Re: [galaxy-dev] [galaxy-user] Problem using Galaxy on the cloud

[Brad Chapman]

Jan;
No problem, sorry I don't have a nicer immediate solution for
you. I appreciate the problem report and hopefully we'll figure out a
clean fix for this.

CloudBioLinux does have Velvet included by default, so you should be
able to use it without needing to compile. Were you having trouble
building, or running it? Velvet and other assemblers are memory hungry,
so the issue you were seeing may be due to running out of memory. 'top'
is a useful way to monitor memory usage from the console.

If it is a memory issue, AWS does have some high-memory instances you
could try:

http://aws.amazon.com/ec2/instance-types/

I don't have a lot of experience doing assembly so unfortunately don't
have good estimates for memory usage. It might be worth asking on the
Velvet mailing list if you are still running into issues.

Hope this helps,
Brad

> Thanks Brad,
> 
> I will see if I can do what you suggest-even if you are talking
> Klingon now:) .  I really just want to use Velvet, so I may try to
> install it through CloudBioLinux-although last time I tried that I
> seemed to crash everything.  I really need to get better at this
> stuff-or move to a place with bioinformatics support.
> 
> Many Many Thanks,
> Jan
> 
> On Mar 7, 2012, at 9:22 PM, Brad Chapman wrote:
> 
> 
> Jan;
> Thanks for getting back with all the detailed information. I dug into
> this further and understand what is happening:
> 
> - tools/data_source/upload.py calls
>  lib/galaxy/datatypes/sniff.py:stream_to_file
> - stream_to_file uses pythons tempfile module
> - tempfile defaults to using /tmp
> - As large files stream in the temporary space fills up, causing the
>  issue you are seeing.
> 
> The best way to work around this is to have the galaxy user on Amazon
> export TMPDIR to point at a temporary directory on /mnt/galaxyData
> instead of the root filesystem.
> 
> I'm hoping that Enis or Dannon might be able to help out with the best
> place to set this in CloudMan to avoid the issue, I've cc'ed them in.
> 
> If you want to manually fix it to get some work done, you could create a
> directory /mnt/galaxyData/tmp and then symlink /tmp there:
> 
> ln -s /mnt/galaxyData/tmp /tmp
> 
> Hope this helps and we can come up with a more permanent fix. Thanks
> again,
> Brad
> 
> 
> Thanks Brad,
> Sorry it has taken me so long to respond.  I had a meeting sort of day. I 
> started another instance to recreate what is happening to me in more detail.  
> I hope this helps.  I tried to color code things so you could follow 
> everything more easily.
> 
> This is what I have when I start up Galaxy through BioCloudCentral before I 
> import any files...
> 
> Get cloud support with Ubuntu Advantage Cloud Guest
>  http://www.ubuntu.com/business/services/cloud
> ubuntu@ip-10-44-78-218:~$ df -h
> FilesystemSize  Used Avail Use% Mounted on
> /dev/xvda1 20G   13G  6.1G  68% /
> udev  8.4G  4.0K  8.4G   1% /dev
> tmpfs 3.4G  644K  3.4G   1% /run
> none  5.0M 0  5.0M   0% /run/lock
> none  8.4G 0  8.4G   0% /run/shm
> /dev/xvdb 404G  201M  383G   1% /mnt
> 
> After starting to import data (pasted 
> https://s3.amazonaws.com/thunnus/BluefinAQ30_shuffled.fastq), it starts 
> filling up immediately
> 
> FilesystemSize  Used Avail Use% Mounted on
> /dev/xvda1 20G   19G 0 100% /
> udev  8.4G  4.0K  8.4G   1% /dev
> tmpfs 3.4G  660K  3.4G   1% /run
> none  5.0M 0  5.0M   0% /run/lock
> none  8.4G 0  8.4G   0% /run/shm
> /dev/xvdb 404G  201M  383G   1% /mnt
> /dev/xvdg1700G  654G   47G  94% /mnt/galaxyIndices
> /dev/xvdg2 10G  1.7G  8.4G  17% /mnt/galaxyTools
> /dev/xvdg3500G   81M  500G   1% /mnt/galaxyData
> 
> 
> Jan McDowell
> The Virginia Institute of Marine Science
> The College of William and Mary
> Department of Fisheries Science
> Phone: 804-684-7263
> Fax: 804-684-7157
> mcdow...@vims.edu
> 
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[galaxy-dev] local performance

[Charles Gawad]

Hello,
I am new to galaxy and bioinformatics in general.  I have installed galaxy (and 
supporting software) on my mac pro with 8 cores and 24 Gb of memory.  The main 
issue is that it runs really slow.  When I look at CPU and memory allocation to 
python, less than 10% of each are being used.  Is there an easy fix?
thanks,
Chuck
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Re: [galaxy-dev] unable to add tools in tool_conf.xml

[Sivasangari NANDY]

Thanks to bjoern and Peter, it's working now.I've juste change the type string 
to text.

regards, Siva
> Subject: Re: [galaxy-dev] unable to add tools in tool_conf.xml
> From: bjoern.gruen...@pharmazie.uni-freiburg.de
> To: nsi...@hotmail.com
> CC: galaxy-dev@lists.bx.psu.edu
> Date: Thu, 8 Mar 2012 17:13:50 +0100
> 
> Hi Sivasangari ,
> 
> your tools has an error. Tools with an error don't get listed. Can you
> show us the rec_expression.xml file?
> I guess you need to change the 'string' to 'text' or something like
> that.
> 
> Cheers,
> Bjoern
> 
> > 
> > I've got a problem, i'm not able to add a tool in ttol_conf.xml.
> > Actually i can see one tool that i've added but when i put the second
> > Galaxy doesn't take it into account :
> > 
> > 
> >   
> >   
> >  
> >
> > 
> > 
> > My paster.log gives that : 
> > 
> > 
> > galaxy.tools ERROR 2012-03-08 16:07:57,849 error reading tool from
> > path: mytools/rec_expression.xml
> > Traceback (most recent call last):
> >   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> > line 77, in load_tool
> > tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
> >   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> > line 169, in load_tool
> > return ToolClass( config_file, root, self.app )
> >   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> > line 340, in __init__
> > self.parse( root )
> >   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> > line 446, in parse
> > self.parse_inputs( root )
> >   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> > line 528, in parse_inputs
> > display, inputs = self.parse_input_page( page, enctypes )
> >   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> > line 708, in parse_input_page
> > inputs = self.parse_input_elem( input_elem, enctypes )
> >   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> > line 801, in parse_input_elem
> > param = self.parse_param_elem( elem, enctypes, context )
> >   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> > line 813, in parse_param_elem
> > param = ToolParameter.build( self, input_elem )
> >   File
> > "/home/pmontalent/galaxy_dev/lib/galaxy/tools/parameters/basic.py",
> > line 159, in build
> > raise ValueError( "Unknown tool parameter type '%s'" % param_type
> > )
> > ValueError: Unknown tool parameter type 'string'
> > 
> > 
> > Have you got aany idea ?
> > advance thanks,
> > ___
> > 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/
> 
> -- 
> Björn Grüning
> Albert-Ludwigs-Universität Freiburg
> Institute of Pharmaceutical Sciences
> Pharmaceutical Bioinformatics
> Hermann-Herder-Strasse 9
> D-79104 Freiburg i. Br.
> 
> Tel.:  +49 761 203-4872
> Fax.:  +49 761 203-97769
> E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
> Web: http://www.pharmaceutical-bioinformatics.org/
> 
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[galaxy-dev] refresh loc files without restart

[Bossers, Alex]

Early 2011 there was a discussion and feature request to be able to refresh loc 
files on a running galaxy instance.
This is not only convenient for updating loc files for blast, bowtie, bwa and 
such, but also opens possibilities to update and dynamically populate such 
files to be used in other custom tools.
Is there any progress on this?

Or has anyone hacked the system to be able to? Like the tool_refresh option?

Alex




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Re: [galaxy-dev] uploads stuck in history

[Bossers, Alex]

The same for us. We never changed anything on our local dev or prod server. The 
dev server which runs the latest central edition is still suffering from it. 
Earlier there was no problem at all.
Why is it the ngnix issue?
Alex

-Oorspronkelijk bericht-
Van: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Leandro Hermida
Verzonden: donderdag 8 maart 2012 12:43
Aan: Jorrit Boekel
CC: galaxy-dev@lists.bx.psu.edu
Onderwerp: Re: [galaxy-dev] uploads stuck in history

Hello,

We don't use the nginx module

kind regards,
Leandro

On Wed, Mar 7, 2012 at 4:42 PM, Jorrit Boekel  
wrote:
> Hi Nate,
>
> I wasn't before, but I switched to nginx now. Non-uploading is still 
> happening in firefox (10.0.2 on ubuntu 11.10).
>
> I can't be 100% sure that my nginx install was correct, but it's 
> definitely serving galaxy and not complaining. Is there any way to 
> verify uploads are processed through nginx?
>
> jorrit
>
>
>
> On 03/05/2012 08:37 PM, Nate Coraor wrote:
>>
>> By any chance, do you all happen to be using the nginx upload module?  
>> I am guessing not.
>>
>> --nate
>>
>> On Feb 23, 2012, at 3:16 AM, Bossers, Alex wrote:
>>
>>> I confirm the same strange behaviour since some of the last updates 
>>> on the central version. We are at the latest now.
>>> It is also with medium (10Mb+ tarballs) AND large files! Furthermore 
>>> its seems to be in FireFox only They upload fine using IE8 or 9. 
>>> Didn't test other browsers though.
>>>
>>> Annoying it is indeed.
>>>
>>> Alex
>>>
>>>
>>> -Oorspronkelijk bericht-
>>> Van: galaxy-dev-boun...@lists.bx.psu.edu
>>> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Jorrit Boekel
>>> Verzonden: woensdag 22 februari 2012 10:15
>>> Aan: galaxy-dev@lists.bx.psu.edu
>>> Onderwerp: [galaxy-dev] uploads stuck in history
>>>
>>> Dear list,
>>>
>>> I have stumbled on some strange behaviour when uploading files to 
>>> galaxy via the upload.py tool. At times, the upload seems to be 
>>> stalled in history and is never actually performed, followed by a 
>>> seemingly infinite history update (see log below). My system is 
>>> Ubuntu 11.10 and runs Python 2.7.2. I find the behaviour in both my 
>>> own modified galaxy install (based on galaxy-dist), and in a fresh clone 
>>> from galaxy-central.
>>>
>>> I have tried to upload different files, and all seem to sometimes 
>>> trigger the behaviour, but not all the time. A restart of galaxy 
>>> sometimes sorts things out. Common for the debug messages is that it 
>>> seems there is never a job id generated as in 
>>> "galaxy.tools.actions.upload_common INFO 2012-02-22
>>> 10:06:36,186 tool
>>> upload1 created job id 2".
>>>
>>> Has anyone seen similar things or can it be a problem with my system?
>>>
>>> cheers,
>>> jorrit
>>>
>>>
>>>
>>>
>>>
>>>
>>> --Debug messa:
>>>
>>> galaxy.web.framework DEBUG 2012-02-22 09:47:43,730 Error: this 
>>> request returned None from get_history(): http://localhost:8080/
>>> 127.0.0.1 - - [22/Feb/2012:09:47:43 +0200] "GET / HTTP/1.1" 200 - "-"
>>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 
>>> Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /root/tool_menu HTTP/1.1"
>>> 200 - "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux 
>>> x86_64;
>>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /history HTTP/1.1" 
>>> 200 - "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux 
>>> x86_64;
>>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "POST 
>>> /root/user_get_usage HTTP/1.1" 200 - "http://localhost:8080/history"; 
>>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 
>>> Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:47:50 +0200] "GET
>>> /tool_runner?tool_id=upload1 HTTP/1.1" 200 - 
>>> "http://localhost:8080/root/tool_menu"; "Mozilla/5.0 (X11; Ubuntu; 
>>> Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "POST 
>>> /tool_runner/upload_async_create HTTP/1.1" 200 - "http://localhost:8080/";
>>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "GET 
>>> /tool_runner/upload_async_message HTTP/1.1" 200 - "http://localhost:8080/";
>>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "GET /history HTTP/1.1" 
>>> 200 - "http://localhost:8080/tool_runner/upload_async_message"; 
>>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 
>>> Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "POST 
>>> /root/user_get_usage HTTP/1.1" 200 - "http://localhost:8080/history"; 
>>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 
>>> Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:13 +0200] "GET
>>> /tool_runner

Re: [galaxy-dev] unable to add tools in tool_conf.xml

[Sivasangari NANDY]

  
from a choosen one  rec_expression.pl $input $output  
  


Yea i think i must replace this line :  and change the 
type to text maybe, i'll test it in few mins (some problems for the moment) and 
give you the answer.
n.b : no Peter, i've just forgot to put the list email.

> Subject: Re: [galaxy-dev] unable to add tools in tool_conf.xml
> From: bjoern.gruen...@pharmazie.uni-freiburg.de
> To: nsi...@hotmail.com
> CC: galaxy-dev@lists.bx.psu.edu
> Date: Thu, 8 Mar 2012 17:13:50 +0100
> 
> Hi Sivasangari ,
> 
> your tools has an error. Tools with an error don't get listed. Can you
> show us the rec_expression.xml file?
> I guess you need to change the 'string' to 'text' or something like
> that.
> 
> Cheers,
> Bjoern
> 
> > 
> > I've got a problem, i'm not able to add a tool in ttol_conf.xml.
> > Actually i can see one tool that i've added but when i put the second
> > Galaxy doesn't take it into account :
> > 
> > 
> >   
> >   
> >  
> >
> > 
> > 
> > My paster.log gives that : 
> > 
> > 
> > galaxy.tools ERROR 2012-03-08 16:07:57,849 error reading tool from
> > path: mytools/rec_expression.xml
> > Traceback (most recent call last):
> >   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> > line 77, in load_tool
> > tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
> >   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> > line 169, in load_tool
> > return ToolClass( config_file, root, self.app )
> >   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> > line 340, in __init__
> > self.parse( root )
> >   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> > line 446, in parse
> > self.parse_inputs( root )
> >   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> > line 528, in parse_inputs
> > display, inputs = self.parse_input_page( page, enctypes )
> >   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> > line 708, in parse_input_page
> > inputs = self.parse_input_elem( input_elem, enctypes )
> >   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> > line 801, in parse_input_elem
> > param = self.parse_param_elem( elem, enctypes, context )
> >   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> > line 813, in parse_param_elem
> > param = ToolParameter.build( self, input_elem )
> >   File
> > "/home/pmontalent/galaxy_dev/lib/galaxy/tools/parameters/basic.py",
> > line 159, in build
> > raise ValueError( "Unknown tool parameter type '%s'" % param_type
> > )
> > ValueError: Unknown tool parameter type 'string'
> > 
> > 
> > Have you got aany idea ?
> > advance thanks,
> > ___
> > 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/
> 
> -- 
> Björn Grüning
> Albert-Ludwigs-Universität Freiburg
> Institute of Pharmaceutical Sciences
> Pharmaceutical Bioinformatics
> Hermann-Herder-Strasse 9
> D-79104 Freiburg i. Br.
> 
> Tel.:  +49 761 203-4872
> Fax.:  +49 761 203-97769
> E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
> Web: http://www.pharmaceutical-bioinformatics.org/
> 
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Re: [galaxy-dev] unable to add tools in tool_conf.xml

[Björn Grüning]

Hi Sivasangari ,

your tools has an error. Tools with an error don't get listed. Can you
show us the rec_expression.xml file?
I guess you need to change the 'string' to 'text' or something like
that.

Cheers,
Bjoern

> 
> I've got a problem, i'm not able to add a tool in ttol_conf.xml.
> Actually i can see one tool that i've added but when i put the second
> Galaxy doesn't take it into account :
> 
> 
>   
>   
>  
>
> 
> 
> My paster.log gives that : 
> 
> 
> galaxy.tools ERROR 2012-03-08 16:07:57,849 error reading tool from
> path: mytools/rec_expression.xml
> Traceback (most recent call last):
>   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> line 77, in load_tool
> tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
>   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> line 169, in load_tool
> return ToolClass( config_file, root, self.app )
>   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> line 340, in __init__
> self.parse( root )
>   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> line 446, in parse
> self.parse_inputs( root )
>   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> line 528, in parse_inputs
> display, inputs = self.parse_input_page( page, enctypes )
>   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> line 708, in parse_input_page
> inputs = self.parse_input_elem( input_elem, enctypes )
>   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> line 801, in parse_input_elem
> param = self.parse_param_elem( elem, enctypes, context )
>   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py",
> line 813, in parse_param_elem
> param = ToolParameter.build( self, input_elem )
>   File
> "/home/pmontalent/galaxy_dev/lib/galaxy/tools/parameters/basic.py",
> line 159, in build
> raise ValueError( "Unknown tool parameter type '%s'" % param_type
> )
> ValueError: Unknown tool parameter type 'string'
> 
> 
> Have you got aany idea ?
> advance thanks,
> ___
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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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-- 
Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceutical Sciences
Pharmaceutical Bioinformatics
Hermann-Herder-Strasse 9
D-79104 Freiburg i. Br.

Tel.:  +49 761 203-4872
Fax.:  +49 761 203-97769
E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
Web: http://www.pharmaceutical-bioinformatics.org/

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Re: [galaxy-dev] unable to add tools in tool_conf.xml

[Peter Cock]

On Thu, Mar 8, 2012 at 3:54 PM, Sivasangari NANDY  wrote:
> Hi friends,
>
> I've got a problem, i'm not able to add a tool in ttol_conf.xml. Actually i
> can see one tool that i've added but when i put the second Galaxy doesn't
> take it into account :
>
>   
>       
>      
>   
>
> My paster.log gives that :
>
> galaxy.tools ERROR 2012-03-08 16:07:57,849 error reading tool from path:
> mytools/rec_expression.xml
> Traceback (most recent call last):
>   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 77,
> in load_tool
>     tool = self.load_tool( os.path.join( self.tool_root_dir, path ) )
>   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 169,
> in load_tool
>     return ToolClass( config_file, root, self.app )
>   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 340,
> in __init__
>     self.parse( root )
>   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 446,
> in parse
>     self.parse_inputs( root )
>   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 528,
> in parse_inputs
>     display, inputs = self.parse_input_page( page, enctypes )
>   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 708,
> in parse_input_page
>     inputs = self.parse_input_elem( input_elem, enctypes )
>   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 801,
> in parse_input_elem
>     param = self.parse_param_elem( elem, enctypes, context )
>   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 813,
> in parse_param_elem
>     param = ToolParameter.build( self, input_elem )
>   File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/parameters/basic.py",
> line 159, in build
>     raise ValueError( "Unknown tool parameter type '%s'" % param_type )
> ValueError: Unknown tool parameter type 'string'
>
> Have you got aany idea ?
> advance thanks,

It is telling you there is a problem understanding one of the parameters
defined in mytools/rec_expression.xml - can you show us the input
section of your XML file?

Peter

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Re: [galaxy-dev] Galaxy SNPEff Display Bug (2nd Independent Report)

[John David Osborne]

Very helpful, thank you!

I don't see this option in universe_wsgi.ini, but hopefully I will when we
update our galaxy.

Thanks!

 -John



On 3/8/12 9:53 AM, "Dannon Baker"  wrote:

>This was addressed in 6788:e58a87c91bc4.  The reason for the initial
>change that's causing these display issues was to eliminate potential XSS
>vulnerabilities.  There's now a configuration option (sanitize_all_html,
>which is True by default) for local instances where you can disable the
>extra html sanitization.
>
>-Dannon
>
>On Mar 8, 2012, at 10:33 AM, John David Osborne wrote:
>
>> Hi Pablo,
>> 
>> About 3 weeks ago Praveen mentioned a bug in SNPEff such that it no
>>longer correctly displays the HTML report in galaxy ­ we have the exact
>>same error. Is there a workaround for this yet? I found his original
>>report here:
>> http://article.gmane.org/gmane.science.biology.galaxy.user/2418
>> 
>> The report looks great when generated from the command line or even if
>>the files from galaxy are copied over to a local machine and displayed.
>>However in galaxy it appears that the supplementary data file (for
>>example dataset_41.dat.genes.txt) from the original dataset_41.dat is
>>not accessible to the main html file although I can copy it off the
>>server. Perhaps the data file it is being called from elsewhere at this
>>is a path related issue? The html looks for the data file in the same
>>directory which I think is quite reasonable.
>> 
>> I'm not sure which galaxy update broke this, but it is definitely
>>broken and I'm guessing any efforts to display html reports in galaxy
>>that involve other supplementary data files may be broken tooŠ.
>> 
>>  -John
>> 
>> ___
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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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[galaxy-dev] unable to add tools in tool_conf.xml

[Sivasangari NANDY]

Hi friends, 
I've got a problem, i'm not able to add a tool in ttol_conf.xml. Actually i can 
see one tool that i've added but when i put the second Galaxy doesn't take it 
into account :

My paster.log gives that : 
galaxy.tools ERROR 2012-03-08 16:07:57,849 error reading tool from path: 
mytools/rec_expression.xmlTraceback (most recent call last):  File 
"/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 77, in 
load_tooltool = self.load_tool( os.path.join( self.tool_root_dir, path ) )  
File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 169, in 
load_toolreturn ToolClass( config_file, root, self.app )  File 
"/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 340, in 
__init__self.parse( root )  File 
"/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 446, in parse  
  self.parse_inputs( root )  File 
"/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 528, in 
parse_inputsdisplay, inputs = self.parse_input_page( page, enctypes )  File 
"/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 708, in 
parse_input_pageinputs = self.parse_input_elem( input_elem, enctypes )  
File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 801, in 
parse_input_elemparam = self.parse_param_elem( elem, enctypes, context )  
File "/home/pmontalent/galaxy_dev/lib/galaxy/tools/__init__.py", line 813, in 
parse_param_elemparam = ToolParameter.build( self, input_elem )  File 
"/home/pmontalent/galaxy_dev/lib/galaxy/tools/parameters/basic.py", line 159, 
in buildraise ValueError( "Unknown tool parameter type '%s'" % param_type 
)ValueError: Unknown tool parameter type 'string'
Have you got aany idea ?advance thanks, 
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Re: [galaxy-dev] Galaxy SNPEff Display Bug (2nd Independent Report)

[Dannon Baker]

This was addressed in 6788:e58a87c91bc4.  The reason for the initial change 
that's causing these display issues was to eliminate potential XSS 
vulnerabilities.  There's now a configuration option (sanitize_all_html, which 
is True by default) for local instances where you can disable the extra html 
sanitization.

-Dannon

On Mar 8, 2012, at 10:33 AM, John David Osborne wrote:

> Hi Pablo,
> 
> About 3 weeks ago Praveen mentioned a bug in SNPEff such that it no longer 
> correctly displays the HTML report in galaxy – we have the exact same error. 
> Is there a workaround for this yet? I found his original report here:
> http://article.gmane.org/gmane.science.biology.galaxy.user/2418
> 
> The report looks great when generated from the command line or even if the 
> files from galaxy are copied over to a local machine and displayed.  However 
> in galaxy it appears that the supplementary data file (for example 
> dataset_41.dat.genes.txt) from the original dataset_41.dat is not accessible 
> to the main html file although I can copy it off the server. Perhaps the data 
> file it is being called from elsewhere at this is a path related issue? The 
> html looks for the data file in the same directory which I think is quite 
> reasonable.
> 
> I'm not sure which galaxy update broke this, but it is definitely broken and 
> I'm guessing any efforts to display html reports in galaxy that involve other 
> supplementary data files may be broken too….
> 
>  -John
> 
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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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Re: [galaxy-dev] postgres

[Björn Grüning]

Hi Christin,

> I would like to clarify whether we have understood something about the 
> database correctly. Is is right that all calculations with galaxy are 
> stored as a link in the database. And the data are stored somewhereelse? 

Yes, kind of :)

> Is it possible to store the data only in the database?

No and its advisable to do so. Galaxy operates on files and they can be
huge. It does not make much sense to store such data in a database.

Best,
Bjoern

> For some advice, I am very grateful.
> 
> Best regards,
> Christin
> 

-- 
Björn Grüning
Albert-Ludwigs-Universität Freiburg
Institute of Pharmaceutical Sciences
Pharmaceutical Bioinformatics
Hermann-Herder-Strasse 9
D-79104 Freiburg i. Br.

Tel.:  +49 761 203-4872
Fax.:  +49 761 203-97769
E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de
Web: http://www.pharmaceutical-bioinformatics.org/

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[galaxy-dev] Galaxy SNPEff Display Bug (2nd Independent Report)

[John David Osborne]

Hi Pablo,

About 3 weeks ago Praveen mentioned a bug in SNPEff such that it no longer 
correctly displays the HTML report in galaxy – we have the exact same error. Is 
there a workaround for this yet? I found his original report here:
http://article.gmane.org/gmane.science.biology.galaxy.user/2418

The report looks great when generated from the command line or even if the 
files from galaxy are copied over to a local machine and displayed.  However in 
galaxy it appears that the supplementary data file (for example 
dataset_41.dat.genes.txt) from the original dataset_41.dat is not accessible to 
the main html file although I can copy it off the server. Perhaps the data file 
it is being called from elsewhere at this is a path related issue? The html 
looks for the data file in the same directory which I think is quite reasonable.

I'm not sure which galaxy update broke this, but it is definitely broken and 
I'm guessing any efforts to display html reports in galaxy that involve other 
supplementary data files may be broken too….

 -John

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Re: [galaxy-dev] Welcome.html page

[Hans-Rudolf Hotz]

Hi Huayan

> I got a silly question for you. My galaxy is running now but I'd like
> to customize it.
> I've changed the welcome.html page but the galaxy mirror site is
> showing the old one. Do I need to change some other files or other
> configurations?

Are you sure the page is not cached locally?

> Also, I add  in tool_conf.xml file but it does not show up
> either. Is there another file I need to change too?
>

I assume you mean "label", have you restarted your galaxy server?


I hope this helps
Regards, Hans





> Best,
> Huayan
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[galaxy-dev] postgres

[christin weinberg]

Dear all,
I would like to clarify whether we have understood something about the 
database correctly. Is is right that all calculations with galaxy are 
stored as a link in the database. And the data are stored somewhereelse? 
Is it possible to store the data only in the database?


For some advice, I am very grateful.

Best regards,
Christin

--

Christin Weinberg
Institute for Applied Computer Science (IACS)
FH Stralsund - University of Applied Sciences

Phone: +49 3831 456948
E-Mail : christin.weinb...@fh-stralsund.de

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Re: [galaxy-dev] uploads stuck in history

[Leandro Hermida]

Hello,

We don't use the nginx module

kind regards,
Leandro

On Wed, Mar 7, 2012 at 4:42 PM, Jorrit Boekel
 wrote:
> Hi Nate,
>
> I wasn't before, but I switched to nginx now. Non-uploading is still
> happening in firefox (10.0.2 on ubuntu 11.10).
>
> I can't be 100% sure that my nginx install was correct, but it's definitely
> serving galaxy and not complaining. Is there any way to verify uploads are
> processed through nginx?
>
> jorrit
>
>
>
> On 03/05/2012 08:37 PM, Nate Coraor wrote:
>>
>> By any chance, do you all happen to be using the nginx upload module?  I
>> am guessing not.
>>
>> --nate
>>
>> On Feb 23, 2012, at 3:16 AM, Bossers, Alex wrote:
>>
>>> I confirm the same strange behaviour since some of the last updates on
>>> the central version. We are at the latest now.
>>> It is also with medium (10Mb+ tarballs) AND large files! Furthermore its
>>> seems to be in FireFox only They upload fine using IE8 or 9. Didn't test
>>> other browsers though.
>>>
>>> Annoying it is indeed.
>>>
>>> Alex
>>>
>>>
>>> -Oorspronkelijk bericht-
>>> Van: galaxy-dev-boun...@lists.bx.psu.edu
>>> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Jorrit Boekel
>>> Verzonden: woensdag 22 februari 2012 10:15
>>> Aan: galaxy-dev@lists.bx.psu.edu
>>> Onderwerp: [galaxy-dev] uploads stuck in history
>>>
>>> Dear list,
>>>
>>> I have stumbled on some strange behaviour when uploading files to galaxy
>>> via the upload.py tool. At times, the upload seems to be stalled in history
>>> and is never actually performed, followed by a seemingly infinite history
>>> update (see log below). My system is Ubuntu 11.10 and runs Python 2.7.2. I
>>> find the behaviour in both my own modified galaxy install (based on
>>> galaxy-dist), and in a fresh clone from galaxy-central.
>>>
>>> I have tried to upload different files, and all seem to sometimes trigger
>>> the behaviour, but not all the time. A restart of galaxy sometimes sorts
>>> things out. Common for the debug messages is that it seems there is never a
>>> job id generated as in "galaxy.tools.actions.upload_common INFO 2012-02-22
>>> 10:06:36,186 tool
>>> upload1 created job id 2".
>>>
>>> Has anyone seen similar things or can it be a problem with my system?
>>>
>>> cheers,
>>> jorrit
>>>
>>>
>>>
>>>
>>>
>>>
>>> --Debug messa:
>>>
>>> galaxy.web.framework DEBUG 2012-02-22 09:47:43,730 Error: this request
>>> returned None from get_history(): http://localhost:8080/
>>> 127.0.0.1 - - [22/Feb/2012:09:47:43 +0200] "GET / HTTP/1.1" 200 - "-"
>>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101
>>> Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /root/tool_menu HTTP/1.1"
>>> 200 - "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /history HTTP/1.1" 200 -
>>> "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "POST /root/user_get_usage
>>> HTTP/1.1" 200 - "http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu;
>>> Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:47:50 +0200] "GET
>>> /tool_runner?tool_id=upload1 HTTP/1.1" 200 -
>>> "http://localhost:8080/root/tool_menu"; "Mozilla/5.0 (X11; Ubuntu; Linux
>>> x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "POST
>>> /tool_runner/upload_async_create HTTP/1.1" 200 - "http://localhost:8080/";
>>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "GET
>>> /tool_runner/upload_async_message HTTP/1.1" 200 - "http://localhost:8080/";
>>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "GET /history HTTP/1.1" 200 -
>>> "http://localhost:8080/tool_runner/upload_async_message"; "Mozilla/5.0 (X11;
>>> Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "POST /root/user_get_usage
>>> HTTP/1.1" 200 - "http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu;
>>> Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:13 +0200] "GET
>>> /tool_runner?tool_id=upload1 HTTP/1.1" 200 -
>>> "http://localhost:8080/root/tool_menu"; "Mozilla/5.0 (X11; Ubuntu; Linux
>>> x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:15 +0200] "POST
>>> /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history";
>>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>>> rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
>>> 127.0.0.1 - - [22/Feb/2012:09:48:19 +0200] "POST
>>> /root/history_item_updates HTTP/1.1" 200 - "http://localhost:8080/history";
>>> "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
>>> rv:10.0.2)