Re: [galaxy-dev] Mail is not configured for this Galaxy instance.

[shenwiyn]

Hi Hans-Rudolf,
Thank you very much for you help.Actually I want some more information about 
how to configure 'smtp_server' in "universe_wsgi.ini".Could you show me some 
samples to have a look please?





Regards, shenwiyn

From: Hans-Rudolf Hotz
Date: 2013-07-31 23:40
To: shenwiyn
CC: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Mail is not configured for this Galaxy instance.
Hi Shenwiyn

You need to specify a SMTP server. Have a look at the 'smtp_server' 
settings in your "universe_wsgi.ini" file.


Regards, Hans-Rudolf




On 07/31/2013 04:19 PM, shenwiyn wrote:
> Hi everyone,
> In my local Galaxy,when I want to reset my Login password,some error
> occurre
> :"Mail is not configured for this Galaxy instance. Please contact an 
> administrator.
> "Could anyone tell me some imformation about how to configure the mail
> for my Galaxy instance?
> Thank you very much.
> 
> shenwiyn
>
>
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[galaxy-dev] datatype logic

[Ted Goldstein, Ph.D.]

If I share a history, it produces a url with the datasets. This is good. But if 
you click on the eyeball in this view, it shows the dataset in its raw form. 
Its as if the code path does not go through the sophisticated datatype logic. 
Is this deliberate or an oversight?
Thanks,
Ted


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[galaxy-dev] Galaxy cannot start last [server:handlerxx]

[Rodolfo Aramayo]

Hi,

I have a 80 core/1TB RAM Dell server.
In order improve Galaxy performance I modified the universe_wsgi.ini
file so as to improve the Scaling and Load Balancing
as follows:

# Use a threadpool for the web server instead of creating a thread for each
# request.
use_threadpool = True

# Number of threads in the web server thread pool.
threadpool_workers = 200


[server:web0]
use = egg:Paste#http
port = 8090
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web1]
use = egg:Paste#http
port = 8091
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web2]
use = egg:Paste#http
port = 8092
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web3]
use = egg:Paste#http
port = 8093
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web4]
use = egg:Paste#http
port = 8094
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web5]
use = egg:Paste#http
port = 8095
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web6]
use = egg:Paste#http
port = 8096
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web7]
use = egg:Paste#http
port = 8097
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web8]
use = egg:Paste#http
port = 8098
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web9]
use = egg:Paste#http
port = 8099
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10

[server:web10]
use = egg:Paste#http
port = 8100
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 10


[server:manager]
use = egg:Paste#http
port = 8200
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5


[server:handler0]
use = egg:Paste#http
port = 8300
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler1]
use = egg:Paste#http
port = 8301
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler2]
use = egg:Paste#http
port = 8302
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler3]
use = egg:Paste#http
port = 8303
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler4]
use = egg:Paste#http
port = 8304
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler5]
use = egg:Paste#http
port = 8305
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler6]
use = egg:Paste#http
port = 8306
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler7]
use = egg:Paste#http
port = 8307
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler8]
use = egg:Paste#http
port = 8308
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler9]
use = egg:Paste#http
port = 8309
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler10]
use = egg:Paste#http
port = 8310
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler11]
use = egg:Paste#http
port = 8311
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler12]
use = egg:Paste#http
port = 8312
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler13]
use = egg:Paste#http
port = 8313
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler14]
use = egg:Paste#http
port = 8314
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler15]
use = egg:Paste#http
port = 8315
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler16]
use = egg:Paste#http
port = 8316
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler17]
use = egg:Paste#http
port = 8317
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

[server:handler18]
use = egg:Paste#http
port = 8318
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5

# [server:handler19]
# use = egg:Paste#http
# port = 8319
# host = 127.0.0.1
# use_threadpool = true
# threadpool_workers = 5

# [server:handler20]
# use = egg:Paste#http
# port = 8320
# host = 127.0.0.1
# use_threadpool = true
# threadpool_workers = 5


job_manager = manager
job_handlers = 
handler0,handler1,,handler2,handler3,handler4,handler5,handler6,handler7,handler8,handler9,handler10,handler11,handler12,handler13,handler14,handler15,handler16,handler17,handler18



Now the problem I have is that when I start galaxy I cannot get the
last [server:handler18] to load correclt
I get the following error:

galaxy.web.framework.base DEBUG 2013-08-05 17:08:24,236 Enabling
'library_contents' API controller, class: 

Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

[Rodolfo Aramayo]

Dave,

See below

On Mon, Aug 5, 2013 at 1:55 PM, Dave Bouvier  wrote:
> Rodolfo,
>
> Please keep the thread on the mailing list by using the "Reply all" option.

Apologies

>
> You should now be able to go to the manage repository page, select the tool
> dependency, then select 'Manage tool dependencies' from the repository
> actions dropdown and reinstall the blast+ tool dependency.
>
>--Dave B.


I did and it worked well it installed Blast 2.2.26+

However there are two problems:

1. On the admin page "Installed tool shed repository 'ncbi_blast_plus'"
The name, Version and Type display correct values. However the
'Installation status' shows no text

2. When I run the same blast job I was able to run before (using
Blast+ 2.2.28+...that I installed) I get the following:

error
An error occurred with this dataset: blastn: 2.2.26+ Package: blast
2.2.26, build Aug 5 2013 14:01:30 Fatal error: Exit code 255 () Error:
NCBI C++ Exception:
"/usr/local/galaxy/galaxy-dist/database/tmp/tmpyhSi2d/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp",
line 689: Critical:


Obviously it is the installed Blast that is at fault in here

Thanks

--R
>
>
> On 8/5/13 14:03:14.000, Rodolfo Aramayo wrote:
>>
>> Dear Dave,
>>
>> Answers below...
>>
>> On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier  wrote:
>>>
>>> Rodolfo,
>>>
>>> In order to simplify tracking down this issue, could you provide the
>>> changeset revision of Galaxy that is running on tamu.edu? To retrieve the
>>> revision, execute the following command in your galaxy root directory:
>>>
>>> hg id
>>
>>
>> fd4113962c32+ (stable)
>>
>>>
>>> To clarify, our understanding is that you installed the ncbi_blast_plus
>>> repository from the main tool shed, and it installed correctly. You then
>>> uninstalled the repository, and it also uninstalled properly. You then
>>> attempted to reinstall the repository, and encountered the error message
>>> cited in your email.
>>>
>>> Can you confirm the above?
>>
>>
>> This is correct
>>
>>>
>>> We further understand that the repository is stuck in the 'installing'
>>> state.
>>
>>
>> YES and in the "Manage installed tool shed repositories" says now
>> (after having to restart Galaxy for another reason):
>>
>> "Installed, Missing tool dependencies"
>>
>>
>> What options are available from the popup menu next to the
>>>
>>> ncbi_blast_plus repository on the manage installed repositories page?
>>
>>
>>   If I click on the little arrow, it says:
>>
>> Get updates
>> Deactivate or uninstall
>>
>>> 'Deactivate or uninstall' is available, can you try uninstalling again,
>>> and
>>> see if that functions correctly?
>>
>>
>> It worked!
>>
>> Before I was not able to do it as I was getting an ugly galaxy error page
>> But now it did uninstall and removed and was able to clone correctly.
>> However, the directory:
>>
>>
>> ./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/
>>
>> is empty!
>>
>>
>> Should I repopulate it with the one I have in my backup??
>>
>> Thanks
>>
>> --Rodolfo
>>
>>
>>>
>>> --Dave B.
>>>
>>>
>>> On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote:


 People,

 I successfully installed NCBI_Blast_Plus from the toolshed
 The tool, however, failed to work giving the following error:

 Fatal error: Exit code 255 ()
 Error: NCBI C++ Exception:


 "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp",
 line 689: Critical: ncbi::CObject::ThrowNullPointerException() -
 Attempt to access NULL pointer.

 I then tried uninstalling/reinstalling the tool

 However I now get an eternal 'installing' grey message and when I
 click 'manage the repo' I get:

 #

 URL:

 http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f
 File

 '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
 line 149 in __call__
 app_iter = self.application(environ, sr_checker)
 File

 '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
 line 84 in __call__
 return self.application(environ, start_response)
 File

 '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
 line 633 in __call__
 return self.application(environ, start_response)
 File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
 line 132 in __call__
 return self.handle_request( environ, start_response )
 File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
 line 190 in handle_request
 body = method( trans, **kwargs )
 File
 '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
 line 221 in decorator
 return func( self, trans, *args, **kwargs )
 File

 '/usr/local/galaxy/galax

[galaxy-dev] qa_url = slyfox?

[David Hoover]

Strangely, I had never noticed this before.  On some tools, there is a link at 
the top of the tool page that attempts to connect to  
http://slyfox.bx.psu.edu:8080/, which it can't.  This URL is set via the qa_url 
directive in the universe_wsgi.ini file.  What is this URL, and what should it 
be?

David Hoover
Helix Systems Staff
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Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

[Dave Bouvier]

Rodolfo,

Please keep the thread on the mailing list by using the "Reply all" option.

You should now be able to go to the manage repository page, select the 
tool dependency, then select 'Manage tool dependencies' from the 
repository actions dropdown and reinstall the blast+ tool dependency.


   --Dave B.

On 8/5/13 14:03:14.000, Rodolfo Aramayo wrote:

Dear Dave,

Answers below...

On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier  wrote:

Rodolfo,

In order to simplify tracking down this issue, could you provide the
changeset revision of Galaxy that is running on tamu.edu? To retrieve the
revision, execute the following command in your galaxy root directory:

hg id


fd4113962c32+ (stable)



To clarify, our understanding is that you installed the ncbi_blast_plus
repository from the main tool shed, and it installed correctly. You then
uninstalled the repository, and it also uninstalled properly. You then
attempted to reinstall the repository, and encountered the error message
cited in your email.

Can you confirm the above?


This is correct



We further understand that the repository is stuck in the 'installing'
state.


YES and in the "Manage installed tool shed repositories" says now
(after having to restart Galaxy for another reason):

"Installed, Missing tool dependencies"


What options are available from the popup menu next to the

ncbi_blast_plus repository on the manage installed repositories page?


  If I click on the little arrow, it says:

Get updates
Deactivate or uninstall


'Deactivate or uninstall' is available, can you try uninstalling again, and
see if that functions correctly?


It worked!

Before I was not able to do it as I was getting an ugly galaxy error page
But now it did uninstall and removed and was able to clone correctly.
However, the directory:

./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/

is empty!


Should I repopulate it with the one I have in my backup??

Thanks

--Rodolfo




--Dave B.


On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote:


People,

I successfully installed NCBI_Blast_Plus from the toolshed
The tool, however, failed to work giving the following error:

Fatal error: Exit code 255 ()
Error: NCBI C++ Exception:

"/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp",
line 689: Critical: ncbi::CObject::ThrowNullPointerException() -
Attempt to access NULL pointer.

I then tried uninstalling/reinstalling the tool

However I now get an eternal 'installing' grey message and when I
click 'manage the repo' I get:

#

URL:
http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f
File
'/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__
app_iter = self.application(environ, sr_checker)
File
'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
line 84 in __call__
return self.application(environ, start_response)
File
'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
line 132 in __call__
return self.handle_request( environ, start_response )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
line 190 in handle_request
body = method( trans, **kwargs )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 221 in decorator
return func( self, trans, *args, **kwargs )
File
'/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
line 561 in manage_repository
repository = suc.get_installed_tool_shed_repository( trans,
repository_id )
File
'/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py',
line 515 in get_installed_tool_shed_repository
return trans.sa_session.query( trans.model.ToolShedRepository ).get(
trans.security.decode_id( id ) )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py',
line 60 in decode_id
return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip(
"!" ) )
ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b'

#

How can I totally uninstall and re-install this tool?

Thanks
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 http://l

Re: [galaxy-dev] Running local galaxy installation while another httpd is operating on the same computer

[Boaz Shaanan]

Hi Dannon,


Thanks a lot. I'll do as you suggest.


  Cheers,


                  Boaz
 
Boaz Shaanan, Ph.D.

Dept. of Life Sciences  
Ben-Gurion University of the Negev  
Beer-Sheva 84105    
Israel  
    
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan  
Fax:   972-8-647-2992 or 972-8-646-1710
 
 








From: Dannon Baker [dannon.ba...@gmail.com]
Sent: Monday, August 05, 2013 7:47 PM
To: בעז שאנן
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Running local galaxy installation while another httpd is operating on the same computer




Hi Boaz,


You should be able to edit universe_wsgi.ini (line ~30) to specify any port you'd like -- so simply pick something other than 8080, save the file, and retry.  Remember to remove the hash (#) at the beginning of the line to have it take effect.


-Dannon



On Mon, Aug 5, 2013 at 12:42 PM, Boaz Shaanan 
 wrote:


Hi,


I think I'm running into a problem of getting my local galaxy installation server to start because another httpd server is currently running on the same computer (see attached output of run.sh). Toward the end of the attached file you'll notice that the
 server starts with PID number but then runs into a socket conflict (probably with the other server) and stops. Is there a way to get over this problem? Or am I wrong in my diagnosis? 


I did manage to get the galaxy server to start about 2 weeks ago while no other httpd server was running. I then switched the galaxy server off and now I run into this problem while trying to restart it.


   Thanks for your help.


                     Boaz


 
 
Boaz Shaanan, Ph.D.

Dept. of Life Sciences  
Ben-Gurion University of the Negev  
Beer-Sheva 84105    
Israel  
    
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan  
Fax:   972-8-647-2992 or 972-8-646-1710
 
 









___
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  http://galaxyproject.org/search/mailinglists/










___
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[galaxy-dev] getting large files into a local instance of Galaxy

[Gerald Bothe]

Trying out a local instance of Galaxy. Small files can be uploaded with 
"browse.." but this works only for files under 2Gb. Is there a folder in a 
local copy of galaxy-dist where I can copy a large file and have it show up in 
the Get Data/Upload File/Files uploaded via FTP window so that I can properly 
get it into the local history? Copying it directly into the database seemed not 
to work, it didn't show up anywhere.

Gerald 


>
> From: Rodolfo Aramayo 
>To: Dave Bouvier  
>Cc: galaxy-...@bx.psu.edu; Rodolfo Aramayo  
>Sent: Monday, August 5, 2013 2:07 PM
>Subject: Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed
>  
>
>Dave,
>
>Also, when I click on:
>
>"Get repository update"
>
>I get the following error:
>##
>URL: 
>http://galaxy.tamu.edu/admin_toolshed/check_for_updates?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f
>File 
>'/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
>line 149 in __call__
>  app_iter = self.application(environ, sr_checker)
>File 
>'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
>line 84 in __call__
>  return self.application(environ, start_response)
>File 
>'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
>line 633 in __call__
>  return self.application(environ, start_response)
>File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
>line 132 in __call__
>  return self.handle_request( environ, start_response )
>File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
>line 190 in handle_request
>  body = method( trans, **kwargs )
>File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
>line 221 in decorator
>  return func( self, trans, *args, **kwargs )
>File 
>'/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
>line 202 in check_for_updates
>  repository = suc.get_installed_tool_shed_repository( trans, repository_id )
>File '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py',
>line 515 in get_installed_tool_shed_repository
>  return trans.sa_session.query( trans.model.ToolShedRepository ).get(
>trans.security.decode_id( id ) )
>File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py',
>line 60 in decode_id
>  return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) )
>ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b'
>
>##
>
>Thanks
>
>--R
>
>On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier  wrote:
>> Rodolfo,
>>
>> In order to simplify tracking down this issue, could you provide the
>> changeset revision of Galaxy that is running on tamu.edu? To retrieve the
>> revision, execute the following command in your galaxy root directory:
>>
>> hg id
>>
>> To clarify, our understanding is that you installed the ncbi_blast_plus
>> repository from the main tool shed, and it installed correctly. You then
>> uninstalled the repository, and it also uninstalled properly. You then
>> attempted to reinstall the repository, and encountered the error message
>> cited in your email.
>>
>> Can you confirm the above?
>>
>> We further understand that the repository is stuck in the 'installing'
>> state. What options are available from the popup menu next to the
>> ncbi_blast_plus repository on the manage installed repositories page? If
>> 'Deactivate or uninstall' is available, can you try uninstalling again, and
>> see if that functions correctly?
>>
>>    --Dave B.
>>
>>
>> On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote:
>>>
>>> People,
>>>
>>> I successfully installed NCBI_Blast_Plus from the toolshed
>>> The tool, however, failed to work giving the following error:
>>>
>>> Fatal error: Exit code 255 ()
>>> Error: NCBI C++ Exception:
>>>
>>> "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp",
>>> line 689: Critical: ncbi::CObject::ThrowNullPointerException() -
>>> Attempt to access NULL pointer.
>>>
>>> I then tried uninstalling/reinstalling the tool
>>>
>>> However I now get an eternal 'installing' grey message and when I
>>> click 'manage the repo' I get:
>>>
>>> #
>>>
>>> URL:
>>> http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f
>>> File
>>> '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
>>> line 149 in __call__
>>>    app_iter = self.application(environ, sr_checker)
>>> File
>>> '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
>>> line 84 in __call__
>>>    return self.application(environ, start_response)
>>> File
>>> '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
>>> line 633 in __call__
>>>    return self.application(environ, start_response)
>>> File '/u

Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

[Rodolfo Aramayo]

Greg,

Please see my previous responses to Dave
I believe there are issues with the Tool Shed itself

Thanks

--R

On Mon, Aug 5, 2013 at 1:42 PM, Greg Von Kuster  wrote:
> The statement "there are still issues with the Tool Shed itself" is not
> confirmed, correct?  I believe we're still waiting on the response to Dave's
> initial response below.  Or did I miss it???
>
> On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier  wrote:
>
> Rodolfo,
>
> In order to simplify tracking down this issue, could you provide the
> changeset revision of Galaxy that is running on tamu.edu? To retrieve the
> revision, execute the following command in your galaxy root directory:
>
> hg id
>
> To clarify, our understanding is that you installed the ncbi_blast_plus
> repository from the main tool shed, and it installed correctly. You then
> uninstalled the repository, and it also uninstalled properly. You then
> attempted to reinstall the repository, and encountered the error message
> cited in your email.
>
> Can you confirm the above?
>
> We further understand that the repository is stuck in the 'installing'
> state. What options are available from the popup menu next to the
> ncbi_blast_plus repository on the manage installed repositories page? If
> 'Deactivate or uninstall' is available, can you try uninstalling again, and
> see if that functions correctly?
>
>   --Dave B.
>
>
>
> On Aug 5, 2013, at 2:35 PM, Peter Cock  wrote:
>
> On Mon, Aug 5, 2013 at 6:50 PM, Rodolfo Aramayo  wrote:
>
> Dear Peter,
>
> APOLOGIES for the delayed response
>
> Please see below for details..
>
>
> OK, so there are still issues with the Tool Shed itself,
> but the BLAST issue seems to have gone away when
> using a newer version (compiled). I'm working on using
> the NCBI provided binaries if possible, but updating
> the Galaxy BLAST+ bundle to a newer version of
> the underlying BLAST tools is planned.
>
> Thanks,
>
> Peter
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
>
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Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

[Greg Von Kuster]

The statement "there are still issues with the Tool Shed itself" is not 
confirmed, correct?  I believe we're still waiting on the response to Dave's 
initial response below.  Or did I miss it???

On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier  wrote:
> Rodolfo,
> 
> In order to simplify tracking down this issue, could you provide the
> changeset revision of Galaxy that is running on tamu.edu? To retrieve the
> revision, execute the following command in your galaxy root directory:
> 
> hg id
> 
> To clarify, our understanding is that you installed the ncbi_blast_plus
> repository from the main tool shed, and it installed correctly. You then
> uninstalled the repository, and it also uninstalled properly. You then
> attempted to reinstall the repository, and encountered the error message
> cited in your email.
> 
> Can you confirm the above?
> 
> We further understand that the repository is stuck in the 'installing'
> state. What options are available from the popup menu next to the
> ncbi_blast_plus repository on the manage installed repositories page? If
> 'Deactivate or uninstall' is available, can you try uninstalling again, and
> see if that functions correctly?
> 
>   --Dave B.


On Aug 5, 2013, at 2:35 PM, Peter Cock  wrote:

> On Mon, Aug 5, 2013 at 6:50 PM, Rodolfo Aramayo  wrote:
>> Dear Peter,
>> 
>> APOLOGIES for the delayed response
>> 
>> Please see below for details..
>> 
> 
> OK, so there are still issues with the Tool Shed itself,
> but the BLAST issue seems to have gone away when
> using a newer version (compiled). I'm working on using
> the NCBI provided binaries if possible, but updating
> the Galaxy BLAST+ bundle to a newer version of
> the underlying BLAST tools is planned.
> 
> Thanks,
> 
> Peter
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>  http://lists.bx.psu.edu/
> 
> To search Galaxy mailing lists use the unified search at:
>  http://galaxyproject.org/search/mailinglists/

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Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

[Peter Cock]

On Mon, Aug 5, 2013 at 6:50 PM, Rodolfo Aramayo  wrote:
> Dear Peter,
>
> APOLOGIES for the delayed response
>
> Please see below for details..
>

OK, so there are still issues with the Tool Shed itself,
but the BLAST issue seems to have gone away when
using a newer version (compiled). I'm working on using
the NCBI provided binaries if possible, but updating
the Galaxy BLAST+ bundle to a newer version of
the underlying BLAST tools is planned.

Thanks,

Peter
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Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

[Rodolfo Aramayo]

Dave,

Also, when I click on:

"Get repository update"

I get the following error:
##
URL: 
http://galaxy.tamu.edu/admin_toolshed/check_for_updates?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f
File 
'/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__
  app_iter = self.application(environ, sr_checker)
File 
'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
line 84 in __call__
  return self.application(environ, start_response)
File 
'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__
  return self.application(environ, start_response)
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
line 132 in __call__
  return self.handle_request( environ, start_response )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
line 190 in handle_request
  body = method( trans, **kwargs )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
line 221 in decorator
  return func( self, trans, *args, **kwargs )
File 
'/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
line 202 in check_for_updates
  repository = suc.get_installed_tool_shed_repository( trans, repository_id )
File '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py',
line 515 in get_installed_tool_shed_repository
  return trans.sa_session.query( trans.model.ToolShedRepository ).get(
trans.security.decode_id( id ) )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py',
line 60 in decode_id
  return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) )
ValueError: invalid literal for int() with base 10: 'cb73864b36ce6a1b'

##

Thanks

--R

On Thu, Aug 1, 2013 at 9:44 AM, Dave Bouvier  wrote:
> Rodolfo,
>
> In order to simplify tracking down this issue, could you provide the
> changeset revision of Galaxy that is running on tamu.edu? To retrieve the
> revision, execute the following command in your galaxy root directory:
>
> hg id
>
> To clarify, our understanding is that you installed the ncbi_blast_plus
> repository from the main tool shed, and it installed correctly. You then
> uninstalled the repository, and it also uninstalled properly. You then
> attempted to reinstall the repository, and encountered the error message
> cited in your email.
>
> Can you confirm the above?
>
> We further understand that the repository is stuck in the 'installing'
> state. What options are available from the popup menu next to the
> ncbi_blast_plus repository on the manage installed repositories page? If
> 'Deactivate or uninstall' is available, can you try uninstalling again, and
> see if that functions correctly?
>
>--Dave B.
>
>
> On 8/1/13 07:38:22.000, Rodolfo Aramayo wrote:
>>
>> People,
>>
>> I successfully installed NCBI_Blast_Plus from the toolshed
>> The tool, however, failed to work giving the following error:
>>
>> Fatal error: Exit code 255 ()
>> Error: NCBI C++ Exception:
>>
>> "/usr/local/galaxy/galaxy-dist/database/tmp/tmpwL5OFq/ncbi-blast-2.2.26+-src/c++/src/corelib/ncbiobj.cpp",
>> line 689: Critical: ncbi::CObject::ThrowNullPointerException() -
>> Attempt to access NULL pointer.
>>
>> I then tried uninstalling/reinstalling the tool
>>
>> However I now get an eternal 'installing' grey message and when I
>> click 'manage the repo' I get:
>>
>> #
>>
>> URL:
>> http://galaxy.tamu.edu/admin_toolshed/manage_repository?id=ff08d6222f8e14990ad98c3bdd778cf31920e6108c41c80f
>> File
>> '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
>> line 149 in __call__
>>app_iter = self.application(environ, sr_checker)
>> File
>> '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
>> line 84 in __call__
>>return self.application(environ, start_response)
>> File
>> '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
>> line 633 in __call__
>>return self.application(environ, start_response)
>> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
>> line 132 in __call__
>>return self.handle_request( environ, start_response )
>> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py',
>> line 190 in handle_request
>>body = method( trans, **kwargs )
>> File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py',
>> line 221 in decorator
>>return func( self, trans, *args, **kwargs )
>> File
>> '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py',
>> line 561 in manage_repository
>>repository = suc.get_installed_tool_shed_repository( trans,
>> repository_id )
>> File
>> '/usr/local/galaxy/galaxy-dist/lib/tool_shed/util/shed_util_common.py',
>> line 515 in get_installed_tool_shed_repositor

Re: [galaxy-dev] How to Uninstall NCBI_Blast_Plus from ToolShed

[Rodolfo Aramayo]

Dear Peter,

APOLOGIES for the delayed response

Please see below for details..

On Thu, Aug 1, 2013 at 8:51 AM, Peter Cock  wrote:
> On Thu, Aug 1, 2013 at 2:47 PM, Rodolfo Aramayo  wrote:
>> On Thu, Aug 1, 2013 at 8:40 AM, Peter Cock  wrote:
>
> I've seen that kind of error from NCBI BLAST+ before - do you
> know which of the BLAST tools was this, and what the query
> was?

 The repo was:
 repos/devteam/ncbi_blast_plus/9dabbfd73c8a/ncbi_blast_plus

 The query was:
 Output from velvetoptimiser
 /repos/simon-gladman/velvet_optimiser/43c89d82a7d3/velvet_optimiser
>>>
>>> OK, so this was a nucleotide FASTA file from an assembly, right?
>>
>> Yes
>>
>>> What were you searching with BLAST? e.g. BLASTN against NT,
>>> BLASTX against NR, etc.
>>
>> Search was blastn, task megablast of the assembly as query against an
>> in-house made (and installed into galaxy) of a blastn database for
>> Chromosomes 1 to 7 of Neurospora crassa
>> Database was produced with:
>> makeblastdb -in Ncrassa_wt_Chr01.Chr07_v12 -dbtype nucl -title
>> Ncrassa_wt_Chr01.Chr07_v12 -parse_seqids -hash_index
>> and "installed" into the "blastdb.loc" file as required
>
> Can you run this blastn search 'by hand' at the terminal?

Yes, yes and no

> Does that crash too?

No and I do not know

Please let me explain.
I have set up the user galaxy account such that it has access to a
directory called 'bioinfosoft' where all bioinformatics-related
software is installed, including Blast+
Galaxy has 'access' to this directory and there I have compiled Blast+ 2.2.28+
Now, when I installed Blast+ via the toolshed, the toolshed Blast+
package did download and install what I believe it was the 2.2.26+
version of Blast+?
If I recall correctly, I got an error message that went away while the
Blast+ package was being compiled by the toolshed
The errors I got running Blast did all occur when using that
particular version of Blast+ (2.2.26)
I then removed or uninstalled the packaged and tried to re-install
again, but, as I said, it hanged there forever, installing...
To my surprise when I re-run the jobs, they all worked well. This is,
Blast worked like a charm BUT it did because it is NOT using the Blast
packaged that was installed by the toolshed but the Blast package I
compiled myself (2.2.28+) (SEE LOG AT END OF THIS MESSAGE...)

Comparing the directory of galaxy with those of my backups I can see
that the packaged Blast 2.2.26+ that was installed by the toolshed in
the directory:

./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/bin/

is no longer there..

The directory:

./bioinfosoft/galaxy_dependencies/blast+/2.2.26+/devteam/ncbi_blast_plus/9dabbfd73c8a/

is present but it is empty

Therefore to answer your questions:

> Can you run this blastn search 'by hand' at the terminal?

Yes, I can but I would be using a different version of Blast+

> Does that crash too?

No, because I would be using a different version of Blast+

>
> The error sounds very similar to this report which turned out
> to be due to a corrupted BLAST database - so also try
> recreating your DB:
> http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=644962

Regarding this last comment..basically a corrupt database is not the
problem in this case as demonstrated by the fact that I can run Blast
on those databases

Having said that, yes I have observed that depending on how one runs
the makeblastdb command and depending on the type of fasta files used,
you can end up with corrupt output. Some identifiers and symbols
present in the fasta ID can interfere with makeblastdb (especially
some produced by the JGI)

In summary, yes Blast+ is working but because is not using the
compiled Blast+ binaries installed by the toolshed package

The problem I have is that I would like to be able to properly
uninstall and re-install the Blast+ toolsheed so that things work as
they were originally supossed to

On the other hand, if you guys upgrade the package, this might be a
non-issue as the toolshed would just simply generate new directories...

Last, I noticed the command used in the compilation is different from
the one I normally use

The command I use is:

tar -xzvf ncbi-blast-2.2.28+-src.tar.gz
cd ncbi-blast-2.2.28+-src/c++
./configure --prefix=/usr/local/galaxy/bioinfosoft/blast-2.2.28+
--with-64 --with-bincopy --with-mt --without-debug --with-static | tee
c.log
make | tee m.log
make check
make install

Many Thanks


--Rodolfo

>
> Peter

LOG:

galaxy.jobs.handler INFO 2013-08-05 12:11:30,841 (2405) Job dispatched

galaxy.tools DEBUG 2013-08-05 12:11:31,018 Building dependency shell
command for dependency 'blastn'

galaxy.tools WARNING 2013-08-05 12:11:31,018 Failed to resolve
dependency on 'blastn', ignoring

galaxy.tools DEBUG 2013-08-05 12:11:31,018 Building dependency shell
command for dependency 'blast+'

galaxy.tools WARNING 2013-08-05 12:11:31,018 Failed to resolve
dependency on 'blast+', ignoring

galaxy.job

[galaxy-dev] 2014 Galaxy Training Survey

[Dave Clements]

Hello all,

The Galaxy Project is asking for your help on how we should focus our
training efforts for the coming year.  If you are interested in Galaxy
Training, please take a few minutes to let us know what you would like to
see offered, and where you would like training to be held:
  http://bit.ly/gxy14training

Thanks in advance for your time and input,

Dave C

-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://wiki.galaxyproject.org/
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Re: [galaxy-dev] Running local galaxy installation while another httpd is operating on the same computer

[Dannon Baker]

Hi Boaz,

You should be able to edit universe_wsgi.ini (line ~30) to specify any port
you'd like -- so simply pick something other than 8080, save the file, and
retry.  Remember to remove the hash (#) at the beginning of the line to
have it take effect.

-Dannon


On Mon, Aug 5, 2013 at 12:42 PM, Boaz Shaanan  wrote:

>  Hi,
>
>  I think I'm running into a problem of getting my local galaxy
> installation server to start because another httpd server is currently
> running on the same computer (see attached output of run.sh). Toward the
> end of the attached file you'll notice that the server starts with PID
> number but then runs into a socket conflict (probably with the other
> server) and stops. Is there a way to get over this problem? Or am I wrong
> in my diagnosis?
>
>  I did manage to get the galaxy server to start about 2 weeks ago while
> no other httpd server was running. I then switched the galaxy server off
> and now I run into this problem while trying to restart it.
>
> Thanks for your help.
>
>   Boaz
>
>
>
> *Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
>
> E-mail: bshaa...@bgu.ac.il
> Phone: 972-8-647-2220  Skype: boaz.shaanan
> Fax:   972-8-647-2992 or 972-8-646-1710*
> **
> **
> *
>
> *
>
> ___
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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/
>
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>   http://galaxyproject.org/search/mailinglists/
>
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Re: [galaxy-dev] lessc compiler error on blue_colors.ini

[Carl Eberhard]

Nice catch. Maybe an old version of bootstrap's less. I'll see what I can
do about that.

Thanks for the help.


On Mon, Aug 5, 2013 at 12:17 PM, Seth Sims  wrote:

> Dear Carl,
>
>lessc 1.3.3 successfully compiles the scripts. So you've got a bit of a
> goldielocks situation going on. Looks like only 1.3.* versions of less are
> useable with galaxy as it stands.
>
> - Seth
>
>
> On Mon, Aug 5, 2013 at 12:09 PM, Seth Sims  wrote:
>
>> Dear Carl,
>>
>>OK, I have been casting about to find out what the problem was;
>> invoking lessc on the ini was just something I tried since the error from
>> the makefile is completely opaque. I already had PIL and pyparsing
>> installed, just checked again to make sure...
>>
>> After fighting a bit with npm to get lessc installed I now have
>> lessc-1.4.2 which is giving this error:
>>
>> /srv/galaxy-dist/static/style$ sudo make OUT=blue
>> make[1]: Entering directory `/srv/galaxy-dist/static/style/blue'
>> lessc -x ../base.less base.css
>> util.error: Use console.error instead
>> ParseError: Unrecognised input in
>> /srv/galaxy-dist/static/style/bootstrap/mixins.less on line 561, column 7:
>> 560 .spanX (@index) when (@index > 0) {
>> 561   (~".span@{index}") { .span(@index); }
>> 562   .spanX(@index - 1);
>>
>> make[1]: *** [base.css] Error 1
>> make[1]: Leaving directory `/srv/galaxy-dist/static/style/blue'
>> make: *** [all] Error 2
>>
>> So now I guess i'm going to try and downgrade specifically to lessc 1.3.3
>>
>> - Seth
>>
>>
>> On Mon, Aug 5, 2013 at 11:56 AM, Carl Eberhard 
>> wrote:
>>
>>> The ini file is not a .less file so it will error if you call lessc
>>> directly with it.
>>>
>>> It may be that you're lacking some (not obvious) dependencies. Do you
>>> have pyparsing and PIL installed and available in your terminal (pip
>>> install will work with both)?
>>>
>>> You can also use npm to update/install your node modules (sudo npm
>>> install -g less) if you have npm installed.
>>>
>>>
>>> On Mon, Aug 5, 2013 at 11:28 AM, Seth Sims  wrote:
>>>
 Dear Carl,

 You are using a more recent version of lessc then I am so it is
 probably just a versioning error. Ubuntu Precise Pangolin's repositories
 are still at lessc-1.2.1. So apparently I need to manually install a more
 recent version of the compiler. Here is a description of the error if
 anyone else has this problem:

 I have not edited anything, when attempting to compile the vanilla
 blue_colors.ini from the repo I receive an error like so:

 $sudo lessc blue_colors.ini
 ParseError: Syntax Error on line 1 in
 /srv/galaxy-dist/static/style/blue_colors.ini:1:9
 1 base_text=#303030
 2 base_bg_top=#FF

 However the only reason I used that command is because the makefile
 gives a different error:

 $ sudo make OUT=blue
 make[1]: Entering directory `/srv/galaxy-dist/static/style/blue'
 lessc -x ../base.less base.css
 TypeError: Cannot call method 'charAt' of undefined
 at getLocation (/usr/lib/nodejs/less/parser.js:204:34)
 at new LessError (/usr/lib/nodejs/less/parser.js:213:19)
 at Object.toCSS (/usr/lib/nodejs/less/parser.js:379:31)
 at /usr/bin/lessc:103:28
 at /usr/lib/nodejs/less/parser.js:428:40
 at /usr/lib/nodejs/less/parser.js:94:48
 at /usr/lib/nodejs/less/index.js:113:15
 at /usr/lib/nodejs/less/parser.js:428:40
 at /usr/lib/nodejs/less/parser.js:94:48
 at /usr/lib/nodejs/less/index.js:113:15
 make[1]: *** [base.css] Error 2
 make[1]: Leaving directory `/srv/galaxy-dist/static/style/blue'
 make: *** [all] Error 2

 Which is apparently a bug in the version of lessc I have.


 On Mon, Aug 5, 2013 at 11:09 AM, Carl Eberhard >>> > wrote:

> Hey, Seth
>
> I'm using npm less 1.3.3. That error isn't a known issue, no.
>
> Is that the full stack trace/error report? Which files have you edited?
>
> Thanks,
> Carl
>
>
>
> On Tue, Jul 30, 2013 at 2:39 PM, Seth Sims wrote:
>
>> Dear Galaxy devs,
>>
>> I am attempting to create a style directory to match my school's
>> look and feel. I am mainly trying to get the development environment 
>> setup
>> to do this right now. My current problem is that when I attempt to 
>> compile
>> the standard blue_colors.ini which comes with galaxy I am receiving a
>> syntax error:
>>
>> ParseError: Syntax Error on line 1 in
>> /srv/galaxy-dist/static/style/blue_colors.ini:1:10
>> 1 base_text=#303030
>> 2 base_bg_top=#FF
>>
>> I have not edited that file at all. So the first question is, what
>> version of lessc is being used to compile the styles for the basic
>> installation? Also are there any pitfalls I should be aware of with this
>> process.
>>
>> - Seth
>>
>> 

Re: [galaxy-dev] lessc compiler error on blue_colors.ini

[Seth Sims]

Dear Carl,

   lessc 1.3.3 successfully compiles the scripts. So you've got a bit of a
goldielocks situation going on. Looks like only 1.3.* versions of less are
useable with galaxy as it stands.

- Seth


On Mon, Aug 5, 2013 at 12:09 PM, Seth Sims  wrote:

> Dear Carl,
>
>OK, I have been casting about to find out what the problem was;
> invoking lessc on the ini was just something I tried since the error from
> the makefile is completely opaque. I already had PIL and pyparsing
> installed, just checked again to make sure...
>
> After fighting a bit with npm to get lessc installed I now have
> lessc-1.4.2 which is giving this error:
>
> /srv/galaxy-dist/static/style$ sudo make OUT=blue
> make[1]: Entering directory `/srv/galaxy-dist/static/style/blue'
> lessc -x ../base.less base.css
> util.error: Use console.error instead
> ParseError: Unrecognised input in
> /srv/galaxy-dist/static/style/bootstrap/mixins.less on line 561, column 7:
> 560 .spanX (@index) when (@index > 0) {
> 561   (~".span@{index}") { .span(@index); }
> 562   .spanX(@index - 1);
>
> make[1]: *** [base.css] Error 1
> make[1]: Leaving directory `/srv/galaxy-dist/static/style/blue'
> make: *** [all] Error 2
>
> So now I guess i'm going to try and downgrade specifically to lessc 1.3.3
>
> - Seth
>
>
> On Mon, Aug 5, 2013 at 11:56 AM, Carl Eberhard wrote:
>
>> The ini file is not a .less file so it will error if you call lessc
>> directly with it.
>>
>> It may be that you're lacking some (not obvious) dependencies. Do you
>> have pyparsing and PIL installed and available in your terminal (pip
>> install will work with both)?
>>
>> You can also use npm to update/install your node modules (sudo npm
>> install -g less) if you have npm installed.
>>
>>
>> On Mon, Aug 5, 2013 at 11:28 AM, Seth Sims  wrote:
>>
>>> Dear Carl,
>>>
>>> You are using a more recent version of lessc then I am so it is
>>> probably just a versioning error. Ubuntu Precise Pangolin's repositories
>>> are still at lessc-1.2.1. So apparently I need to manually install a more
>>> recent version of the compiler. Here is a description of the error if
>>> anyone else has this problem:
>>>
>>> I have not edited anything, when attempting to compile the vanilla
>>> blue_colors.ini from the repo I receive an error like so:
>>>
>>> $sudo lessc blue_colors.ini
>>> ParseError: Syntax Error on line 1 in
>>> /srv/galaxy-dist/static/style/blue_colors.ini:1:9
>>> 1 base_text=#303030
>>> 2 base_bg_top=#FF
>>>
>>> However the only reason I used that command is because the makefile
>>> gives a different error:
>>>
>>> $ sudo make OUT=blue
>>> make[1]: Entering directory `/srv/galaxy-dist/static/style/blue'
>>> lessc -x ../base.less base.css
>>> TypeError: Cannot call method 'charAt' of undefined
>>> at getLocation (/usr/lib/nodejs/less/parser.js:204:34)
>>> at new LessError (/usr/lib/nodejs/less/parser.js:213:19)
>>> at Object.toCSS (/usr/lib/nodejs/less/parser.js:379:31)
>>> at /usr/bin/lessc:103:28
>>> at /usr/lib/nodejs/less/parser.js:428:40
>>> at /usr/lib/nodejs/less/parser.js:94:48
>>> at /usr/lib/nodejs/less/index.js:113:15
>>> at /usr/lib/nodejs/less/parser.js:428:40
>>> at /usr/lib/nodejs/less/parser.js:94:48
>>> at /usr/lib/nodejs/less/index.js:113:15
>>> make[1]: *** [base.css] Error 2
>>> make[1]: Leaving directory `/srv/galaxy-dist/static/style/blue'
>>> make: *** [all] Error 2
>>>
>>> Which is apparently a bug in the version of lessc I have.
>>>
>>>
>>> On Mon, Aug 5, 2013 at 11:09 AM, Carl Eberhard 
>>> wrote:
>>>
 Hey, Seth

 I'm using npm less 1.3.3. That error isn't a known issue, no.

 Is that the full stack trace/error report? Which files have you edited?

 Thanks,
 Carl



 On Tue, Jul 30, 2013 at 2:39 PM, Seth Sims  wrote:

> Dear Galaxy devs,
>
> I am attempting to create a style directory to match my school's
> look and feel. I am mainly trying to get the development environment setup
> to do this right now. My current problem is that when I attempt to compile
> the standard blue_colors.ini which comes with galaxy I am receiving a
> syntax error:
>
> ParseError: Syntax Error on line 1 in
> /srv/galaxy-dist/static/style/blue_colors.ini:1:10
> 1 base_text=#303030
> 2 base_bg_top=#FF
>
> I have not edited that file at all. So the first question is, what
> version of lessc is being used to compile the styles for the basic
> installation? Also are there any pitfalls I should be aware of with this
> process.
>
> - Seth
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search a

Re: [galaxy-dev] lessc compiler error on blue_colors.ini

[Seth Sims]

Dear Carl,

   OK, I have been casting about to find out what the problem was; invoking
lessc on the ini was just something I tried since the error from the
makefile is completely opaque. I already had PIL and pyparsing installed,
just checked again to make sure...

After fighting a bit with npm to get lessc installed I now have
lessc-1.4.2 which is giving this error:

/srv/galaxy-dist/static/style$ sudo make OUT=blue
make[1]: Entering directory `/srv/galaxy-dist/static/style/blue'
lessc -x ../base.less base.css
util.error: Use console.error instead
ParseError: Unrecognised input in
/srv/galaxy-dist/static/style/bootstrap/mixins.less on line 561, column 7:
560 .spanX (@index) when (@index > 0) {
561   (~".span@{index}") { .span(@index); }
562   .spanX(@index - 1);

make[1]: *** [base.css] Error 1
make[1]: Leaving directory `/srv/galaxy-dist/static/style/blue'
make: *** [all] Error 2

So now I guess i'm going to try and downgrade specifically to lessc 1.3.3

- Seth


On Mon, Aug 5, 2013 at 11:56 AM, Carl Eberhard wrote:

> The ini file is not a .less file so it will error if you call lessc
> directly with it.
>
> It may be that you're lacking some (not obvious) dependencies. Do you have
> pyparsing and PIL installed and available in your terminal (pip install
> will work with both)?
>
> You can also use npm to update/install your node modules (sudo npm install
> -g less) if you have npm installed.
>
>
> On Mon, Aug 5, 2013 at 11:28 AM, Seth Sims  wrote:
>
>> Dear Carl,
>>
>> You are using a more recent version of lessc then I am so it is
>> probably just a versioning error. Ubuntu Precise Pangolin's repositories
>> are still at lessc-1.2.1. So apparently I need to manually install a more
>> recent version of the compiler. Here is a description of the error if
>> anyone else has this problem:
>>
>> I have not edited anything, when attempting to compile the vanilla
>> blue_colors.ini from the repo I receive an error like so:
>>
>> $sudo lessc blue_colors.ini
>> ParseError: Syntax Error on line 1 in
>> /srv/galaxy-dist/static/style/blue_colors.ini:1:9
>> 1 base_text=#303030
>> 2 base_bg_top=#FF
>>
>> However the only reason I used that command is because the makefile gives
>> a different error:
>>
>> $ sudo make OUT=blue
>> make[1]: Entering directory `/srv/galaxy-dist/static/style/blue'
>> lessc -x ../base.less base.css
>> TypeError: Cannot call method 'charAt' of undefined
>> at getLocation (/usr/lib/nodejs/less/parser.js:204:34)
>> at new LessError (/usr/lib/nodejs/less/parser.js:213:19)
>> at Object.toCSS (/usr/lib/nodejs/less/parser.js:379:31)
>> at /usr/bin/lessc:103:28
>> at /usr/lib/nodejs/less/parser.js:428:40
>> at /usr/lib/nodejs/less/parser.js:94:48
>> at /usr/lib/nodejs/less/index.js:113:15
>> at /usr/lib/nodejs/less/parser.js:428:40
>> at /usr/lib/nodejs/less/parser.js:94:48
>> at /usr/lib/nodejs/less/index.js:113:15
>> make[1]: *** [base.css] Error 2
>> make[1]: Leaving directory `/srv/galaxy-dist/static/style/blue'
>> make: *** [all] Error 2
>>
>> Which is apparently a bug in the version of lessc I have.
>>
>>
>> On Mon, Aug 5, 2013 at 11:09 AM, Carl Eberhard 
>> wrote:
>>
>>> Hey, Seth
>>>
>>> I'm using npm less 1.3.3. That error isn't a known issue, no.
>>>
>>> Is that the full stack trace/error report? Which files have you edited?
>>>
>>> Thanks,
>>> Carl
>>>
>>>
>>>
>>> On Tue, Jul 30, 2013 at 2:39 PM, Seth Sims  wrote:
>>>
 Dear Galaxy devs,

 I am attempting to create a style directory to match my school's
 look and feel. I am mainly trying to get the development environment setup
 to do this right now. My current problem is that when I attempt to compile
 the standard blue_colors.ini which comes with galaxy I am receiving a
 syntax error:

 ParseError: Syntax Error on line 1 in
 /srv/galaxy-dist/static/style/blue_colors.ini:1:10
 1 base_text=#303030
 2 base_bg_top=#FF

 I have not edited that file at all. So the first question is, what
 version of lessc is being used to compile the styles for the basic
 installation? Also are there any pitfalls I should be aware of with this
 process.

 - Seth

 ___
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>>>
>>>
>>
>
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Re: [galaxy-dev] lessc compiler error on blue_colors.ini

[Carl Eberhard]

The ini file is not a .less file so it will error if you call lessc
directly with it.

It may be that you're lacking some (not obvious) dependencies. Do you have
pyparsing and PIL installed and available in your terminal (pip install
will work with both)?

You can also use npm to update/install your node modules (sudo npm install
-g less) if you have npm installed.


On Mon, Aug 5, 2013 at 11:28 AM, Seth Sims  wrote:

> Dear Carl,
>
> You are using a more recent version of lessc then I am so it is
> probably just a versioning error. Ubuntu Precise Pangolin's repositories
> are still at lessc-1.2.1. So apparently I need to manually install a more
> recent version of the compiler. Here is a description of the error if
> anyone else has this problem:
>
> I have not edited anything, when attempting to compile the vanilla
> blue_colors.ini from the repo I receive an error like so:
>
> $sudo lessc blue_colors.ini
> ParseError: Syntax Error on line 1 in
> /srv/galaxy-dist/static/style/blue_colors.ini:1:9
> 1 base_text=#303030
> 2 base_bg_top=#FF
>
> However the only reason I used that command is because the makefile gives
> a different error:
>
> $ sudo make OUT=blue
> make[1]: Entering directory `/srv/galaxy-dist/static/style/blue'
> lessc -x ../base.less base.css
> TypeError: Cannot call method 'charAt' of undefined
> at getLocation (/usr/lib/nodejs/less/parser.js:204:34)
> at new LessError (/usr/lib/nodejs/less/parser.js:213:19)
> at Object.toCSS (/usr/lib/nodejs/less/parser.js:379:31)
> at /usr/bin/lessc:103:28
> at /usr/lib/nodejs/less/parser.js:428:40
> at /usr/lib/nodejs/less/parser.js:94:48
> at /usr/lib/nodejs/less/index.js:113:15
> at /usr/lib/nodejs/less/parser.js:428:40
> at /usr/lib/nodejs/less/parser.js:94:48
> at /usr/lib/nodejs/less/index.js:113:15
> make[1]: *** [base.css] Error 2
> make[1]: Leaving directory `/srv/galaxy-dist/static/style/blue'
> make: *** [all] Error 2
>
> Which is apparently a bug in the version of lessc I have.
>
>
> On Mon, Aug 5, 2013 at 11:09 AM, Carl Eberhard wrote:
>
>> Hey, Seth
>>
>> I'm using npm less 1.3.3. That error isn't a known issue, no.
>>
>> Is that the full stack trace/error report? Which files have you edited?
>>
>> Thanks,
>> Carl
>>
>>
>>
>> On Tue, Jul 30, 2013 at 2:39 PM, Seth Sims  wrote:
>>
>>> Dear Galaxy devs,
>>>
>>> I am attempting to create a style directory to match my school's
>>> look and feel. I am mainly trying to get the development environment setup
>>> to do this right now. My current problem is that when I attempt to compile
>>> the standard blue_colors.ini which comes with galaxy I am receiving a
>>> syntax error:
>>>
>>> ParseError: Syntax Error on line 1 in
>>> /srv/galaxy-dist/static/style/blue_colors.ini:1:10
>>> 1 base_text=#303030
>>> 2 base_bg_top=#FF
>>>
>>> I have not edited that file at all. So the first question is, what
>>> version of lessc is being used to compile the styles for the basic
>>> installation? Also are there any pitfalls I should be aware of with this
>>> process.
>>>
>>> - Seth
>>>
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>   http://lists.bx.psu.edu/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
>
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[galaxy-dev] Problems with running jobs on Galaxy

[Philipp Kapranov]

Hello,

I have submitted some simple jobs to Galaxy Main last Friday and they are
still waiting to be run. Are there any issues with the cluster?

Thank you,

Phil

Philipp Kapranov, PhD
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[galaxy-dev] rsync questions

[Gerald Bothe]

Here are a couple of questions on rsync: 
1. the amount of files for hg19 and mm9 is extremely different (over 600 vs. 88 
Gb) - why is that so? They are both mammalian genomes ... are there redundant 
files in hg19, is mm9 incomplete...?
2. if I list the directories for hg19 and mm9, there seems to be a group of 
files for bowtie2 in hg19, but not in mm9 - where are the ones for mm9?
3. genome sequences such as mm9.fa are not in /indexes, there are only pointers 
(mm9/bowtie_index/mm9.fa -> ../seq/mm9.fa ) can the sequence files be 'rsync'ed 
from somewhere?


Gerald  ___
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Re: [galaxy-dev] lessc compiler error on blue_colors.ini

[Seth Sims]

Dear Carl,

You are using a more recent version of lessc then I am so it is
probably just a versioning error. Ubuntu Precise Pangolin's repositories
are still at lessc-1.2.1. So apparently I need to manually install a more
recent version of the compiler. Here is a description of the error if
anyone else has this problem:

I have not edited anything, when attempting to compile the vanilla
blue_colors.ini from the repo I receive an error like so:

$sudo lessc blue_colors.ini
ParseError: Syntax Error on line 1 in
/srv/galaxy-dist/static/style/blue_colors.ini:1:9
1 base_text=#303030
2 base_bg_top=#FF

However the only reason I used that command is because the makefile gives a
different error:

$ sudo make OUT=blue
make[1]: Entering directory `/srv/galaxy-dist/static/style/blue'
lessc -x ../base.less base.css
TypeError: Cannot call method 'charAt' of undefined
at getLocation (/usr/lib/nodejs/less/parser.js:204:34)
at new LessError (/usr/lib/nodejs/less/parser.js:213:19)
at Object.toCSS (/usr/lib/nodejs/less/parser.js:379:31)
at /usr/bin/lessc:103:28
at /usr/lib/nodejs/less/parser.js:428:40
at /usr/lib/nodejs/less/parser.js:94:48
at /usr/lib/nodejs/less/index.js:113:15
at /usr/lib/nodejs/less/parser.js:428:40
at /usr/lib/nodejs/less/parser.js:94:48
at /usr/lib/nodejs/less/index.js:113:15
make[1]: *** [base.css] Error 2
make[1]: Leaving directory `/srv/galaxy-dist/static/style/blue'
make: *** [all] Error 2

Which is apparently a bug in the version of lessc I have.


On Mon, Aug 5, 2013 at 11:09 AM, Carl Eberhard wrote:

> Hey, Seth
>
> I'm using npm less 1.3.3. That error isn't a known issue, no.
>
> Is that the full stack trace/error report? Which files have you edited?
>
> Thanks,
> Carl
>
>
>
> On Tue, Jul 30, 2013 at 2:39 PM, Seth Sims  wrote:
>
>> Dear Galaxy devs,
>>
>> I am attempting to create a style directory to match my school's look
>> and feel. I am mainly trying to get the development environment setup to do
>> this right now. My current problem is that when I attempt to compile the
>> standard blue_colors.ini which comes with galaxy I am receiving a syntax
>> error:
>>
>> ParseError: Syntax Error on line 1 in
>> /srv/galaxy-dist/static/style/blue_colors.ini:1:10
>> 1 base_text=#303030
>> 2 base_bg_top=#FF
>>
>> I have not edited that file at all. So the first question is, what
>> version of lessc is being used to compile the styles for the basic
>> installation? Also are there any pitfalls I should be aware of with this
>> process.
>>
>> - Seth
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
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Re: [galaxy-dev] lessc compiler error on blue_colors.ini

[Carl Eberhard]

Hey, Seth

I'm using npm less 1.3.3. That error isn't a known issue, no.

Is that the full stack trace/error report? Which files have you edited?

Thanks,
Carl



On Tue, Jul 30, 2013 at 2:39 PM, Seth Sims  wrote:

> Dear Galaxy devs,
>
> I am attempting to create a style directory to match my school's look
> and feel. I am mainly trying to get the development environment setup to do
> this right now. My current problem is that when I attempt to compile the
> standard blue_colors.ini which comes with galaxy I am receiving a syntax
> error:
>
> ParseError: Syntax Error on line 1 in
> /srv/galaxy-dist/static/style/blue_colors.ini:1:10
> 1 base_text=#303030
> 2 base_bg_top=#FF
>
> I have not edited that file at all. So the first question is, what version
> of lessc is being used to compile the styles for the basic installation?
> Also are there any pitfalls I should be aware of with this process.
>
> - Seth
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
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Re: [galaxy-dev] History & Visualization list empty

[Benjamin Schuster-Boeckler]

Fantastic, it works now, thank you! I was on 10200, now I'm testing the default 
HEAD and all is looking good!

--
Benjamin Schuster-Böckler
Leadership Fellow for Bioinformatics

☎ +44 1865 617481
✉ benjamin.schuster-boeck...@ludwig.ox.ac.uk

Ludwig Institute for Cancer Research
University of Oxford
Old Road Campus Research Building
Oxford OX3 7DQ
United Kingdom

On 5 Aug 2013, at 13:53, Dannon Baker 
 wrote:

> Hi Ben,
> 
> I think you're seeing a bug that has been fixed as of revision 
> 10230:3985ecec291f.  What version of galaxy are you running, and is 
> log_actions set to True in your universe_wsgi.ini?
> 
> 
> On Fri, Aug 2, 2013 at 2:22 PM, Benjamin Schuster-Boeckler 
>  wrote:
> Hi there,
> 
> I've set up a local galaxy installation that so far is working very nicely. 
> However one little issue that I'm having is that the "Saved Visualizations" 
> and "Saved Histories" lists are empty, even though I have multiple histories 
> and multiple visualizations. In fact, when I choose to visualize a dataset in 
> Trackster and select "View in saved visualization", I DO see the list of 
> existing visualizations. Pictures attached. The identical problem appears 
> with Histories. Any idea what the problem might be? I tried in Chrome and 
> Safari, I logged out and back in, I restarted the server, but nothing fixed 
> the issue...
> 
> Thanks in advance for the help,
> Ben
> 
> --
> Benjamin Schuster-Böckler
> Leadership Fellow for Bioinformatics
> 
> Ludwig Institute for Cancer Research
> University of Oxford
> Old Road Campus Research Building
> Oxford OX3 7DQ
> United Kingdom
>  19.13.21.png>
> 
> ___
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> and other Galaxy lists, please use the interface at:
>   http://lists.bx.psu.edu/
> 
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
> 


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