you saying that "composite multiple file dataset" isn't required and 
> won't be implemented?
>
> We are using your implementation of multifiles dataset ("m:xxx" type) and 
> hope that eventually it will be pushed into main Galaxy implementation.
>
> As we are using Galaxy for CT reconstruction tools, where input and output 
> can consist of a couple thousand files, other options are not feasible, i.e. 
> grouping datasets.
>
> -Alex
>
> -Original Message-
> From: 
> galaxy-dev-boun...@lists.bx.psu.edu
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu]
>  On Behalf Of John Chilton
> Sent: Thursday, 28 February 2013 2:06 AM
> To: Jeremy Goecks
> Cc: Jim Johnson; mailto:galaxy-...@bx.psu.edu>>
> Subject: Re: [galaxy-dev] Composite datatype output for Cuffdiff
>
> Hey Jeremy,
>
>   I am trying to think about a path fo

Re: [galaxy-dev] [External] Re: data from galaxy

[Sun, Wenping [USA]]

I've already terminated the cluster, since it was for short term use.
It is strange that the admins were not on the user list.
Would you provide some hints for next time re-launching instance, if the same 
thing happens?
Kathryn

From: Dannon Baker [mailto:dannon.ba...@gmail.com]
Sent: Sunday, March 03, 2013 6:56 PM
To: Sun, Wenping [USA]
Cc: Galaxy Dev
Subject: Re: [External] Re: data from galaxy

Can you share the cluster log with me and I'll try to figure out what's 
happened here?

The fact that the admin users are listed indicates that you're definitely 
working with the same instance and a re-mounted data volume (these are parsed 
from universe_wsgi.ini), but I'm struggling to come up with what would yield 
you a working galaxy database, without the users.

-Dannon

On Fri, Mar 1, 2013 at 10:08 AM, Sun, Wenping [USA] 
mailto:sun_wenp...@bah.com>> wrote:
When galaxy instance was launched, I have two user listed as admin on cloud 
admin panel. However, in galaxy site, I couldn't log in with either user. When 
I added additional user at cloud panel to access galaxy's admin, in "manage 
users" there is no user there.

Thanks for the help,
Kathryn

From: Dannon Baker 
[mailto:dannon.ba...@gmail.com]
Sent: Friday, March 01, 2013 9:06 AM
To: Sun, Wenping [USA]
Cc: Galaxy Dev

Subject: Re: [External] Re: data from galaxy

I'm a little confused about the state of this instance.  In the cloud admin 
panel, you have a user listed.  And, in galaxy, you can log in as that user and 
act as an admin?  But when you go to "Manage users" there are no users listed?

Lastly, I've cc'd galaxy-dev here.  Please do try to email the list with these 
questions, and not individual developers directly.

-Dannon


On Wed, Feb 27, 2013 at 4:38 PM, Sun, Wenping [USA] 
mailto:sun_wenp...@bah.com>> wrote:
Hi Dannon,
I just found that the problem of user and data history from below email that 
happened again today. The galaxy cloud cluster was terminated 1-2 weeks ago. I 
have tried once 1 weeks ago to re-launch and it seemed everything was fine, 
both with users and data history.

However, I just tried to re-launch galaxy and found that all the users not 
there. the admin email still on the galaxy launch page, however, on "manage 
users" from galaxy interface, there was no user there (it suppose 2 user, same 
as the admin I added in the first place). All the data history was not 
available because of that as well.

I really appreciate your help on this at your early convenience!! I need to 
retrieve them for tomorrow morning meeting.
Kathryn

-Original Message-
From: Dannon Baker [mailto:dannonba...@me.com]
Sent: Monday, January 21, 2013 9:51 AM
To: Sun, Wenping [USA]
Subject: Re: [External] Re: data from galaxy

Different -- the point is to create a *new* admin user since the password was 
lost for the other one.


On Jan 21, 2013, at 9:50 AM, "Sun, Wenping [USA]" 
mailto:sun_wenp...@bah.com>> wrote:

> Use different email address or the same?
>
> -Original Message-
> From: Dannon Baker [mailto:dannonba...@me.com]
> Sent: Monday, January 21, 2013 9:50 AM
> To: Sun, Wenping [USA]
> Subject: Re: [External] Re: data from galaxy
>
> Add a new user as an admin in the cloudman interface, and then register and 
> log in as that new user.  Then look at the Admin section of Galaxy and you 
> can reset the password for your other user there.
>
> On Jan 21, 2013, at 9:47 AM, "Sun, Wenping [USA]" 
> mailto:sun_wenp...@bah.com>> wrote:
>
>> No, I tried and it said not recognized. I even cannot reset the password, 
>> here is the error for reset password "Mail is not configured for this Galaxy 
>> instance. Please contact an administrator."
>> I have lot of data and don't have time to reproduce them. Please help me 
>> with this.
>> Thanks a lot!
>> Kathryn
>>
>> -Original Message-
>> From: Dannon Baker [mailto:dannonba...@me.com]
>> Sent: Monday, January 21, 2013 9:45 AM
>> To: Sun, Wenping [USA]
>> Subject: [External] Re: data from galaxy
>>
>> You should be able to log back in with the same username and password you 
>> used before.  Is it not working?
>>
>> -Dannon
>>
>>
>> On Jan 21, 2013, at 9:43 AM, "Sun, Wenping [USA]" 
>> mailto:sun_wenp...@bah.com>> wrote:
>>
>>> Hi Dannon,
>>>
>>> I have the whole processed data from galaxy on cloudman and they are on 
>>> during the weekend. However, I found out that I was logged out this 
>>> morning. My user name is still in admin. I tried to log in but I could not. 
>>> This data takes time and would you please direct me how to get back to my 
>>> data?
>>>
>>> Thank you in advance!
>>> Kathryn
>>
>


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Re: [galaxy-dev] Datatype dropdown only 8px wide

[Kelvin Chan]

Nevermind, I noticed that the wiki page on Install galaxy was recently
updated to show how to do this.

-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Kelvin Chan
Sent: Monday, March 04, 2013 9:50 AM
To: 'Nate Coraor'; 'Björn Grüning'
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Datatype dropdown only 8px wide

Hi Nate,

I have checked and I am indeed in the Default branch. Is there an easy way
to switch over to the stable branch via command line?

-Kelvin

-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nate Coraor
Sent: Monday, March 04, 2013 8:52 AM
To: Björn Grüning
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Datatype dropdown only 8px wide

All,

Could you check whether you are running the "default" or "stable" branch of
galaxy-dist?  You can find out with the `hg branch` command.  I believe this
problem should only exist if you're running the "default" (development)
branch, which is not recommended.

Thanks,
--nate

On Mar 4, 2013, at 1:17 AM, Björn Grüning wrote:

> Hi Peter,
> 
> i think it was fixed in 0ea9f51. You need to adopt 
> static/style/base.less.
> 
> Cheers,
> Bjoern
> 
>> I'm seeing something similar with a local galaxy-dist install that 
>> was also installed from bitbucket about 1.5-2 weeks ago, however, in 
>> my case, the width is set to 6px, e.g. > id="s2id_autogen2" style="width: 6px>.
>> 
>> 
>> In fact, I started seeing this after I upgraded a previous install - 
>> and based on this behavior, I did a complete re-install, but am still 
>> getting it.
>> 
>> 
>> Does anyone know whether or not this has been fixed and pushed back 
>> to repository so we can pull the fix?
>> 
>> On Fri, Mar 1, 2013 at 3:59 PM, Kelvin Chan 
>> 
>> wrote:
>>Hello,
>> 
>> 
>> 
>>I am having a slight issue with the Datatype tab of the edit
>>page. I am using a locally installed version of galaxy-dist
>>obtained from bitbucket. I cannot see anything in the dropdown
>>menu to change the datatype. According to the HTML, the box is
>>only 8px wide. >id="s2id_autogen2" style="width: 8px> Is there any way to fix
>>this problem without having to re-install galaxy?
>> 
>> 
>> 
>>Thanks,
>> 
>>Kelvin
>> 
>> 
>> 
>>___
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>>and other Galaxy lists, please use the interface at:
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>> 
>> 
>> 
>> 
>> --
>> Peter Waltman, Ph.D. 
>> pwalt...@ucsc.edu
>> 617.347.1876
>> 
>> ___
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>> Galaxy lists, please use the interface at:
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> 
> 
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Re: [galaxy-dev] Datatype dropdown only 8px wide

[Kelvin Chan]

Hi Nate,

I have checked and I am indeed in the Default branch. Is there an easy way
to switch over to the stable branch via command line?

-Kelvin

-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Nate Coraor
Sent: Monday, March 04, 2013 8:52 AM
To: Björn Grüning
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Datatype dropdown only 8px wide

All,

Could you check whether you are running the "default" or "stable" branch of
galaxy-dist?  You can find out with the `hg branch` command.  I believe this
problem should only exist if you're running the "default" (development)
branch, which is not recommended.

Thanks,
--nate

On Mar 4, 2013, at 1:17 AM, Björn Grüning wrote:

> Hi Peter,
> 
> i think it was fixed in 0ea9f51. You need to adopt 
> static/style/base.less.
> 
> Cheers,
> Bjoern
> 
>> I'm seeing something similar with a local galaxy-dist install that 
>> was also installed from bitbucket about 1.5-2 weeks ago, however, in 
>> my case, the width is set to 6px, e.g. > id="s2id_autogen2" style="width: 6px>.
>> 
>> 
>> In fact, I started seeing this after I upgraded a previous install - 
>> and based on this behavior, I did a complete re-install, but am still 
>> getting it.
>> 
>> 
>> Does anyone know whether or not this has been fixed and pushed back 
>> to repository so we can pull the fix?
>> 
>> On Fri, Mar 1, 2013 at 3:59 PM, Kelvin Chan 
>> 
>> wrote:
>>Hello,
>> 
>> 
>> 
>>I am having a slight issue with the Datatype tab of the edit
>>page. I am using a locally installed version of galaxy-dist
>>obtained from bitbucket. I cannot see anything in the dropdown
>>menu to change the datatype. According to the HTML, the box is
>>only 8px wide. >id="s2id_autogen2" style="width: 8px> Is there any way to fix
>>this problem without having to re-install galaxy?
>> 
>> 
>> 
>>Thanks,
>> 
>>Kelvin
>> 
>> 
>> 
>>___
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>>in your mail client.  To manage your subscriptions to this
>>and other Galaxy lists, please use the interface at:
>> 
>>  http://lists.bx.psu.edu/
>> 
>> 
>> 
>> 
>> --
>> Peter Waltman, Ph.D. 
>> pwalt...@ucsc.edu
>> 617.347.1876
>> 
>> ___
>> 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/
> 
> 
> ___
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> Galaxy lists, please use the interface at:
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[galaxy-dev] Broken pipe in server

[Thomas van Gurp]

Dear all,

Our galaxy suffers from frequent hickups, which apparently are due to broken
pipes.

It will give these errors in paster.log


Exception happened during processing of request from ('127.0.0.1', 53234)
Traceback (most recent call last):
  File 
"/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpse
rver.py", line 1068, in process_request_in_thread
self.finish_request(request, client_address)
  File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib/python2.7/SocketServer.py", line 641, in __init__
self.finish()
  File "/usr/lib/python2.7/SocketServer.py", line 694, in finish
self.wfile.flush()
  File "/usr/lib/python2.7/socket.py", line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe



Any idea why this might be an what I would need to check?

Cheers,
THomas


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[galaxy-dev] deleted datasets inconsistent

[Sarah Diehl]

Hi all,

it seems my clean-up enthusiasm caused some inconsistencies with datasets' 
deleted status. I encounter the following phenomenon: datasets appear totally 
fine in the data libraries, but once they are loaded into a history, they 
appear as deleted there.

I dug through the database and found out that the following query returns all 
datasets in the libraries that were uploaded before my clean-up:

SELECT * FROM library_dataset_dataset_association INNER JOIN library_dataset ON 
 library_dataset_dataset_association.library_dataset_id = library_dataset.id
WHERE library_dataset_dataset_association.deleted = TRUE AND 
library_dataset.deleted = FALSE;

When I set both deleted to false, only datasets that were added after the 
clean-up appear.

Do I break something, if I reset library_dataset_dataset_association.deleted to 
FALSE for the inconsistent datasets? I tried it for one dataset and that seems 
to have fixed the problem. Is this some bug in the clean-up scripts? I guess 
that actually they should have been removed completely.

Best regards,
Sarah
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Re: [galaxy-dev] Datatype dropdown only 8px wide

[Nate Coraor]

All,

Could you check whether you are running the "default" or "stable" branch of 
galaxy-dist?  You can find out with the `hg branch` command.  I believe this 
problem should only exist if you're running the "default" (development) branch, 
which is not recommended.

Thanks,
--nate

On Mar 4, 2013, at 1:17 AM, Björn Grüning wrote:

> Hi Peter,
> 
> i think it was fixed in 0ea9f51. You need to adopt
> static/style/base.less.
> 
> Cheers,
> Bjoern
> 
>> I'm seeing something similar with a local galaxy-dist install that was
>> also installed from bitbucket about 1.5-2 weeks ago, however, in my
>> case, the width is set to 6px, e.g. > id="s2id_autogen2" style="width: 6px>.
>> 
>> 
>> In fact, I started seeing this after I upgraded a previous install -
>> and based on this behavior, I did a complete re-install, but am still
>> getting it.
>> 
>> 
>> Does anyone know whether or not this has been fixed and pushed back to
>> repository so we can pull the fix?
>> 
>> On Fri, Mar 1, 2013 at 3:59 PM, Kelvin Chan 
>> wrote:
>>Hello,
>> 
>> 
>> 
>>I am having a slight issue with the Datatype tab of the edit
>>page. I am using a locally installed version of galaxy-dist
>>obtained from bitbucket. I cannot see anything in the dropdown
>>menu to change the datatype. According to the HTML, the box is
>>only 8px wide. >id="s2id_autogen2" style="width: 8px> Is there any way to fix
>>this problem without having to re-install galaxy?
>> 
>> 
>> 
>>Thanks,
>> 
>>Kelvin
>> 
>> 
>> 
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>> 
>> 
>> 
>> 
>> -- 
>> Peter Waltman, Ph.D. 
>> pwalt...@ucsc.edu
>> 617.347.1876
>> 
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Re: [galaxy-dev] Search software on public Galaxy servers

[Bernardo Bello]

Hi,

I completely agree with Hans proposal. Creating a new page to list all the
tools would be a good alternative. In addition, this page could offer
categories of bioinformatic tools and more information of the tool in
question. Nevertheless, a Google search box is a very good starting point.

The potential of Galaxy is very high and organizing all the ready-to-use
tools can, on the one hand, save a lot of time to people who needs a
specific tool and, on the other hand, exploit the full potential of Galaxy
Public servers that, in my opinion, the still chaotic mode to use these
servers is limiting Galaxy usability and popularity.

Bernardo




2013/3/4 Hans-Rudolf Hotz 

>
>
> On 03/03/2013 05:18 PM, Dave Clements wrote:
>
>> Hi Bernardo,
>>
>> I'm intrigued by this idea.  It might be possible to build a Google
>> custom search, similar to the Tools tab of the usegalaxy search
>> (http://galaxyproject.org/**search/usegalaxy/).
>>  That's would not be an
>> ideal solution, but it would be quick to implement.
>>
>>
> or adding a new page to listing all the tools (similar to the "Tool
> versions" page you get from the report tools). And this page can easily be
> called and parsed from a central location.
>
> This kind of reminds me to the "good old days" when we checked the list of
> databases available from all the public SRS servers:
>
> http://bioblog.instem.com/**download/srs-parser-and-**
> software-downloads/public-srs-**installations/
>
> where the info is all taken from pages like:
>
> http://www.dkfz.de/menu/cgi-**bin/srs7.1.3.1/wgetz?-page+**databanks
> http://srs.ebi.ac.uk/srsbin/**cgi-bin/wgetz?-page+databanks
>
>
> Such a page listing all the tools would also be nice for the users. Not
> everybody likes search boxes. Some people prefer reading lists.
>
>
> Hans-Rudolf
>
>
>
>
>
>  Let me take a look at this in a week or two (traveling this week) and
>> see if searching ~28 sites is tractable/possible with a free Google
>> custom search.
>>
>> Thanks,
>>
>> Dave C
>>
>>
>> On Thu, Feb 28, 2013 at 8:02 AM, Bernardo Bello > > wrote:
>>
>> Hi community,
>>
>> Due to the increasing Galaxy public servers PublicGalaxyServers
>> 
>> >
>> it would be very
>>
>> useful to have a search tool in order to look for software
>> ready-to-use in the public servers.
>>
>> Since I know this is not available. Will it be feasible?
>>
>> Here is the Trello Card https://trello.com/c/FdF5h17c
>>
>> Regards,
>>
>> Bernardo
>>
>>
>>
>> --
>>
>> *Bernardo Bello Ortí*
>>
>>
>> PhD student
>>
>> CReSA-IRTA
>>
>> Campus de Bellaterra-Universitat Autònoma de Barcelona
>>
>> Edifici CReSA
>>
>> 08193  Bellaterra (Barcelona, Spain)
>>
>> Tel.: 647 42 52 63 *www.cresa.es  *
>>
>> *
>>
>> *
>>
>>
>>
>> __**_
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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>
>> http://lists.bx.psu.edu/
>>
>>
>>
>>
>> --
>> 
>> >http://**galaxyproject.org/ 
>>
>> http://getgalaxy.org/
>> http://usegalaxy.org/
>> http://wiki.galaxyproject.org/
>>
>>
>> __**_
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>>
>>


-- 

*Bernardo Bello Ortí*

PhD student

CReSA-IRTA

Campus de Bellaterra-Universitat Autònoma de Barcelona

Edifici CReSA

08193  Bellaterra (Barcelona, Spain)

Tel.: 647 42 52 63 *www.cresa.es  *

*
*
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Re: [galaxy-dev] tool shed can't install via admin user

[Dave Bouvier]

Shenwiyn,

I have not been able to duplicate that error message in my local 
environment, what changeset revision of Galaxy are you running, and how 
is your server environment configured?


   --Dave B.

On 3/4/13 10:41:36.000, shenwiyn wrote:

Hi,
I want to install our local Galaxy for more than one users. When I want
to install some tools from tool shed via admin user ,and  I followed the
instructions in the follow link:
http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#Installing_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance

but these are some errors:


  Server Error

URL:
http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1ec48b84b33d36d8&changeset_revisions=41bba3e648d1
Module paste.exceptions.errormiddleware:*143* in |__call__|
|>>
app_iter
*=* self*.*application*(*environ*,* start_response*)*|
Module paste.debug.prints:*98* in |__call__|
|>>
environ*,*
self*.*app*)*|
Module paste.wsgilib:*539* in |intercept_output|
|>>
app_iter
*=* application*(*environ*,* replacement_start_response*)*|
Module paste.recursive:*80* in |__call__|
|>>
*return*
self*.*application*(*environ*,* start_response*)*|
Module paste.httpexceptions:*632* in |__call__|
|>>
*return*
self*.*application*(*environ*,* start_response*)*|
Module galaxy.web.framework.base:*160* in |__call__|
|>>
body
*=* method*(* trans*,* kwargs *)*|
Module galaxy.web.framework:*208* in |decorator|
|>>
*return*
func*(* self*,* trans*,* ***args*,* kwargs *)*|
Module galaxy.webapps.galaxy.controllers.admin_toolshed:*1177* in
|prepare_for_install|
|>>
response
*=* urllib2*.*urlopen*(* url *)*|
Module urllib2:*126* in |urlopen|
|>>
*return*
_opener*.*open*(*url*,* data*,* timeout*)*|
Module urllib2:*391* in |open|
|>>
response
*=* self*.*_open*(*req*,* data*)*|
Module urllib2:*409* in |_open|
|>>
'_open'*,*
req*)*|
Module urllib2:*369* in |_call_chain|
|>>
result
*=* func*(args*)*|
Module urllib2:*1172* in |http_open|
|>>
*return*
self*.*do_open*(*httplib*.*HTTPConnection*,* req*)*|
Module urllib2:*1147* in |do_open|
|>>
*raise*
URLError*(*err*)*|

Could anyone tell me why ,and how to solve?
Thanks

shenwiyn


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[galaxy-dev] tool shed can't install via admin user

[shenwiyn]

Hi,
I want to install our local Galaxy for more than one users. When I want to 
install some tools from tool shed via admin user ,and  I followed the 
instructions in the follow link:
http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#Installing_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance
 
but these are some errors:
Server Error
URL: 
http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/&repository_ids=1ec48b84b33d36d8&changeset_revisions=41bba3e648d1
Module paste.exceptions.errormiddleware:143 in __call__
>>  app_iter = self.application(environ, start_response)
Module paste.debug.prints:98 in __call__
>>  environ, self.app)
Module paste.wsgilib:539 in intercept_output
>>  app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__
>>  return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__
>>  return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__
>>  body = method( trans, **kwargs )
Module galaxy.web.framework:208 in decorator
>>  return func( self, trans, *args, **kwargs )
Module galaxy.webapps.galaxy.controllers.admin_toolshed:1177 in 
prepare_for_install
>>  response = urllib2.urlopen( url )
Module urllib2:126 in urlopen
>>  return _opener.open(url, data, timeout)
Module urllib2:391 in open
>>  response = self._open(req, data)
Module urllib2:409 in _open
>>  '_open', req)
Module urllib2:369 in _call_chain
>>  result = func(*args)
Module urllib2:1172 in http_open
>>  return self.do_open(httplib.HTTPConnection, req)
Module urllib2:1147 in do_open
>>  raise URLError(err)

Could anyone tell me why ,and how to solve?

Thanks 



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Re: [galaxy-dev] Implementing dataset collections

[Peter Cock]

On Mon, Mar 4, 2013 at 3:16 PM, John Chilton  wrote:
> Hi Alex and Peter,
>
>   I appreciate the comments, but I am not going to keep talking about
> this issue here, I consider the issue closed. The Galaxy team has
> spoken clearly on this topic. They have accepted dozens of my pull
> requests and I am very happy about all of them, and I need them to
> accept dozens (if not hundreds) more in the future so I cannot afford
> to continue to burn political capital by talking about this in this
> forum.
>
>   Alex, I plan to support some version of multiple file datasets for
> at least the next two years. I will put the code here when it is ready
> - https://bitbucket.org/msiappdev/galaxy-extras. Peter, I have
> responded to your questions here -
> https://groups.google.com/forum/?fromgroups#!forum/galaxy-extras.
>
> Thanks,
> -John

Thank John,

Hopefully I will get a better insight into the internals during some
of the developer orientated GCC2013 training sessions - right now
I know that I only have a partial grasp of the compound datatypes.

Regards,

Peter
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Re: [galaxy-dev] Implementing dataset collections

[John Chilton]

Hi Alex and Peter,

  I appreciate the comments, but I am not going to keep talking about
this issue here, I consider the issue closed. The Galaxy team has
spoken clearly on this topic. They have accepted dozens of my pull
requests and I am very happy about all of them, and I need them to
accept dozens (if not hundreds) more in the future so I cannot afford
to continue to burn political capital by talking about this in this
forum.

  Alex, I plan to support some version of multiple file datasets for
at least the next two years. I will put the code here when it is ready
- https://bitbucket.org/msiappdev/galaxy-extras. Peter, I have
responded to your questions here -
https://groups.google.com/forum/?fromgroups#!forum/galaxy-extras.

Thanks,
-John

On Mon, Mar 4, 2013 at 4:49 AM, Peter Cock  wrote:
> Hi all,
>
> I've retitled this from "Composite datatype output for Cuffdiff" to
> "Implementing dataset collections" to try and link into Jeremy's thread.
> References:
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-February/013574.html
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-March/013634.html
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-March/013636.html
>
> On Mon, Mar 4, 2013 at 4:08 AM,   wrote:
>>> Hi John,
>>>
>>> Are you saying that "composite multiple file dataset" isn't required
>>> and won't be implemented?
>>>
>>> We are using your implementation of multifiles dataset ("m:xxx" type)
>>> and hope that eventually it will be pushed into main Galaxy
>>> implementation.
>>>
>>> As we are using Galaxy for CT reconstruction tools, where input
>>> and output can consist of a couple thousand files, other options
>>> are not feasible, i.e. grouping datasets.
>>>
>>> -Alex
>
> On Mon, Mar 4, 2013 at 5:42 AM, John Chilton  wrote:
>> Hi Alex,
>>
>>   Thanks for the comments. The galaxy team has made it clear here and
>> to me privately that this will NOT be included in the Galaxy main code
>> base. I hope and am I confident that they will make grouping datasets
>> work, hopefully even to thousands of files.
>>
>>   I do not believe the two ideas are mutually exclusive and I will be
>> maintaining a fork of galaxy-central with these additions, I will set
>> this up this week hopefully. I will do my best to respond to support
>> requests and make multiple file datasets and composite types in
>> general as robust as possible, keep up with Galaxy updates, etc
>> Obviously, it is risky to let a code base drift so far from galaxy
>> main's however and you, me, and others who might want to use them will
>> have to carefully weigh the risks when determining if multiple file
>> datasets are worth the headache.
>>
>>   Thanks for all your help and inputs. I am sorry this did not turn
>> out differently, I feel I have really failed here.
>>
>> -John
>
> Hi John,
>
> Does your multiple file system work on composite datatypes? For
> example, given a 'blastdbn' file (several files making up a BLAST
> nucleotide database) could we use 'm:blastdbn' to refer to several
> BLAST databases? Is this at least possible in principle based
> on your work so far?
>
> How different is your m:xxx grouping of multiple files of a given
> datatype at odds with the dataset collections idea as outlined by
> Jeremy Goecks here?
>
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-February/013574.html
> https://trello.com/c/325AXIEr
>
> Jeremy's idea mentions the special case of a unique dataset
> collection object for paired-end reads - well if that was defined
> using the existing core Galaxy functionality as a 'pairedfastq'
> composite datatype (made of two FASTQ files), then could we
> use 'm:pairedfastq' (with your enhancement) for a whole bunch
> of paired FASTQ files.  Nice? :)
>
> Regards,
>
> Peter
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Re: [galaxy-dev] Resizing EBS on Amazon

[Dannon Baker]

Unfortunately the snapshotting process used by the is really slow, as
you've noticed, and there's not much we can do to make that faster.  We've
discussed other methods for growing the filesystem but haven't finished it
yet.

For working with S3, instead of s3fs you're more than welcome to give
Galaxy's S3ObjectStore a shot.  There isn't much documentation available
for it right now, and I'd still say it's a beta feature in need of more
testing and optimization, but to enable it define the following options in
your universe_wsgi.ini:

# Object store mode (valid options are: disk, s3, distributed, hierarchical)
#object_store = s3
#aws_access_key = 
#aws_secret_key = 
#s3_bucket = 
#use_reduced_redundancy = True

# Size (in GB) that the cache used by object store should be limited to.
# If the value is not specified, the cache size will be limited only by the
file
# system size.
object_store_cache_size = 

What this will do is use the EBS volume for working, exactly like galaxy
does currently.  Additionally, it'll push datasets to S3 and delete them
from local disk as necessary (last touched deleted first) to stay beneath
object_store_cache_size.  If something swaps out, it's just fetched back
from S3 as needed, but most of the time you'll be working on disk directly
and pushing to S3 in the background.

I'd be more than happy to work with you if you run into any issues trying
this out, this is something we've wanted to firm up for a while now and
having a real live test case would be useful!

-Dannon


On Tue, Feb 26, 2013 at 7:24 PM, Scooter Willis  wrote:

> Used cloud man to create a new cluster on Feb 22 and picked 500GB as the
> initial size of the data drive. Working with TCGA exome DNA seq data didn't
> take long to fill that up. Used the cloud man admin interface to resize
> from 500GB to 1TB and the resize operation took 15 hours. Not sure if that
> is expected so wanted to give some heads up in case that is an area for
> optimization.
>
> Since I now have a local storage problem as I need to work with more than
> 1TB of data I tried to go the route of setting a S3 bucket using Fuse. Ran
> into a problem where the first s3fs software I tried to install had a
> version issue with Ubuntu 10.
>
> I remember something in a support email that better support for Amazon S3
> was in the works. Can you provide any guidance or thoughts on how to work
> with more than 1TB of data using cost effective S3 versus expensive EBS?
> The same applies for storing results at S3.
>
> With s3fs the file system can hide many of the complexities of moving
> files back and forth with caching where working with 30GB+ files isn't
> going to be fun.
>
> Thanks
>
> Scooter
>
>
>
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Re: [galaxy-dev] Error when upgrading the database to version 110

[Dannon Baker]

On Mon, Mar 4, 2013 at 7:59 AM, Hans-Rudolf Hotz  wrote:

> @ Dannon
>
>
> > While we definitely do recommend that if you have the option to
> > choose, go with postgres, Galaxy should function both now and in the
> > future with MySQL.  In this case, your galaxy will function just fine
> > without that index.
>
> I assume there are a lot of 'old' Galaxy servers using MySQL around, where
> the 'galaxy admin' (like me) would love to switch to postgres. Maybe we can
> do a community effort putting together a "MySQL-to-postgres" protocol for a
> defined Galaxy release? And after that release, only postgres is supported.
> I am sure this would make a lot of things easier.something to discuss
> in Oslo?
>

Sure, it's definitely something to discuss if we keep running into these
issues, but my hope is really that upgrading SqlAlchemy will obviate the
need to deal with this at all, and that everything will 'just work' going
forward with whatever database folks want to use.  That said, if there are
others who want to just go ahead and migrate from MySQL to postgres a
tested protocol for doing so would be a great thing to try and put together
as a community and I'd be happy to help.

-Dannon
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Re: [galaxy-dev] Bug in handling user job limits (due to dynamic job runner code?)

[Nate Coraor]

Hi Hans,

Thanks for "bumping" this thread.  The issue has been fixed in development and 
will be included in the next release.

--nate

On Mar 4, 2013, at 5:48 AM, Hans-Rudolf Hotz wrote:

> Hi Lance
> 
> I was just running into the same issue as part of upgrading our production 
> server from release 2012_10_05 to 2013_02_08 (unfortunately, I didn't catch 
> it last week, when I did our test server, as the job limit was not set there).
> 
> I added a little comment to your trello "ticket", but I thought it might be 
> useful to know for a the wider community. The user job limit has been very 
> handy for us. And I am sure other Galaxy installations rely on this as well.
> 
> 
> Regards, Hans-Rudolf
> 
> On 01/18/2013 11:28 PM, Lance Parsons wrote:
>> Just an update on this issue. Upon further investigation, it looks like
>> the dynamic job runner code in commit 6f3b4e8 broke this. I haven't been
>> able to parse through everything going on yet to propose a fix, but I've
>> discovered two things:
>> 
>> 1) Moving the self.__clear_user_job_count() call outside of the if
>> block, does indeed fix that issue
>> 2) Fixing that leads the __check_user_jobs method to fail since it does
>> not check `self.track_jobs_in_database`, but instead assumes that jobs
>> are in the database, resulting in a different exception regarding
>> invalid columns.
>> 
>> Lance Parsons wrote:
>>> I submitted a trello "ticket" [(https://trello.com/c/6vxkqdjT)
>>> regarding this, but wanted to make sure I brought it to someone's
>>> attention (it's causing me some queue issues with my instance of galaxy).
>>> 
>>> When registered_user_job_limit and anonymous_user_job_limit are set in
>>> universe.wsgi jobs cannot be run, instead the following error occurs:
>>> 
>>> galaxy.jobs.handler ERROR 2012-12-04 12:44:51,869 failure running job
>>> 22396
>>> Traceback (most recent call last):
>>>  File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py",
>>> line 183, in __monitor_step
>>>job_state = self.__check_if_ready_to_run( job )
>>>  File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py",
>>> line 253, in __check_if_ready_to_run
>>>state = self.__check_user_jobs( job )
>>>  File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py",
>>> line 274, in __check_user_jobs
>>>if not self.user_job_count:
>>> AttributeError: 'JobHandlerQueue' object has no attribute
>>> 'user_job_count'
>>> 
>>> Commenting out the lines for registered_user_job_limit and
>>> anonymous_user_job_limit in universe.wsgi allows job to be queue one
>>> again.
>>> It looks like this is due to the fact that
>>> `self.__clear_user_job_count()` on line 159 of `handler.py` is only
>>> called when jobs are tracked in the database. If jobs are not tracked
>>> in the database (as in my case), the error occurs. Perhaps the fix
>>> would be to simply move the call outside the `if` block.
>>> 
>>> It appears this was broken in the 2012-11-13 revision (73e05bc).
>>> 
>>> 
>> 
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Re: [galaxy-dev] Composite datatype output for Cuffdiff

[Dannon Baker]

Alex,

To reiterate what Jeremy has already said on the mailing list, this is
definitely something we want, and need, for Galaxy.  While this particular
implementation has a lot of good parts, creating these collections as
first-class composite datasets isn't ideal and we'd be stuck supporting
them going forward, forever.

There's a clear plan for implementing this in Trello (
https://trello.com/c/325AXIEr), most of which is straightforward to
implement.  The 'hard' part is really going to be implementing an ideal UI
for dealing with these collections, something which we could do in phases.

What exactly are your concerns with the implementation as set out in the
Trello card?

-Dannon



On Mon, Mar 4, 2013 at 1:32 AM,  wrote:

> Yeah John,
>
> This is sad, I don't understand why it is such a problem? If it's already
> implemented and used in real projects like ours - then it is needed for the
> community.  I don't think we have other options for our requirements, your
> multiple file datasets implementation was a real saviour for us.
>
> -Alex
>
> -Original Message-
> From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John
> Chilton
> Sent: Monday, 4 March 2013 4:42 PM
> To: Khassapov, Alex (CSIRO IM&T, Clayton)
> Cc: 
> Subject: Re: [galaxy-dev] Composite datatype output for Cuffdiff
>
> Hi Alex,
>
>   Thanks for the comments. The galaxy team has made it clear here and to
> me privately that this will NOT be included in the Galaxy main code base. I
> hope and am I confident that they will make grouping datasets work,
> hopefully even to thousands of files.
>
>   I do not believe the two ideas are mutually exclusive and I will be
> maintaining a fork of galaxy-central with these additions, I will set this
> up this week hopefully. I will do my best to respond to support requests
> and make multiple file datasets and composite types in general as robust as
> possible, keep up with Galaxy updates, etc
> Obviously, it is risky to let a code base drift so far from galaxy main's
> however and you, me, and others who might want to use them will have to
> carefully weigh the risks when determining if multiple file datasets are
> worth the headache.
>
>   Thanks for all your help and inputs. I am sorry this did not turn out
> differently, I feel I have really failed here.
>
> -John
>
>
> On Sun, Mar 3, 2013 at 10:08 PM,   wrote:
> > Hi John,
> >
> > Are you saying that "composite multiple file dataset" isn't required and
> won't be implemented?
> >
> > We are using your implementation of multifiles dataset ("m:xxx" type)
> and hope that eventually it will be pushed into main Galaxy implementation.
> >
> > As we are using Galaxy for CT reconstruction tools, where input and
> output can consist of a couple thousand files, other options are not
> feasible, i.e. grouping datasets.
> >
> > -Alex
> >
> > -Original Message-
> > From: galaxy-dev-boun...@lists.bx.psu.edu
> > [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of John Chilton
> > Sent: Thursday, 28 February 2013 2:06 AM
> > To: Jeremy Goecks
> > Cc: Jim Johnson; 
> > Subject: Re: [galaxy-dev] Composite datatype output for Cuffdiff
> >
> > Hey Jeremy,
> >
> >   I am trying to think about a path forward with this composite multiple
> file dataset implementation. It seems there is consensus among the galaxy
> team that it shouldn't be included because grouping actual datasets would
> be superior. In that light, I am revisiting this e-mail, because depending
> on the implementation of what you described multiple file datasets are a
> specific case of this concept with some likely uncontroversial enhancements
> for the specific case of composite datatypes that are a homogeneous list of
> files. Does that make any sense?
> >
> >   If I implemented (i) and (ii) in such a way that the multiple file
> dataset stuff flowed out more organically is there any chance than it could
> be included in galaxy-central. If no and the implicit datatypes and
> parallelism stuff would remain no-gos implementing what you described would
> still benefit the multiple file datasets implementation, so I still might
> do this, would a clean implementation of just what you described be
> accepted?
> >
> >   Any thoughts you or anyone has on the future direction of composite
> datatypes in general would be appreciated?
> >
> > Thanks for your time,
> > -John
> >
> >
> > On Fri, Oct 12, 2012 at 2:44 PM, Jeremy Goecks 
> wrote:
> >> Hi Jim,
> >>
> >> This is nice and is a path forward for the immediate future.
> >>
> >> That said, a couple extensions to Galaxy to better support composite
> >> datatypes would enable cummerbund without the additional tools:
> >>
> >> (i) extending the composite datatype to include definition of
> >> individual outputs in the collection;
> >> (ii) extend the history panel to allow usage/selection of (1) the
> >> complete composite set of files or (2) individual items in a
> >> composite datatype
> >>
> >> Once (i) is do

Re: [galaxy-dev] Error when upgrading the database to version 110

[Hans-Rudolf Hotz]

Hi Derrick and Dannon


@ Derrick


Yours happened when upgrading from 108 - 109 (which didn't happen to me).

If you have a chance to upgrade to release_2013.02.08, your database
will be upgrade from 109 - 110, I am very interested to see if the index
creation error happens to you as well.



We are talking about the same step (it is all part of our upgrade to the 
2013.02.08 release which in my case involved changing the db from 107 to 
110), see: 
~/lib/galaxy/model/migrate/versions0109_add_repository_dependency_tables.py


Nevertheless, thanks for identifying the actual cause of the problem ie:
>There is identifier length limit in MySQL which is 64


So I am just puzzled, why I don't get this particular error message. I 
asked our sysadmin again, and he claims not to see this error in the 
logs (for our developments server upgraded last week and our production 
server upgraded today).



@ Dannon

> While we definitely do recommend that if you have the option to
> choose, go with postgres, Galaxy should function both now and in the
> future with MySQL.  In this case, your galaxy will function just fine
> without that index.

I assume there are a lot of 'old' Galaxy servers using MySQL around, 
where the 'galaxy admin' (like me) would love to switch to postgres. 
Maybe we can do a community effort putting together a 
"MySQL-to-postgres" protocol for a defined Galaxy release? And after 
that release, only postgres is supported. I am sure this would make a 
lot of things easier.something to discuss in Oslo?



Regards, Hans-Rudolf

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Re: [galaxy-dev] Reloading *.loc files

[Peter Cock]

On Fri, Mar 1, 2013 at 2:55 PM, Peter Cock  wrote:
> Hello all,
>
> Re: BitBucket Issue 538 - Admin action to reload ".loc" files without
> restarting Galaxy
> https://trello.com/card/538-admin-action-to-reload-loc-files-without-restarting-galaxy/506338ce32ae458f6d15e4b3/475
>
> Currently Galaxy administrators can reload a tool's XML configuration
> file, which is very helpful (especially as a developer working on
> changes to a single tool). Similarly it would be useful to be able to
> reload one (or all) of the *.loc files (e.g. if a new BLAST database
> is added), without having to restart Galaxy.
>
> Further to this, it would be useful to trigger this from a script via
> the Galaxy API or otherwise. Should this be filed as a new issue, or a
> comment on the existing issue?
>
> Another idea for enhancement would be to monitor the loc files for
> *automatic* reloading without user or script intervention (but that
> might be too much magic), or simply (re)loading loc files on demand
> rather than at startup.
>
> Do the Galaxy team have any plans in this area?
>
> Thanks,
>
> Peter

One example I had in mind was a tool using a loc file for a list of
databases, with a special entry "latest". If told to use the latest
DB, the tool would check the source website/FTP site. If the
latest file is already downloaded locally, it would just use that.
If not, it would download the latest file and use it. That part is
all quite doable in a tool wrapper script (assuming write
permissions in the desired database folder).

Now for the 'clever' part - the new database could be added to
the loc file for explicit selection by future users. It could be added
at the top to make it the default if desired. Then somehow we'd
need Galaxy to reload the loc file.

Of course, from a reproducibility point of view, the 'latest' version
of a database is not ideal (especially when there are versioned
or dated snapshots), but it is commonly requested all the same.

Peter
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Re: [galaxy-dev] Implementing dataset collections

[Peter Cock]

Hi all,

I've retitled this from "Composite datatype output for Cuffdiff" to
"Implementing dataset collections" to try and link into Jeremy's thread.
References:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-February/013574.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-March/013634.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-March/013636.html

On Mon, Mar 4, 2013 at 4:08 AM,   wrote:
>> Hi John,
>>
>> Are you saying that "composite multiple file dataset" isn't required
>> and won't be implemented?
>>
>> We are using your implementation of multifiles dataset ("m:xxx" type)
>> and hope that eventually it will be pushed into main Galaxy
>> implementation.
>>
>> As we are using Galaxy for CT reconstruction tools, where input
>> and output can consist of a couple thousand files, other options
>> are not feasible, i.e. grouping datasets.
>>
>> -Alex

On Mon, Mar 4, 2013 at 5:42 AM, John Chilton  wrote:
> Hi Alex,
>
>   Thanks for the comments. The galaxy team has made it clear here and
> to me privately that this will NOT be included in the Galaxy main code
> base. I hope and am I confident that they will make grouping datasets
> work, hopefully even to thousands of files.
>
>   I do not believe the two ideas are mutually exclusive and I will be
> maintaining a fork of galaxy-central with these additions, I will set
> this up this week hopefully. I will do my best to respond to support
> requests and make multiple file datasets and composite types in
> general as robust as possible, keep up with Galaxy updates, etc
> Obviously, it is risky to let a code base drift so far from galaxy
> main's however and you, me, and others who might want to use them will
> have to carefully weigh the risks when determining if multiple file
> datasets are worth the headache.
>
>   Thanks for all your help and inputs. I am sorry this did not turn
> out differently, I feel I have really failed here.
>
> -John

Hi John,

Does your multiple file system work on composite datatypes? For
example, given a 'blastdbn' file (several files making up a BLAST
nucleotide database) could we use 'm:blastdbn' to refer to several
BLAST databases? Is this at least possible in principle based
on your work so far?

How different is your m:xxx grouping of multiple files of a given
datatype at odds with the dataset collections idea as outlined by
Jeremy Goecks here?

http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-February/013574.html
https://trello.com/c/325AXIEr

Jeremy's idea mentions the special case of a unique dataset
collection object for paired-end reads - well if that was defined
using the existing core Galaxy functionality as a 'pairedfastq'
composite datatype (made of two FASTQ files), then could we
use 'm:pairedfastq' (with your enhancement) for a whole bunch
of paired FASTQ files.  Nice? :)

Regards,

Peter
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Re: [galaxy-dev] Bug in handling user job limits (due to dynamic job runner code?)

[Hans-Rudolf Hotz]

Hi Lance

 I was just running into the same issue as part of upgrading our 
production server from release 2012_10_05 to 2013_02_08 (unfortunately, 
I didn't catch it last week, when I did our test server, as the job 
limit was not set there).


I added a little comment to your trello "ticket", but I thought it might 
be useful to know for a the wider community. The user job limit has been 
very handy for us. And I am sure other Galaxy installations rely on this 
as well.



Regards, Hans-Rudolf

On 01/18/2013 11:28 PM, Lance Parsons wrote:

Just an update on this issue. Upon further investigation, it looks like
the dynamic job runner code in commit 6f3b4e8 broke this. I haven't been
able to parse through everything going on yet to propose a fix, but I've
discovered two things:

1) Moving the self.__clear_user_job_count() call outside of the if
block, does indeed fix that issue
2) Fixing that leads the __check_user_jobs method to fail since it does
not check `self.track_jobs_in_database`, but instead assumes that jobs
are in the database, resulting in a different exception regarding
invalid columns.

Lance Parsons wrote:

I submitted a trello "ticket" [(https://trello.com/c/6vxkqdjT)
regarding this, but wanted to make sure I brought it to someone's
attention (it's causing me some queue issues with my instance of galaxy).

When registered_user_job_limit and anonymous_user_job_limit are set in
universe.wsgi jobs cannot be run, instead the following error occurs:

galaxy.jobs.handler ERROR 2012-12-04 12:44:51,869 failure running job
22396
Traceback (most recent call last):
  File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py",
line 183, in __monitor_step
job_state = self.__check_if_ready_to_run( job )
  File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py",
line 253, in __check_if_ready_to_run
state = self.__check_user_jobs( job )
  File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py",
line 274, in __check_user_jobs
if not self.user_job_count:
AttributeError: 'JobHandlerQueue' object has no attribute
'user_job_count'

Commenting out the lines for registered_user_job_limit and
anonymous_user_job_limit in universe.wsgi allows job to be queue one
again.
It looks like this is due to the fact that
`self.__clear_user_job_count()` on line 159 of `handler.py` is only
called when jobs are tracked in the database. If jobs are not tracked
in the database (as in my case), the error occurs. Perhaps the fix
would be to simply move the call outside the `if` block.

It appears this was broken in the 2012-11-13 revision (73e05bc).





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Re: [galaxy-dev] Search software on public Galaxy servers

[Hans-Rudolf Hotz]

On 03/03/2013 05:18 PM, Dave Clements wrote:

Hi Bernardo,

I'm intrigued by this idea.  It might be possible to build a Google
custom search, similar to the Tools tab of the usegalaxy search
(http://galaxyproject.org/search/usegalaxy/).  That's would not be an
ideal solution, but it would be quick to implement.



or adding a new page to listing all the tools (similar to the "Tool 
versions" page you get from the report tools). And this page can easily 
be called and parsed from a central location.


This kind of reminds me to the "good old days" when we checked the list 
of databases available from all the public SRS servers:


http://bioblog.instem.com/download/srs-parser-and-software-downloads/public-srs-installations/

where the info is all taken from pages like:

http://www.dkfz.de/menu/cgi-bin/srs7.1.3.1/wgetz?-page+databanks
http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+databanks


Such a page listing all the tools would also be nice for the users. Not 
everybody likes search boxes. Some people prefer reading lists.



Hans-Rudolf






Let me take a look at this in a week or two (traveling this week) and
see if searching ~28 sites is tractable/possible with a free Google
custom search.

Thanks,

Dave C


On Thu, Feb 28, 2013 at 8:02 AM, Bernardo Bello mailto:popn...@gmail.com>> wrote:

Hi community,

Due to the increasing Galaxy public servers PublicGalaxyServers
 it would be very
useful to have a search tool in order to look for software
ready-to-use in the public servers.

Since I know this is not available. Will it be feasible?

Here is the Trello Card https://trello.com/c/FdF5h17c

Regards,

Bernardo



--

*Bernardo Bello Ortí*

PhD student

CReSA-IRTA

Campus de Bellaterra-Universitat Autònoma de Barcelona

Edifici CReSA

08193  Bellaterra (Barcelona, Spain)

Tel.: 647 42 52 63 *www.cresa.es  *

*
*



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--
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://wiki.galaxyproject.org/


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