[galaxy-dev] About the creation of a new folder

[Ciara Ledero]

Hi all,

I would just like to ask if it's possible to create a new folder (via
script) in the galaxy-dist folder.

Cheers,

CL
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Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

[Greg Edwards]

Clare,

I'm running an AWS Cloudman instance (on US East region) from Sydney for a
developing suite of proteomics PTM tools in Perl, for use mainly by
http://sydney.edu.au/science/molecular_bioscience/  and
http://www.sdu.dk/en/om_sdu/institutter_centre/bmb_biokemi_og_molekylaer_biologi

Hard to say if a local group is fully needed yet, but we could try. A
multi-site audio or video conference is pretty easy these days. There are
always unexpected insights from talking direct to others. I'd be happy to
take part. But the main Galaxy dev team in US are so good on the mailing
lists, we don't want to impact that.

Not a very insightful comment ! I used to be indecisive but now I'm not so
sure ...

Greg Edwards


On Thu, May 10, 2012 at 3:20 PM, Clare Sloggett  wrote:

> Hi all,
>
> I'm at one of the places Ross mentions (VLSCI), with Enis - among
> other things we're deploying Galaxy CloudMan on the new "Australian
> Research Cloud".
>
> Just from talking to people I feel that local institutions that have
> installed their own Galaxy, and are customising it, wrapping tools for
> the researchers they support etc, do end up struggling with a lot of
> the same problems. I think though that as Ross is suggesting in a lot
> of cases these needs could be filled by the existing galaxy-user and
> galaxy-dev mailing lists (I find sometimes people can be quite
> hesitant to post a question until they have spent a lot of time on the
> problem).
>
> I do like the idea of a "local" Australia-New Zealand Galaxy group for
> developers / techie bioinformaticians, but more for the sake of
> face-to-face interaction and perhaps local-timezone teleconferences; I
> don't want to end up just duplicating existing mailing lists. I'm not
> sure of the best way to make such a group take off or how much
> interest there would be. If there are other Australian / New Zealand
> or local timezone groups reading this list and you're interested, let
> us know!
>
> Clare
>
> On 30 April 2012 13:35, Ross  wrote:
> > To all interested in Dave's suggestion:
> >
> > IMHO, an Australian/New Zealand Galaxy user/deployer/developer group
> > will be worth setting up and will be viable if it solves specific
> > problems that aren't adequately addressed by existing networks and
> > communication channels - otherwise it will be JAFUG (just another
> > fleeting user group) and will likely fizzle due to lack of genuine
> > utility to potential participants.
> >
> > EG: One challenge for us when it comes to (eg) the proposed
> > teleconferences is the tyranny of time zones - being 14 hours ahead of
> > EST eg in Melbourne/Sydney. The other big challenge is that travel to
> > meetings in Europe or the USA is expensive and exhausting, so
> > workshops and hands on training are harder to get to. In general, I
> > think we're probably going to be able to find plenty of problems to do
> > with geographic isolation and maybe even some specific Australian
> > challenges - but let's be clear about exactly what those are before we
> > start building any structures. One problem I keep seeing is that there
> > are many organisations happy to invest in hardware infrastructure, but
> > far less willing to invest in the training and staff development
> > needed for success.
> >
> > Two things I'd like to suggest to help with planning:
> >
> > 1) to get a better idea of scope, it would be very handy to assemble a
> > register of potential organisations and their primary contacts. I
> > already know of some large Australian organisations investing heavily
> > in Galaxy deployment - eg - VLSCI in Melbourne; UQ in Brisbane, CSIRO
> > all over the place, the Victorian DPI, AGRF, and the BakerIDI where
> > I'm based - no doubt there are plenty of others too?
> >
> > 2) to make sure the idea is viable, it would be useful to collect some
> > specific deployment challenges that people are experiencing that some
> > kind of local user's group could help overcome?
> >
> > One focus I have a personal interest in exploring would be in face to
> > face educational activities: eg for local Galaxy instance system
> > administrators? Local tool developers? Local biologist users in
> > specific contexts like short read sequencing?
> >
> > Suggestions welcomed...
> >
> >
> > On Mon, Apr 30, 2012 at 12:37 PM, Dave Clements
> >  wrote:
> >> Hi Ryan, Ann, and everyone else
> >>
> >> I second what Nate says (I always do :-).  I too like that it is user
> >> driven.  And, while I am not a developer, I do plan on being on the
> call as
> >> often as possible.
> >>
> >> I can also offer my support for logistical and any other support.  Ann,
> >> please let me know if you want help with getting this going and getting
> the
> >> word out.
> >>
> >>
> >> On a related note,   With Matloob's email, we have at least 3
> >> organizations in Australia and New Zealand that are interested. I know
> that
> >> there are many more Galaxy installations in that part of the world (and
> you
> >> have Enis a

[galaxy-dev] ⇝ IOError: [Errno 13] Permission denied: u'/home/koala2/galaxy-central/database/compiled_templates/base_panels.mako.py'

[Luciano Cosme]

Hi Everyone,
   I was just using my local galaxy instance. I closed it up (from
terminal), open IGV to look at some genes, then I restarted it from the
terminal and when I tried to access it I got the error message below. I
just don't know what happened in these few minutes. Any suggestion how to
fix it?
Thank you.

Luciano

URL: http://127.0.0.1:8080/
File
'/home/koala2/galaxy-central/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py',
line 364 in respond
  app_iter = self.application(environ, detect_start_response)
File
'/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py',
line 98 in __call__
  environ, self.app)
File
'/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py',
line 539 in intercept_output
  app_iter = application(environ, replacement_start_response)
File
'/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/recursive.py',
line 80 in __call__
  return self.application(environ, start_response)
File
'/home/koala2/galaxy-central/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py',
line 632 in __call__
  return self.application(environ, start_response)
File '/home/koala2/galaxy-central/lib/galaxy/web/framework/base.py', line
160 in __call__
  body = method( trans, **kwargs )
File '/home/koala2/galaxy-central/lib/galaxy/web/controllers/root.py', line
25 in index
  m_c=m_c, m_a=m_a )
File '/home/koala2/galaxy-central/lib/galaxy/web/framework/__init__.py',
line 733 in fill_template
  return self.fill_template_mako( filename, **kwargs )
File '/home/koala2/galaxy-central/lib/galaxy/web/framework/__init__.py',
line 744 in fill_template_mako
  return template.render( **data )
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/template.py',
line 296 in render
  return runtime._render(self, self.callable_, args, data)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 660 in _render
  **_kwargs_for_callable(callable_, data))
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 691 in _render_context
  (inherit, lclcontext) = _populate_self_namespace(context, tmpl)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 637 in _populate_self_namespace
  ret = template.module._mako_inherit(template, context)
File '/home/koala2/galaxy-central/database/compiled_templates/root/
index.mako.py', line 25 in _mako_inherit
  return runtime._inherit_from(context,
u'/webapps/galaxy/base_panels.mako', _template_uri)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 609 in _inherit_from
  ret = callable_(template, lclcontext)
File
'/home/koala2/galaxy-central/database/compiled_templates/webapps/galaxy/
base_panels.mako.py', line 25 in _mako_inherit
  return runtime._inherit_from(context, u'/base_panels.mako', _template_uri)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 596 in _inherit_from
  template = _lookup_template(context, uri, calling_uri)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py',
line 626 in _lookup_template
  return lookup.get_template(uri)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/lookup.py',
line 218 in get_template
  return self._load(srcfile, uri)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/lookup.py',
line 283 in _load
  **self.template_args)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/template.py',
line 218 in __init__
  module = self._compile_from_file(path, filename)
File
'/home/koala2/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/template.py',
line 245 in _compile_from_file
  module = imp.load_source(self.module_id, path, open(path, 'rb'))
IOError: [Errno 13] Permission denied:
u'/home/koala2/galaxy-central/database/compiled_templates/
base_panels.mako.py'
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Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

[Edward Hills]

RE: The chat about NZ/AUS communication us here at Otago University
(Dunedin, NZ) are very very keen for this.

Please email us at edward.hi...@otago.ac.nz if this does decide to take off :)

Cheers,
Ed
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Re: [galaxy-dev] Loc file configuration question

[Federico De Masi]

Hi,
I agree that *.loc files should be consolidated or, at least, we should 
have proper documentation about which loc file is required for each tool...

Took me quite some time to find that solution.

I would suggest can we have a open wiki where these things are 
annotated. ie: if I find a "trick" or a shortcut to something, shouldn't 
we have a centralised place to share it with the community, rather than 
having Nate and co waste their precious time answering over and over the 
same questions?


Mailing lists are cool, but sometimes heavy to search and to find the 
proper answers..


my 2p or maybe I missed something...

Cheers,

Fred


On 10/05/2012 15:35, Raja Kelkar wrote:

Hi Fred,

Thanks for the tip on the alignseq file. It did work (I do now have
sequence that came back from the tool, will have to check if it correct).

Anyone have a logical explanation?

Perhaps these myriad loc files can be streamlined down to something
simple in future.

Thanks.

Dan: The entries I had in local loc files were all tab delimited.

On Wed, May 9, 2012 at 4:49 PM, Federico De Masi mailto:fred.dem...@gmail.com>> wrote:

Hi,

I was having the same issue just today and my solution was to add:

seq mm9 /path_to/twobit/mm9.2bit

in the alignseq.loc file as .nib has been replaced by 2bit.
Plus all necessaty entries in all_fasta.loc and twobit.loc

That worked :)

Hope this helps.

Fred



On 09/05/2012 22:40, Daniel Blankenberg wrote:

Hi Raja,

Can you check that your fields are tab separated and not spaces
(they
are spaces below, but that could be a copy and paste artifact)?


Thanks for using Galaxy,

Dan


On May 9, 2012, at 9:45 AM, Raja Kelkar wrote:

Hi Jen,

Thank you for your response. I seem to have all the relevant
entries
in the two "*.loc" files you mentioned (paths in all_fasta
files and
the twobit files are different because of the way we have
the files
stored. I also converted the 2bit files to .fa and have them
available
in the same twobit directory).

But the feature extraction is still not working.

Here are the relevant entries in files (I have redacted
specific file
paths and replaced them with "path_to"):

twobit.loc

hg18 /path_to/twobit/hg18.2bit
hg19 /path_to/twobit/hg19.2bit
mm9 /path_to/twobit/mm9.2bit
mm8 /path_to/twobit/mm8.2bit

all_fasta.loc

hg19full hg19 Human (Homo sapiens): hg19 Full
/path_to/hg19/bwa_path/hg19___all.fa
hg19_chr_only hg19_chr Human (Homo sapiens): hg19_chrom_only
/path_to/hg19/bwa_path/hg19.fa
hg18full hg18 Human (Homo sapiens): hg18 Full
/path_to/hg18/bwa_path/hg18___all.fa
hg18_chr_only hg18_chr Human (Homo sapiens): hg18_chrom_only
/path_to/hg18/bwa_path/hg18___chrom_only.fa


I assume that the second field in the (all_fasta.loc) file
 has
to match the builds.txt file in the "ucsc" directory. Is
that correct?
It does in this case. I think I am missing something subtle
here.

The "*.loc.sample" files are great but the information
contained in
those is confusing. I am not sure why there are two examples
of the
same info (as far as I can tell) in most sample loc files.

Thanks.


On Tue, May 8, 2012 at 6:48 PM, Jennifer Jackson
mailto:j...@bx.psu.edu>
>> wrote:

Hi Raja,

This tool uses a .2bit file to extract
sequence data
when the 'Locally cashed' option is used. The 
is a
genome that you install locally. ".2bit" format was
developed by
UCSC and they are the source for many genomes in this format
already and for tools (compiled and uncompiled) to
transform fasta
data into/from .2bit format (faTwoToBit and twoBitToFa):
http://hgdownload.cse.ucsc.edu/downloads.html

> (genomes +
source)
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

>
(compiled
utilities)

For the extract tool, the builds list is required:
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration

Re: [galaxy-dev] Loc file configuration question

[Raja Kelkar]

Hi Fred,

Thanks for the tip on the alignseq file. It did work (I do now have
sequence that came back from the tool, will have to check if it correct).

Anyone have a logical explanation?

Perhaps these myriad loc files can be streamlined down to something simple
in future.

Thanks.

Dan: The entries I had in local loc files were all tab delimited.

On Wed, May 9, 2012 at 4:49 PM, Federico De Masi wrote:

> Hi,
>
> I was having the same issue just today and my solution was to add:
>
> seq mm9 /path_to/twobit/mm9.2bit
>
> in the alignseq.loc file as .nib has been replaced by 2bit.
> Plus all necessaty entries in all_fasta.loc and twobit.loc
>
> That worked :)
>
> Hope this helps.
>
> Fred
>
>
>
> On 09/05/2012 22:40, Daniel Blankenberg wrote:
>
>> Hi Raja,
>>
>> Can you check that your fields are tab separated and not spaces (they
>> are spaces below, but that could be a copy and paste artifact)?
>>
>>
>> Thanks for using Galaxy,
>>
>> Dan
>>
>>
>> On May 9, 2012, at 9:45 AM, Raja Kelkar wrote:
>>
>>  Hi Jen,
>>>
>>> Thank you for your response. I seem to have all the relevant entries
>>> in the two "*.loc" files you mentioned (paths in all_fasta files and
>>> the twobit files are different because of the way we have the files
>>> stored. I also converted the 2bit files to .fa and have them available
>>> in the same twobit directory).
>>>
>>> But the feature extraction is still not working.
>>>
>>> Here are the relevant entries in files (I have redacted specific file
>>> paths and replaced them with "path_to"):
>>>
>>> twobit.loc
>>>
>>> hg18 /path_to/twobit/hg18.2bit
>>> hg19 /path_to/twobit/hg19.2bit
>>> mm9 /path_to/twobit/mm9.2bit
>>> mm8 /path_to/twobit/mm8.2bit
>>>
>>> all_fasta.loc
>>>
>>> hg19full hg19 Human (Homo sapiens): hg19 Full
>>> /path_to/hg19/bwa_path/hg19_**all.fa
>>> hg19_chr_only hg19_chr Human (Homo sapiens): hg19_chrom_only
>>> /path_to/hg19/bwa_path/hg19.fa
>>> hg18full hg18 Human (Homo sapiens): hg18 Full
>>> /path_to/hg18/bwa_path/hg18_**all.fa
>>> hg18_chr_only hg18_chr Human (Homo sapiens): hg18_chrom_only
>>> /path_to/hg18/bwa_path/hg18_**chrom_only.fa
>>>
>>>
>>> I assume that the second field in the (all_fasta.loc) file  has
>>> to match the builds.txt file in the "ucsc" directory. Is that correct?
>>> It does in this case. I think I am missing something subtle here.
>>>
>>> The "*.loc.sample" files are great but the information contained in
>>> those is confusing. I am not sure why there are two examples of the
>>> same info (as far as I can tell) in most sample loc files.
>>>
>>> Thanks.
>>>
>>>
>>> On Tue, May 8, 2012 at 6:48 PM, Jennifer Jackson >> > wrote:
>>>
>>>Hi Raja,
>>>
>>>This tool uses a .2bit file to extract sequence data
>>>when the 'Locally cashed' option is used. The  is a
>>>genome that you install locally. ".2bit" format was developed by
>>>UCSC and they are the source for many genomes in this format
>>>already and for tools (compiled and uncompiled) to transform fasta
>>>data into/from .2bit format (faTwoToBit and twoBitToFa):
>>>http://hgdownload.cse.ucsc.__**edu/downloads.html
>>>
>>>
>>> >
>>> (genomes + source)
>>>http://hgdownload.cse.ucsc.__**edu/admin/exe/linux.x86_64/
>>>
>>>
>>> >
>>> (compiled
>>>utilities)
>>>
>>>For the extract tool, the builds list is required:
>>>
>>> http://wiki.g2.bx.psu.edu/__**Admin/Data%20Integration
>>>
>>>
>>> 
>>> >
>>>
>>>You don't actually need to have more NGS set up beyond that.
>>>Still, this wiki can help.
>>>
>>> http://wiki.g2.bx.psu.edu/__**Admin/NGS%20Local%20Setup
>>>
>>>
>>> 
>>> >
>>>
>>>For example, the .2bit file could be placed with your
>>>.fa files like:
>>>
>>>/galaxy-dist/tool-data/genome/**__/seq/.**__2bit
>>> <<
>>>/galaxy-dist/tool-data/genome/**__/seq/.**fa
>>>/galaxy-dist/tool-data/genome/**__/bowtie/
>>>/galaxy-dist/tool-data/genome/**__/sam/
>>>/galaxy-dist/tool-data/genome/**__/seq/.**__2bit
>>> <<
>>>/galaxy-dist/tool-data/genome/**__/seq/.**fa
>>>/galaxy-dist/tool-data/genome/**__/seq/.**__2bit
>>> <<
>>>/galaxy-dist/tool-data/genome/**__/seq/.**fa
>>>/galaxy-dist/tool-data/genome/**__/seq/.**__2bit
>>> <<
>>>/galaxy-dist/tool-data/genome/**__/seq/.**fa
>>>
>>>
>>>Then the .loc file is here:
>>>
>>>/galaxy-dist/tool-data/twobit.**__loc.sample
>>>
>>>
>>>You will probably have this for all genomes as well:
>

Re: [galaxy-dev] Error when exporting history to file

[Jeremy Goecks]

Fixed in galaxy-central changeset cc70c3dcd6f7

Sarah, thanks for taking the time to reproduce on the public server.

Best,
J.

On May 10, 2012, at 10:17 AM, Sarah Diehl wrote:

> Hi Jeremy,
> 
> I was able to reproduce the error on the public Galaxy server. I shared the 
> history with you (jeremy.goe...@emory.edu). It's named "export history to 
> file bug".
> 
> Thanks.
> Sarah
> 
> 
> - Original Message -
> From: "Sarah Diehl" 
> To: "Jeremy Goecks" 
> Cc: "galaxy-dev@lists.bx.psu.edu List" 
> Sent: Wednesday, May 9, 2012 11:40:50 AM
> Subject: Re: [galaxy-dev] Error when exporting history to file
> 
> Hi Jeremy,
> 
> I'm using galaxy-dist, but it's quite possible that I'm a version or two 
> behind. I'm not yet able to reproduce the problem on the public server, 
> but I'm still missing some steps from the input to the problematic 
> dataset. I'll get back to you if I'm able to reproduce it or if it still 
> persist when I have updated our Galaxy server.
> Thanks for your help!
> 
> Best regards,
> Sarah
> 
> 
> On 05/09/2012 02:09 AM, Jeremy Goecks wrote:
>> Sarah,
>> 
>> I'm not able to reproduce your issue using galaxy-central. This could mean 
>> that this bug has been fixed in galaxy-central but hasn't made it to 
>> galaxy-dist yet—it appears you are using galaxy-dist—or there's other 
>> information needed to reproduce this issue. A couple more questions:
>> 
>> Are you using galaxy-dist?
>> Can you reproduce the issue on our public server using the problematic 
>> dataset and/or workflow?
>> 
>> Thanks,
>> J.
>> 
>> 
>> On May 7, 2012, at 12:33 PM, Sarah Diehl wrote:
>> 
>>> Sort (version 1.0.1)
>>> 
>>> on column: c5
>>> with flavor: Numerical sort
>>> everything in: Descending order
>>> 
>>> 
>>> On 05/07/2012 06:28 PM, Jeremy Goecks wrote:
 Sarah,
 
 What tool was used to create the problematic dataset?
 
 Thanks,
 J.
 
 On May 7, 2012, at 12:17 PM, Sarah Diehl wrote:
 
> Hi all,
> 
> I get the following error when I try to export a specific history to file:
> 
> 10.1.5.190 - - [07/May/2012:18:01:08 +0200] "GET /history/export_archive 
> HTTP/1.1" 500 - "http://galaxy.immunbio.mpg.de/"; "Mozilla/5.0 (X11; U; 
> Linux x86_64; en-US; rv:1.9.2.24) Gecko/2008 Fedora/3.6.24-1.fc14 
> Firefox/3.6.24"
> Error - 'exceptions.TypeError'>: object at 0x8ba67d0>   is not JSON serializable
> URL: http://galaxy.immunbio.mpg.de/history/export_archive
> File 
> '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py',
>  line 143 in __call__
> app_iter = self.application(environ, start_response)
> File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', 
> line 80 in __call__
> return self.application(environ, start_response)
> File 
> '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', 
> line 632 in __call__
> return self.application(environ, start_response)
> File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 
> in __call__
> body = method( trans, **kwargs )
> File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 
> 678 in export_archive
> history_exp_tool.execute( trans, incoming = params, set_output_hid = True 
> )
> File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in 
> execute
> return self.tool_action.execute( self, trans, incoming=incoming, 
> set_output_hid=set_output_hid, history=history, **kwargs )
> File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', 
> line 106 in execute
> include_deleted=incoming[ 'include_deleted' ] )
> File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 
> 428 in setup_job
> jobs_attrs_out.write( to_json_string( jobs_attrs, 
> cls=HistoryDatasetAssociationEncoder ) )
> File 
> '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py',
>  line 268 in dumps
> File 
> '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py',
>  line 214 in encode
> File 
> '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py',
>  line 282 in iterencode
> File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 
> 327 in default
> return simplejson.JSONEncoder.default( self, obj )
> File 
> '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py',
>  line 190 in default
> TypeError: 0x8ba67d0>   is not JSON serializable
> 
> 
> I tracked the problem down to a single bed file. I copied it into a new 
> empty history and I can still not export this history to a file. This 
> file doesn't have any special characters in either its name, info or 
> annotation. I c

Re: [galaxy-dev] Running Galaxy on PBS/Torque cluster

[Dorset, Daniel C]

Thanks Nate! I'm looking forward to it!

-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu] 
Sent: Thursday, May 10, 2012 11:02 AM
To: Dorset, Daniel C
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Running Galaxy on PBS/Torque cluster

On May 3, 2012, at 3:42 PM, Dorset, Daniel C wrote:

> I have had Galaxy running on a local BAS, and after success with that we're 
> ready to create an instance on our local cluster computing service. The local 
> cluster uses PBS/Torque.
>  
> I'm familiar with the basics of configuration, but our particular scheduler 
> rewards those who specify accurate walltimes. I would like to be able to 
> define specific walltimes for each tool. I'm mapping out a strategy for how 
> best to specify accurate walltimes. For instance, if someone is running 
> tophat, it will take longer if they're mapping against a complex reference 
> genome like human, as opposed to nematode. I'd like to use different 
> walltimes to account for that.
>  
> Is there anyone who has tackled this and would be willing to share their 
> approach with me?

Hi Dan,

This doesn't currently exist in Galaxy, but John Chilton at UMN has written 
enhancements that do what you're looking for:

  
https://bitbucket.org/galaxy/galaxy-central/pull-request/12/dynamic-job-runners

Unfortunately the patches no longer apply cleanly against galaxy-central, but I 
will work on getting them integrated soon.

--nate

>  
> Thanks!
>  
> Dan
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Re: [galaxy-dev] Running Galaxy on PBS/Torque cluster

[Fields, Christopher J]

On May 10, 2012, at 11:02 AM, Nate Coraor wrote:

> On May 3, 2012, at 3:42 PM, Dorset, Daniel C wrote:
> 
>> I have had Galaxy running on a local BAS, and after success with that we’re 
>> ready to create an instance on our local cluster computing service. The 
>> local cluster uses PBS/Torque.
>> 
>> I’m familiar with the basics of configuration, but our particular scheduler 
>> rewards those who specify accurate walltimes. I would like to be able to 
>> define specific walltimes for each tool. I’m mapping out a strategy for how 
>> best to specify accurate walltimes. For instance, if someone is running 
>> tophat, it will take longer if they’re mapping against a complex reference 
>> genome like human, as opposed to nematode. I’d like to use different 
>> walltimes to account for that.
>> 
>> Is there anyone who has tackled this and would be willing to share their 
>> approach with me?
> 
> Hi Dan,
> 
> This doesn't currently exist in Galaxy, but John Chilton at UMN has written 
> enhancements that do what you're looking for:
> 
>  
> https://bitbucket.org/galaxy/galaxy-central/pull-request/12/dynamic-job-runners
> 
> Unfortunately the patches no longer apply cleanly against galaxy-central, but 
> I will work on getting them integrated soon.
> 
> --nate

That would be really nice for our local users as well.  I think the current 
hack around this was to have two versions of the same tools, configured 
differently, which is definitely suboptimal.

chris
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Re: [galaxy-dev] Running Galaxy on PBS/Torque cluster

[Nate Coraor]

On May 3, 2012, at 3:42 PM, Dorset, Daniel C wrote:

> I have had Galaxy running on a local BAS, and after success with that we’re 
> ready to create an instance on our local cluster computing service. The local 
> cluster uses PBS/Torque.
>  
> I’m familiar with the basics of configuration, but our particular scheduler 
> rewards those who specify accurate walltimes. I would like to be able to 
> define specific walltimes for each tool. I’m mapping out a strategy for how 
> best to specify accurate walltimes. For instance, if someone is running 
> tophat, it will take longer if they’re mapping against a complex reference 
> genome like human, as opposed to nematode. I’d like to use different 
> walltimes to account for that.
>  
> Is there anyone who has tackled this and would be willing to share their 
> approach with me?

Hi Dan,

This doesn't currently exist in Galaxy, but John Chilton at UMN has written 
enhancements that do what you're looking for:

  
https://bitbucket.org/galaxy/galaxy-central/pull-request/12/dynamic-job-runners

Unfortunately the patches no longer apply cleanly against galaxy-central, but I 
will work on getting them integrated soon.

--nate

>  
> Thanks!
>  
> Dan
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Re: [galaxy-dev] Installing Galaxy on Mac OS X 10.7: pyglet issue

[Nate Coraor]

On May 6, 2012, at 5:11 AM, Arnav Moudgil wrote:

> Hi folks,
> 
> I'm trying to install Galaxy locally on my Mac running OS X 10.7 and Python 
> 2.7.3. After cloning the repository and running sh run.sh the first time, the 
> following error occurs:
> 
> [Fetches series of eggs…]
> Fetch successful.
> Traceback (most recent call last):
>   File "./scripts/paster.py", line 34, in 
> command.run()
>   File 
> "/Users/username/Downloads/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
>  line 73, in run
> commands = get_commands()
>   File 
> "/Users/username/Downloads/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
>  line 115, in get_commands
> plugins = pluginlib.resolve_plugins(plugins)
>   File 
> "/Users/username/Downloads/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/pluginlib.py",
>  line 81, in resolve_plugins
> pkg_resources.require(plugin)
>   File "/Users/username/Downloads/galaxy-dist/lib/galaxy/eggs/__init__.py", 
> line 413, in require
> return pkg_resources.working_set.require( req_str )
>   File "/Users/username/Downloads/galaxy-dist/lib/pkg_resources.py", line 
> 666, in require
> needed = self.resolve(parse_requirements(requirements))
>   File "/Users/username/Downloads/galaxy-dist/lib/pkg_resources.py", line 
> 565, in resolve
> raise DistributionNotFound(req)  # XXX put more info here
> pkg_resources.DistributionNotFound: Not Found: pyglet-1.1.4-py2.6 (did you 
> run python setup.py develop?)
> 
> I have downloaded and installed pyglet for both Python 2.7 and 2.6 (both 
> versions are on my system, but 2.7 is default), and the error still persists. 
> Any ideas what's going on here?

Hi Arnav,

pyglet is not a Galaxy dependency, so I have no idea where that is coming from, 
but I suspect it has something to do with your python environment.  Could you 
set up a virtualenv as described here:

http://usegalaxy.org/production

And see if that makes a difference?

--nate

> 
> 
> Thanks!
> 
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[galaxy-dev] Submitting Jobs as User

[Daniel Patrick Sullivan]

Hi, Galaxy Developers,

I have a hopefully quick question regarding configuring Galaxy cluster
integration;  I've configured our universe_wsgi.ini to include the
options specified in this document:

http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Submitting_Jobs_as_the_Real_User

set_metadata_externally = True
set_metadata_externally = True
drmaa_external_runjob_script = scripts/drmaa_external_runner.py
drmaa_external_killjob_script = scripts/drmaa_external_killer.py

I have also given the galaxy account full sudo privileges.

My question is that even after re-starting Galaxy and launching a job,
when I schedule a job through galaxy, the job is still being scheduled
as the galaxy user (if I run qstat, for example).  Could anybody
possibly provide some insight as to why this would be occurring?  Do I
need to set any other configuration options other than what I have
specified above?

Thank-you so much,

Dan Sullivan
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Re: [galaxy-dev] [galaxy-user] Help on installing cutadapt

[Nate Coraor]

On May 9, 2012, at 10:37 AM, Tilahun Abebe wrote:

> Hi Jen,
> 
> Thank you for the suggestions. I did try to log in to Galaxy under User 
> -->Login. The password is the one I use for the Galaxy Main. However, it 
> gives me the error message "No such user (please note that login is case 
> sensitive)". I do not see a place to set Admin password in the 
> universe_wsgi.ini file. 
> 
> Here is how I setup the Admin permissions under Users and Security in the 
> universe_wsgi.ini file:
> 1. id_secrete = gave a mix of numbers and letters
> 2. use_remote_user = True
> 3. remote_user_maildomain = tilahun.ab...@uni.edu

Hi Tilahun,

If you're using remote_user and your authentication is done upstream (e.g. in 
Apache) then you'll want to modify your remote_user_maildomain.  That parameter 
should be everything after the @ sign, so if you authenticate in Apache and 
Apache sets the REMOTE_USER header to 'Tilahun.Abebe', then 
remote_user_maildomain should be set to 'uni.edu'.

> 4. remote_user_logout_href = None
> 5. Admin_users = tilahun.ab...@uni.edu
> 6. require_login = True
> 7. allow_user_creation = False
> 8. allow_user_deletion = True
> 9. allow_user_impersonation = True
> 10. allow_user_dataset_purge = True
> 11. new_user_dataset_access_role_default_private = True
> 
> Can you check and let me know information I missed?

If remote user authentication is correctly set up, you should not have a "Log 
In" link under the User menu.  You should always see the "Logged in as 
tilahun.ab...@uni.edu" item in the menu instead, and that item would not be 
clickable.

--nate

> 
> Thanks.
> 
> Tilahun
> --
> 
> On Tue, May 8, 2012 at 4:53 PM, Jennifer Jackson  wrote:
> Hello Tilahun,
> 
> Are you logged into your Galaxy instance UI using your admin account? This 
> will display the Admin menu.
> 
> Admin permissions are set up in the universe_wsgi.ini file:
> 
> # -- Users and Security
> 
> < other items >
> 
> # Administrative users - set this to a comma-separated list of valid Galaxy
> # users (email addresses).  These users will have access to the Admin section
> # of the server, and will have access to create users, groups, roles,
> # libraries, and more.  For more information, see:
> # http://wiki.g2.bx.psu.edu/Admin/Interface
> #admin_users = None
> 
> Hopefully this solves the issue. Going forward, you'll probably find that the 
> galaxy-...@bx.psu.edu mailing list is the most helpful for local install 
> questions:
> http://wiki.g2.bx.psu.edu/Support#Mailing_Lists
> 
> Best,
> 
> Jen
> Galaxy team
> 
> 
> On 5/8/12 2:10 PM, Tilahun Abebe wrote:
> Hi Galaxy users,
> 
> I tried to install cutadapt for sequence trimming on a local Galaxy
> instance. I successfully installed Galaxy as an administrator. However,
> when Galaxy starts, I don't see the administrator option in the top menu
> bar with the "Analyze Data, Workflow, Shared Data, Visualization, Help,
> and User". It looks like the only way I can install cutadapt is with an
> administrator option. Any suggestion how I can include the administrator
> option in the menu?
> 
> Thanks for your help.
> 
> Tilahun
> 
> 
> 
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
> 
>   http://lists.bx.psu.edu/listinfo/galaxy-dev
> 
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
> 
>   http://lists.bx.psu.edu/
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> -- 
> Jennifer Jackson
> http://galaxyproject.org
> 
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Re: [galaxy-dev] Server Error when downloading files from history

[Dannon Baker]

This was a temporary issue with the public server that has been fixed.  Let me 
know if you still have issues.  Also, for future reference, galaxy-bugs would 
be the correct list to send this type of problem to.

Thanks!

Dannon


On May 9, 2012, at 7:55 PM, "Rathi D. Thiagarajan"  
wrote:

> Hi there,
> 
> I received the following error when trying to download/save my tabular files 
> with 5k lines:
> 
> Server Error
> 
> An error occurred. See the error logs for more information. (Turn debug on to 
> display exception reports here)
> 
> Please help!
> 
> Thanks in advance.
> 
> Cheers,
> Rathi
> 
> -- 
> Rathi D. Thiagarajan, PhD
> Professional Scientific Collaborator
> UCSD Research Scholar
> Dept. of Chemical Physiology
> Center for Regenerative Medicine
> The Scripps Research Institute
> 3030 Science Park Rd,
> La Jolla, CA 92035, USA
> 
> Mail:SP30-3021
> W: 858.784.7753
> E: ra...@scripps.edu
> E: rthiagara...@ucsd.edu
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Re: [galaxy-dev] Error when exporting history to file

[Sarah Diehl]

Hi Jeremy,

I was able to reproduce the error on the public Galaxy server. I shared the 
history with you (jeremy.goe...@emory.edu). It's named "export history to file 
bug".

Thanks.
Sarah


- Original Message -
From: "Sarah Diehl" 
To: "Jeremy Goecks" 
Cc: "galaxy-dev@lists.bx.psu.edu List" 
Sent: Wednesday, May 9, 2012 11:40:50 AM
Subject: Re: [galaxy-dev] Error when exporting history to file

Hi Jeremy,

I'm using galaxy-dist, but it's quite possible that I'm a version or two 
behind. I'm not yet able to reproduce the problem on the public server, 
but I'm still missing some steps from the input to the problematic 
dataset. I'll get back to you if I'm able to reproduce it or if it still 
persist when I have updated our Galaxy server.
Thanks for your help!

Best regards,
Sarah


On 05/09/2012 02:09 AM, Jeremy Goecks wrote:
> Sarah,
>
> I'm not able to reproduce your issue using galaxy-central. This could mean 
> that this bug has been fixed in galaxy-central but hasn't made it to 
> galaxy-dist yet—it appears you are using galaxy-dist—or there's other 
> information needed to reproduce this issue. A couple more questions:
>
> Are you using galaxy-dist?
> Can you reproduce the issue on our public server using the problematic 
> dataset and/or workflow?
>
> Thanks,
> J.
>
>
> On May 7, 2012, at 12:33 PM, Sarah Diehl wrote:
>
>> Sort (version 1.0.1)
>>
>> on column: c5
>> with flavor: Numerical sort
>> everything in: Descending order
>>
>>
>> On 05/07/2012 06:28 PM, Jeremy Goecks wrote:
>>> Sarah,
>>>
>>> What tool was used to create the problematic dataset?
>>>
>>> Thanks,
>>> J.
>>>
>>> On May 7, 2012, at 12:17 PM, Sarah Diehl wrote:
>>>
 Hi all,

 I get the following error when I try to export a specific history to file:

 10.1.5.190 - - [07/May/2012:18:01:08 +0200] "GET /history/export_archive 
 HTTP/1.1" 500 - "http://galaxy.immunbio.mpg.de/"; "Mozilla/5.0 (X11; U; 
 Linux x86_64; en-US; rv:1.9.2.24) Gecko/2008 Fedora/3.6.24-1.fc14 
 Firefox/3.6.24"
 Error ->>> 'exceptions.TypeError'>:>>> object at 0x8ba67d0>   is not JSON serializable
 URL: http://galaxy.immunbio.mpg.de/history/export_archive
 File 
 '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py',
  line 143 in __call__
 app_iter = self.application(environ, start_response)
 File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', 
 line 80 in __call__
 return self.application(environ, start_response)
 File 
 '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', 
 line 632 in __call__
 return self.application(environ, start_response)
 File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in 
 __call__
 body = method( trans, **kwargs )
 File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 
 678 in export_archive
 history_exp_tool.execute( trans, incoming = params, set_output_hid = True )
 File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in 
 execute
 return self.tool_action.execute( self, trans, incoming=incoming, 
 set_output_hid=set_output_hid, history=history, **kwargs )
 File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', 
 line 106 in execute
 include_deleted=incoming[ 'include_deleted' ] )
 File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 
 428 in setup_job
 jobs_attrs_out.write( to_json_string( jobs_attrs, 
 cls=HistoryDatasetAssociationEncoder ) )
 File 
 '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py',
  line 268 in dumps
 File 
 '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py',
  line 214 in encode
 File 
 '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py',
  line 282 in iterencode
 File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 
 327 in default
 return simplejson.JSONEncoder.default( self, obj )
 File 
 '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py',
  line 190 in default
 TypeError:>>> 0x8ba67d0>   is not JSON serializable


 I tracked the problem down to a single bed file. I copied it into a new 
 empty history and I can still not export this history to a file. This file 
 doesn't have any special characters in either its name, info or 
 annotation. I can't find anything special about this file...

 Any help is greatly appreciated!

 Best regards,
 Sarah
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Re: [galaxy-dev] Trackster - not showing data.

[Jeremy Goecks]

Mo,

This was a temporary problem and has been fixed. 

However, the datasets you tried to visualize are now in an error state, so 
you'll have to copy them (History Menu --> Copy Datasets) to create new ones, 
which you can then visualize. You can copy datasets to the same history without 
problems.

Best,
J. 

On May 10, 2012, at 7:30 AM, Mohammad Heydarian wrote:

> Hi,
> I have been trying to use trackster on the main Galaxy server for a couple of 
> days now. It was working fine for me early yesterday, I was looking at 
> (larger) BAM files, then it just stopped and would not display the data of 
> the loaded tracks (but did display the track title). I have tried to start 
> Trackster with smaller sized tracks, as well as using another Galaxy account, 
> and still cannot get Trackster to display data (though it will show the track 
> title).
> 
> Any help would be greatly appreciated!
> 
> 
> Cheers, 
> Mo Heydarian
> 
> 
> 
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[galaxy-dev] Server Error when downloading files from history

[Rathi D. Thiagarajan]

Hi there,

I received the following error when trying to download/save my tabular  
files with 5k lines:


Server Error

An error occurred. See the error logs for more information. (Turn debug on  
to display exception reports here)


Please help!

Thanks in advance.

Cheers,
Rathi




--
Rathi D. Thiagarajan, PhD
Professional Scientific Collaborator
UCSD Research Scholar
Dept. of Chemical Physiology
Center for Regenerative Medicine
The Scripps Research Institute
3030 Science Park Rd,
La Jolla, CA 92035, USA

Mail:SP30-3021
W: 858.784.7753
E: ra...@scripps.edu
E: rthiagara...@ucsd.edu
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[galaxy-dev] problems with running jobs on Galaxy

[Philipp Kapranov]

Hello,

I keep on getting this error today: Error executing tool: [Errno 13]
Permission denied: '/galaxy/main_pool/pool4/files/004' .

What is wrong?

Thank you!

Phil
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Re: [galaxy-dev] Loc file configuration question

[Federico De Masi]

Hi,

I was having the same issue just today and my solution was to add:

seq mm9 /path_to/twobit/mm9.2bit

in the alignseq.loc file as .nib has been replaced by 2bit.
Plus all necessaty entries in all_fasta.loc and twobit.loc

That worked :)

Hope this helps.

Fred


On 09/05/2012 22:40, Daniel Blankenberg wrote:

Hi Raja,

Can you check that your fields are tab separated and not spaces (they
are spaces below, but that could be a copy and paste artifact)?


Thanks for using Galaxy,

Dan


On May 9, 2012, at 9:45 AM, Raja Kelkar wrote:


Hi Jen,

Thank you for your response. I seem to have all the relevant entries
in the two "*.loc" files you mentioned (paths in all_fasta files and
the twobit files are different because of the way we have the files
stored. I also converted the 2bit files to .fa and have them available
in the same twobit directory).

But the feature extraction is still not working.

Here are the relevant entries in files (I have redacted specific file
paths and replaced them with "path_to"):

twobit.loc

hg18 /path_to/twobit/hg18.2bit
hg19 /path_to/twobit/hg19.2bit
mm9 /path_to/twobit/mm9.2bit
mm8 /path_to/twobit/mm8.2bit

all_fasta.loc

hg19full hg19 Human (Homo sapiens): hg19 Full
/path_to/hg19/bwa_path/hg19_all.fa
hg19_chr_only hg19_chr Human (Homo sapiens): hg19_chrom_only
/path_to/hg19/bwa_path/hg19.fa
hg18full hg18 Human (Homo sapiens): hg18 Full
/path_to/hg18/bwa_path/hg18_all.fa
hg18_chr_only hg18_chr Human (Homo sapiens): hg18_chrom_only
/path_to/hg18/bwa_path/hg18_chrom_only.fa


I assume that the second field in the (all_fasta.loc) file  has
to match the builds.txt file in the "ucsc" directory. Is that correct?
It does in this case. I think I am missing something subtle here.

The "*.loc.sample" files are great but the information contained in
those is confusing. I am not sure why there are two examples of the
same info (as far as I can tell) in most sample loc files.

Thanks.


On Tue, May 8, 2012 at 6:48 PM, Jennifer Jackson mailto:j...@bx.psu.edu>> wrote:

Hi Raja,

This tool uses a .2bit file to extract sequence data
when the 'Locally cashed' option is used. The  is a
genome that you install locally. ".2bit" format was developed by
UCSC and they are the source for many genomes in this format
already and for tools (compiled and uncompiled) to transform fasta
data into/from .2bit format (faTwoToBit and twoBitToFa):
http://hgdownload.cse.ucsc.__edu/downloads.html
 (genomes + source)
http://hgdownload.cse.ucsc.__edu/admin/exe/linux.x86_64/
 (compiled
utilities)

For the extract tool, the builds list is required:
http://wiki.g2.bx.psu.edu/__Admin/Data%20Integration


You don't actually need to have more NGS set up beyond that.
Still, this wiki can help.
http://wiki.g2.bx.psu.edu/__Admin/NGS%20Local%20Setup


For example, the .2bit file could be placed with your
.fa files like:

/galaxy-dist/tool-data/genome/__/seq/.__2bit <<
/galaxy-dist/tool-data/genome/__/seq/.fa
/galaxy-dist/tool-data/genome/__/bowtie/
/galaxy-dist/tool-data/genome/__/sam/
/galaxy-dist/tool-data/genome/__/seq/.__2bit <<
/galaxy-dist/tool-data/genome/__/seq/.fa
/galaxy-dist/tool-data/genome/__/seq/.__2bit <<
/galaxy-dist/tool-data/genome/__/seq/.fa
/galaxy-dist/tool-data/genome/__/seq/.__2bit <<
/galaxy-dist/tool-data/genome/__/seq/.fa

Then the .loc file is here:

/galaxy-dist/tool-data/twobit.__loc.sample

You will probably have this for all genomes as well:

/galaxy-dist/tool-data/all___fasta.loc.sample

Remove the ".sample" before using these. Instructions for how to
populate each are in the files themselves.

The only gtf/gff files associated with this tool would be datasets
from the history, so there are no gtf/gff data to stage before
using the tool. To have the tool use a particular genome, set the
query dataset (interval, bed, gtf) to have the same database
identifier as you used for the "" part of the
".2bit" file. (This is why the builds list is required).

If you make changes to data, don't forget to restart your server
to see the changes.

Hopefully this helps,

Jen
Galaxy team


On 5/8/12 12:46 PM, Raja Kelkar wrote:

I have two questions that pertain to a local install of galaxy:

1. I have been having trouble getting the “fetch sequences” à
“extract
genomic DNA” tool to work. Can someone identify the specific
*.loc file
that needs to have the info about the location of the genome
sequence files?

I get the following error when I run the extract tool:

/No sequences are available for 'hg19’, request them by
reporti

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[galaxy-dev] permission error

[Alex Strunnikov]

Hello, I am trying  to use MACS on galaxy at https://main.g2.bx.psu.edu/, but I 
get permission error:

Error executing tool: [Errno 13] Permission denied: 
'/galaxy/main_pool/pool3/files/004'

Could you help, please

Sincerely, alex strunnikov

my login is
a...@gibh.org___
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[galaxy-dev] Trackster - not showing data.

[Mohammad Heydarian]

Hi,
I have been trying to use trackster on the main Galaxy server for a couple
of days now. It was working fine for me early yesterday, I was looking at
(larger) BAM files, then it just stopped and would not display the data of
the loaded tracks (but did display the track title). I have tried to start
Trackster with smaller sized tracks, as well as using another Galaxy
account, and still cannot get Trackster to display data (though it will
show the track title).

Any help would be greatly appreciated!


Cheers,
Mo Heydarian
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Re: [galaxy-dev] debugging jobs in 'new' state

[Peter Cock]

On Thu, Jul 28, 2011 at 11:03 PM, Shantanu Pavgi  wrote:
>
> We experienced an issue where some of the galaxy jobs were sitting in the
> 'new' state for a quite long time. They were not waiting for cluster resources
> to become available, but haven't been even queued up through DRMAA.
> We are currently using non-debug mode and following were my observations:
> * No indication of new jobs in paster.log file
> * database/pbs script didn't contain any associated job scripts
> * in backend database - job table contained their galaxy job id but no
> command_line input was recorded
>
> Also, not all the jobs are waiting in the 'new' state. Many jobs submitted 
> after
> above waiting jobs got completed successfully on the cluster. Is there any
> job submission logic within galaxy which is being used for submitting jobs?
> Any clues on how to debug this issue will be really helpful.

I've just been searching the archives for any other cases of new jobs not
getting queued (either with the local runner or via DRMAA) but sitting
in state new - and I found your query.

Did you ever solve your issue Shantanu?

We had something similar just happen, but it affected all new jobs,
unlike what you described. Fortunately I could work out what the cause
was - our Galaxy partition had run out of disk space. I did some
cleanup, and then I could submit and run new jobs - but the existing
stalled jobs remained stalled.

Peter
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