[galaxy-dev] Job handler keeps crashing

[Derrick Lin]

Hi guys,

We have updated our galaxy to 20 Dec 2012 release. Recently we found that
some submitted jobs could not start (stay gray forever).

We found that it was caused by the job manager sent jobs to a handler
(handler0) whose python process crashed and died.

>From the handler log we found the last messages right before the crash:

galaxy.jobs.handler DEBUG 2013-01-18 15:00:34,481 Stopping job 3032:
galaxy.jobs.handler DEBUG 2013-01-18 15:00:34,481 stopping job 3032 in
drmaa runner

We restarted the galaxy, handler0 is up for few seconds then died again
with the same error messages except the job number moved to the next one.

We observed that the jobs it was trying to stop are all previous jobs whose
status is either "deleted" or "deleted_new".

We have never seen this in the past, so wondering if there is bugs in the
new release?

Cheers,
Derrick
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[galaxy-dev] Programming error in my new tool for shapeit.

[James Boocock]

ProgrammingError: (ProgrammingError) You must not use 8-bit
bytestrings unless you use a text_factory that can interpret 8-bit
bytestrings (like text_factory = str). It is highly recommended that
you instead just switch your application to Unicode strings. u'UPDATE
job SET update_time=?, state=?, stdout=?, stderr=? WHERE job.id = ?'
['2013-01-14 07:17:20.417990', 'error', '',
'\n\n\x1b[33mS\x1b[0megmented \x1b[33mHAP\x1b[0mlotype
\x1b[33mE\x1b[0mstimation & \x1b[33mI\x1b[0mmputation
\x1b[33mT\x1b[0mool\

That is just a sample of the stderr from the galaxy stack trace. I
think that shapeit is using 8 bit character codes in the stdout and
galaxy is failing on adding to the database. Has anyone experienced
this problem and could help me.

Cheers James
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[galaxy-dev] Programming error in my new tool shape for shape it

[James Boocock]

ProgrammingError: (ProgrammingError) You must not use 8-bit
bytestrings unless you use a text_factory that can interpret 8-bit
bytestrings (like text_factory = str). It is highly recommended that
you instead just switch your application to Unicode strings. u'UPDATE
job SET update_time=?, state=?, stdout=?, stderr=? WHERE job.id = ?'
['2013-01-14 07:17:20.417990', 'error', '',
'\n\n\x1b[33mS\x1b[0megmented \x1b[33mHAP\x1b[0mlotype
\x1b[33mE\x1b[0mstimation & \x1b[33mI\x1b[0mmputation
\x1b[33mT\x1b[0mool\

That is just a sample of the stderr from the galaxy stack trace. I
think that shapeit is using 8 bit character codes in the stdout and
galaxy is failing on adding to the database. Has anyone experienced
this problem and could help me.

Cheers James
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Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy

[Jeremy Goecks]

I have a very basic STAR wrapper that works:

https://bitbucket.org/jgoecks/jeremys-code/src/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml?at=default

For now, the wrapper does two things: maps RNA-seq reads and identifies 
chimeric reads/junctions. There are tons of options that aren't yet 
implemented, but the basics are there.

Eventually I'll put the wrapper in the toolshed, but if you want to use it now, 
you'll need to create your own star_indexes.loc table (identical in structure 
to the bowtie_indexes.loc table) and add the appropriate entry to 
tool_data_table_conf.xml This page explains the details of these files:

http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

If you're interested in helping to flesh out the wrapper, pull requests or 
patches are welcome.

Thanks,
J. 



On Jan 16, 2013, at 7:05 AM, Sorn, Patrick wrote:

> Hi all,
>  
> I want to integrate STAR Aligner v2.2.0c into Galaxy and I was wondering if 
> anyone else is working on this? If nobody is, I would do this.
>  
> Best regards,
>  
> Patrick Sorn
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Re: [galaxy-dev] Galaxy with Univa Grid Engine (UGE) instead of SGE?

[Peter Cock]

On Thursday, January 17, 2013, Carlos Borroto wrote:

> On Wed, Jan 16, 2013 at 7:28 AM, Peter Cock 
> >
> wrote:
> >> Renaming the file to replace the colon with (say) an underscore allows
> >> a manual qsub to work fine with UGE. I've edited Galaxy to avoid the
> >> colons (patch below) but the submission still fails.
> >>
>
> Hi Peter,
>
> After seeing your email I now wonder if the problem I described
> here[1] and didn't get any answer about it is related to your findings
> while trying UGE.
>
> [1]
> http://dev.list.galaxyproject.org/Issue-when-enabling-use-tasked-jobs-with-torque-and-nfs-td4657294.html
>
> I noticed the only mayor different I can notice between jobs
> submission with and without tasked option enabled is a colon in the
> name.
>

Some overlap yes, and I do normally have BLAST running with
task splitting. That does probably explain the source of the colon.
I now suspect the colon is only a problem in SGE / UGE at the
command line using qsub - it may work via the Python API.

I have also seen some similar problems with sub-jobs failing
yet Galaxy still had the task as a green success (not sure
if that has happens recently or not).

Yesterday while our UGE cluster was under load, often one
or more of my split task jobs would fail (Galaxy could not
collect the output files - presumably network related for
accessing the shared storage), but Galaxy was correctly
flagging these as red failed jobs.

Cluster problems are hard to debug - especially on
a live cluster where there are other users active :(

Peter
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Re: [galaxy-dev] Blank history panel / Error in history API at listing contents

[Peter Cock]

On Thursday, January 17, 2013, Carl Eberhard wrote:

> Hello, Peter
>
> The blank panel should definitely be handled more gracefully in this
> situation - I'll work on that.
>
>
Great :)


> Have you noticed though, since your patch, any particular pattern to which
> metadata names are turning out to equal None (some obviously missing
> metadata field)? Is there a particular datatype?
>

No, and thus far I've only had it on my development Galaxy install which
has (compared to a production system) been exposed to plenty of cluster
oddities and other corner cases. It is also running on SQLite (easy to
reset and it is just me running jobs so contention is not normally an
issue).

Note that without adding more debugging or looking directly in the database
there is no easy way to tell what the datasets causing this problem were,
or what file type.


>
>
Have you seen the assertion fail?
> C
>
>
Not yet, no. The fact the two fields were both None suggests to me
sometimes an entry was not recorded properly...

Regards,

Peter
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Re: [galaxy-dev] Error trying to remove trackster visualization in latest galaxy-dist

[James Taylor]

On Thu, Jan 17, 2013 at 1:16 PM, Anthonius deBoer  wrote:

> Not to be ungrateful for the hard work you guys are all doing and
> please don't get this the wrong way, but is there any QA that is
> being done on the galaxy-dist when it is being released?

No worries Thon, we appreciate your feedback.

> Maybe its an idea to install galaxy-dist on the main galaxy server
> for a few weeks, before releasing it to the public so we know it has
> been running and stable...

For what it is worth, this actually is our release process. The code that
gets pulled from galaxy-central to galaxy-dist is a revision that has been
running on Galaxy main for some period of time. We also have
automated tests that run on every commit. However, neither of
these techniques catches every bug.

We're never happy when bugs go out in dist. There are likely a few
causes of the increase in this problem. One is the wide variety of
functionality now available in Galaxy, with increasing contributions
from a wide developer community, means there are many more
corner cases to test.

This has been particularly exacerbated by increasing use of more
interactive client side web technologies. These have enabled some
powerful new features, but are also significantly more difficult to test
well. We're currently working on a new framework for client side
automated testing which will hopefully improve our ability to catch
regressions.

> Again...I know we are dealing with opensource and free software

True, but our goal is still to deliver a stable product (while still
innovating quickly). We're always evolving and improving our
QA process and would appreciate your suggestions.
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Re: [galaxy-dev] Blank history panel / Error in history API at listing contents

[Carl Eberhard]

Hello, Peter

The blank panel should definitely be handled more gracefully in this
situation - I'll work on that.

Have you noticed though, since your patch, any particular pattern to which
metadata names are turning out to equal None (some obviously missing
metadata field)? Is there a particular datatype?

Have you seen the assertion fail?
C



On Wed, Jan 16, 2013 at 11:31 AM, Peter Cock wrote:

> Hello all,
>
> I've noticed on my test setup (tracking galaxy-central) a problem with
> some histories not displaying. If I click on saved histories, I am show
> a list. Some will load (slower than I recall), but others result in a blank
> right hand pane - with the following error from run.sh
>
> galaxy.webapps.galaxy.api.history_contents ERROR 2013-01-16
> 15:24:22,726 Error in history API at listing contents:  'exceptions.TypeError'>, cannot concatenate 'str' and 'NoneType'
> objects
>
> The same error and blank pane happens if I click on the reload
> history icon. A screenshot is attached.
>
> This error is coming from HistoryContentsController in file
> lib/galaxy/webapps/galaxy/api/history_contents.py - specifically
> in the call to get_hda_dict. I tried modifying this for loop so that
> any individual transaction with an error is ignored (but a debug
> message logged), and I could then load the rest of the problem
> histories.
>
> The error from get_hda_dict is from the first line, which takes
> the galaxy.model.HistoryDatasetAssociation object and asks:
>
> hda_dict = hda.get_api_value( view='element' )
>
> That takes us to lib/galaxy/model/__init__.py and the root of
> the problem: I am seeing entries where both name and val
> are None, meaning this line fails with the TypeError above:
>
> rval['metadata_' + name] = val
>
> Clearly some of my histories now have some 'bad' data in them,
> and currently Galaxy is failing to cope. Based on the ID numbers
> this has been happening for a while, so not a recent regression.
>
> Here is a patch which seems to help.
>
> Peter
>
> $ hg diff lib/galaxy/model/__init__.py
> diff -r 81c3b8a6a621 lib/galaxy/model/__init__.py
> --- a/lib/galaxy/model/__init__.py  Wed Jan 16 15:14:04 2013 +
> +++ b/lib/galaxy/model/__init__.py  Wed Jan 16 16:26:28 2013 +
> @@ -1530,7 +1530,11 @@
>  val = val.file_name
>  elif isinstance( val, list ):
>  val = ', '.join( [str(v) for v in val] )
> -rval['metadata_' + name] = val
> +if name is None:
> +log.debug("get_api_value(view=%r) : name %r, val %r"
> % (view, name, val))
> +assert val is None, "get_api_value(view=%r) : name
> %r, val %r" % (view, name, val)
> +else:
> +rval['metadata_' + name] = val
>  return rval
>
>  class HistoryDatasetAssociationDisplayAtAuthorization( object ):
>
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Re: [galaxy-dev] Galaxy with Univa Grid Engine (UGE) instead of SGE?

[Carlos Borroto]

On Wed, Jan 16, 2013 at 7:28 AM, Peter Cock  wrote:
>> Renaming the file to replace the colon with (say) an underscore allows
>> a manual qsub to work fine with UGE. I've edited Galaxy to avoid the
>> colons (patch below) but the submission still fails.
>>

Hi Peter,

After seeing your email I now wonder if the problem I described
here[1] and didn't get any answer about it is related to your findings
while trying UGE.

[1]http://dev.list.galaxyproject.org/Issue-when-enabling-use-tasked-jobs-with-torque-and-nfs-td4657294.html

I noticed the only mayor different I can notice between jobs
submission with and without tasked option enabled is a colon in the
name. See the relevant output from "qstat -f JOBID" below.

Without tasked:
Error_Path = 
/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/34/34.drmerr
Output_Path = 
/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/34/34.drmout

Job finishes and galaxy is able to collect drmerr and drmout files.

With tasked:
Error_Path = 
/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmerr
Output_Path = 
/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmout

sched_hint = Post job file processing error; job 40.head.local on host
node01.local/7+node01.local/6+node01.local/5+node01.local/4+node01.local/3+node01.local/2+node01.local/1+node01.brel.local/0

Unable to copy file /var/spool/torque/spool/40.head.local.OU to
galaxy@/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmout
*** error from copy
cp: cannot create regular file
`galaxy@/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmout':
No such file or directory
*** end error output
Output retained on that host in: /var/spool/torque/undelivered/40.head.local.OU

Unable to copy file /var/spool/torque/spool/40.head.local.ER to
galaxy@/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmerr
*** error from copy
cp: cannot create regular file
`galaxy@/local/opt/galaxy/galaxy-dist.torque/database/job_working_directory/000/33/task_4/33:30.drmerr':
No such file or directory
*** end error output
Output retained on that host in: /var/spool/torque/undelivered/40.head.local.ER

Job finishes, galaxy is not able to collect drmerr and drmout files
and job turns green in the history panels but includes partial
information about not being able to collect drmerr and drmout files.

I will try to see if switching from using colon to underscore could
help in this situation also. Although I'm also worry about "galaxy@"
in the file path. I don't understand why is there.

I'm using latest Galaxy Dist, Torque 4.1.4, Maui 3.3.1 and pbs-drmaa
1.0.12. I tried using pbs-python but that failed for me. I also tried
libdrmaa from this Torque version with the same exact results.

Best,
Carlos
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Re: [galaxy-dev] Error trying to remove trackster visualization in latest galaxy-dist

[Anthonius deBoer]

Not to be ungrateful for the hard work you guys are all doing and please don't get this the wrong way, but is there any QA that is being done on the galaxy-dist when it is being released? I have been a QA manager and I know how hard it is to test UI, but the last few releases on galaxy-dist have been rather broken in one way or another and for a production server this is scary...I am trying to get more people to use galaxy in my organization, but I am hesitant since there are so many simple things that are broken with every release...I know I should do my own QA before I install galaxy-dist on a production server, but I was sorta hoping that the whole reason for galaxy-dev and galaxy-dist was to have a test bed for any fixed in galaxy-dev, so when it was time for a production version for galaxy-dist, it would at least been tested a few weeks...Maybe its an idea to install galaxy-dist on the main galaxy server for a few weeks, before releasing it to the public so we know it has been running and stable...Again...I know we are dealing with opensource and free software and it has been very valuable to me and my organization. I have been happily testing and reporting each release when I was just running it for my self, but since every release I got was broken in one way or another, I had to get the next galaxy-dist just to be able to run my tests, let alone be able to release it to a larger audienceMaybe its time for a more formal release policy of galaxy-dist (other than me just waiting for bug reports before getting it)?Thanks,A very grateful Thon...On Jan 17, 2013, at 05:23 AM, Jeremy Goecks  wrote:This has been fixed in -central and will be available in the next Galaxy distribution.Thanks,J.On Jan 16, 2013, at 10:02 PM, Anthonius deBoer wrote:Hi,Tried to remove a trackster visualization in the latest galaxy-dist and got this error:Error Traceback:View as:   Interactive  |  Text  |  XML (full)⇝ NameError: global name 'util' is not definedURL: http://srv151/visualization/list?f-sharing=All&sort=-update_time&f-tags=All&operation=Delete&f-title=All&id=f2db41e1fa331b3eModule weberror.evalexception.middleware:364 in respond      view>>  app_iter = self.application(environ, detect_start_response)Module paste.debug.prints:98 in __call__      view>>  environ, self.app)Module paste.wsgilib:539 in intercept_output      view>>  app_iter = application(environ, replacement_start_response)Module paste.recursive:80 in __call__      view>>  return self.application(environ, start_response)Module galaxy.web.framework.middleware.remoteuser:91 in __call__      view>>  return self.app( environ, start_response )Module paste.httpexceptions:632 in __call__      view>>  return self.application(environ, start_response)Module galaxy.web.framework.base:160 in __call__      view>>  body = method( trans, **kwargs )Module galaxy.web.framework:94 in decorator      view>>  return func( self, trans, *args, **kwargs )Module galaxy.webapps.galaxy.controllers.visualization:320 in list      view>>  ids = util.listify( kwargs['id'] )NameError: global name 'util' is not definedExtra Features>>Display the lines of code near each part of the tracebackShow a debug prompt to allow you to directly debug the code at the tracebackRe-GET Page___Please keep all replies on the list by using "reply all"in your mail client.  To manage your subscriptions to thisand other Galaxy lists, please use the interface at:  http://lists.bx.psu.edu/___
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Re: [galaxy-dev] JAVAscript error after initiating tool

[Carl Eberhard]

Joachim,

That certainly helps. Thanks.

Do you recall if this error happened (or happens more often) with a
published or shared history? Or if it was imported or copied from a
published or shared history?

Thanks for the info,
C



On Thu, Jan 17, 2013 at 9:58 AM, Joachim Jacob  wrote:

> Hi,
>
> In the server logs I've found:
>
> web0.log: galaxy.webapps.galaxy.api.**histories ERROR 2013-01-11
> 19:56:21,071 Error in history API at showing history detail: History is not
> accessible to the current user
> web1.log: galaxy.webapps.galaxy.api.**histories ERROR 2013-01-11
> 19:55:14,341 Error in history API at showing history detail: History is not
> accessible to the current user
> web5.log: galaxy.webapps.galaxy.api.**histories ERROR 2013-01-11
> 20:29:11,138 Error in history API at showing history detail: History is not
> accessible to the current user
>
> The specific situation here is that I am almost at my 100% quotum of
> storage space... Don't know if this gives some hint. The problem appear
> sporadically, not reproducibabilibity :-)
>
>
> Cheers,
> Joachim
>
>
>
>
> Joachim Jacob
>
> Rijvisschestraat 120, 9052 Zwijnaarde
> Tel: +32 9 244.66.34
> Bioinformatics Training and Services (BITS)
> http://www.bits.vib.be
> @bitsatvib
>
> On 01/16/2013 05:33 PM, Carl Eberhard wrote:
>
>> Hi, Joachim
>>
>> If you have access to your server logs, do you see any log messages
>> containing 'Error in history API' around the time those happen?
>>
>> Is there a situation where this happens more often (or a way to reliably
>> reproduce)?
>>
>> I'm unable to reproduce this locally so far.
>>
>> The error definitely can be handled better on the javascript side, but
>> I'd like to track down the API error as well before I change the javascript.
>>
>> Thanks for the help,
>> C
>>
>>
>>
>>
>> On Wed, Jan 16, 2013 at 7:57 AM, Joachim Jacob > joachim.ja...@vib.be>> wrote:
>>
>> Hi all,
>>
>> For who is interested. Occasionally I get this strange Javascript
>> error, just after clicking 'run' on a tool.
>>
>> ERROR updating hdas from api history contents:e47699a32b93ce7f
>>
>> The tool gets running, but the history panel is not updated. I
>> click 'analyse data' to see the updated history.
>>
>>
>> Cheers,
>> Joachim
>>
>> -- Joachim Jacob
>>
>> Rijvisschestraat 120, 9052 Zwijnaarde
>> Tel: +32 9 244.66.34 
>>
>> Bioinformatics Training and Services (BITS)
>> http://www.bits.vib.be
>> @bitsatvib
>>
>> __**_
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>>
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>>
>>
>>
>
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[galaxy-dev] Migration of tools

[Joachim Jacob |VIB|]

Hi,

Has the devteam a schedule of the order of the tools they plan to 
migrate to the tool shed?



Thanks,

Joachim.

--
Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

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Re: [galaxy-dev] Error trying to remove trackster visualization in latest galaxy-dist

[Jeremy Goecks]

This has been fixed in -central and will be available in the next Galaxy 
distribution.

Thanks,
J.

On Jan 16, 2013, at 10:02 PM, Anthonius deBoer wrote:

> Hi,
> 
> Tried to remove a trackster visualization in the latest galaxy-dist and got 
> this error:
> 
> Error Traceback:
> View as:   Interactive  |  Text  |  XML (full)
> ⇝ NameError: global name 'util' is not defined
> URL: 
> http://srv151/visualization/list?f-sharing=All&sort=-update_time&f-tags=All&operation=Delete&f-title=All&id=f2db41e1fa331b3e
> Module weberror.evalexception.middleware:364 in respond  view
> >>  app_iter = self.application(environ, detect_start_response)
> Module paste.debug.prints:98 in __call__  view
> >>  environ, self.app)
> Module paste.wsgilib:539 in intercept_output  view
> >>  app_iter = application(environ, replacement_start_response)
> Module paste.recursive:80 in __call__  view
> >>  return self.application(environ, start_response)
> Module galaxy.web.framework.middleware.remoteuser:91 in __call__  view
> >>  return self.app( environ, start_response )
> Module paste.httpexceptions:632 in __call__  view
> >>  return self.application(environ, start_response)
> Module galaxy.web.framework.base:160 in __call__  view
> >>  body = method( trans, **kwargs )
> Module galaxy.web.framework:94 in decorator  view
> >>  return func( self, trans, *args, **kwargs )
> Module galaxy.webapps.galaxy.controllers.visualization:320 in list  
> view
> >>  ids = util.listify( kwargs['id'] )
> NameError: global name 'util' is not defined
> 
> 
> 
> Extra Features
> >>Display the lines of code near each part of the traceback
>   Show a debug prompt to allow you to directly debug the code at the 
> traceback
> Re-GET Page
> 
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Re: [galaxy-dev] JAVAscript error after initiating tool

[Joachim Jacob]

Hi,

In the server logs I've found:

web0.log: galaxy.webapps.galaxy.api.histories ERROR 2013-01-11 
19:56:21,071 Error in history API at showing history detail: History is 
not accessible to the current user
web1.log: galaxy.webapps.galaxy.api.histories ERROR 2013-01-11 
19:55:14,341 Error in history API at showing history detail: History is 
not accessible to the current user
web5.log: galaxy.webapps.galaxy.api.histories ERROR 2013-01-11 
20:29:11,138 Error in history API at showing history detail: History is 
not accessible to the current user


The specific situation here is that I am almost at my 100% quotum of 
storage space... Don't know if this gives some hint. The problem appear 
sporadically, not reproducibabilibity :-)



Cheers,
Joachim



Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 01/16/2013 05:33 PM, Carl Eberhard wrote:

Hi, Joachim

If you have access to your server logs, do you see any log messages 
containing 'Error in history API' around the time those happen?


Is there a situation where this happens more often (or a way to 
reliably reproduce)?


I'm unable to reproduce this locally so far.

The error definitely can be handled better on the javascript side, but 
I'd like to track down the API error as well before I change the 
javascript.


Thanks for the help,
C




On Wed, Jan 16, 2013 at 7:57 AM, Joachim Jacob > wrote:


Hi all,

For who is interested. Occasionally I get this strange Javascript
error, just after clicking 'run' on a tool.

ERROR updating hdas from api history contents:e47699a32b93ce7f

The tool gets running, but the history panel is not updated. I
click 'analyse data' to see the updated history.


Cheers,
Joachim

-- 
Joachim Jacob


Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34 
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

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Re: [galaxy-dev] upload files by cluster with pbs-python returns empty files

[Fields, Christopher J]

I saw this same problem with our upload1 set to run on the cluster (it had 
worked properly a few months prior).  I found out that the cluster sysadmins 
had set the nodes for local access only (no web access), direct file uploads 
and FTP to local disk worked but URL-based uploads did not.  

The job indicated success, however the file was empty.  Interestingly the 
'info' box had the error:

Unable to fetch 
ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Agrobacterium_tumefaciens_C58_uid57865/NC_003063.fna
[Errno ftp error] [Errno 113] No route to host

Switching it back to the local job runner fixed it.

chris

On Aug 31, 2012, at 9:27 AM, Nate Coraor  wrote:

> On Aug 31, 2012, at 8:33 AM, Geert Vandeweyer wrote:
> 
>> Hi Nate,
>> 
>> The datafile is really empty on the disk (size 0, checked at the "full path" 
>> etnry from the dataset info).
>> 
>> Best regards,
>> 
>> Geert Vandeweyer
> 
> Although it should generate an error rather than an empty file, can you 
> ensure that new_file_path in Galaxy's config is pointed at a filesystem that 
> is shared between the cluster and the Galaxy server?  If it is, you may need 
> to add some debugging to the upload tool to figure out exactly where the 
> problem is.
> 
> --nate
> 
>> 
>> 
>> 
>> On 08/29/2012 06:05 PM, Nate Coraor wrote:
>>> On Jul 16, 2012, at 6:14 AM, Geert Vandeweyer wrote:
>>> 
 Hi,
 
 We have set up a local instance of galaxy-dist, using pbs-python to 
 communicate with our HPC. Everything is working great, except for the 
 upload functionality.
 
 When I assign the upload1 to local:/// , uploading of small files through 
 the web-site works, and upload of large files by ftp works as well. When I 
 let upload1 to be handled by the default_cluster_job_runner ( = pbs:///), 
 I get empty data sets. Galaxy does not report any errors however and the 
 data state is ok.
 
 Has anybody seen this issue and solved it? Using the local:/// job handler 
 causes a massive performance hit on the galaxy process.
 
 Best regards,
 
 Geert Vandeweyer
>>> Hi Geert,
>>> 
>>> Sorry for the delayed response.  If you're still having this issue, if you 
>>> view the empty dataset, can you see the data it's supposed to contain?  
>>> i.e. does the underlying output file for the upload tool actually contain 
>>> the data, or is it really empty on disk?
>>> 
>>> --nate
>>> 
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>> 
>> 
>> -- 
>> 
>> Geert Vandeweyer, Ph.D.
>> Department of Medical Genetics
>> University of Antwerp
>> Prins Boudewijnlaan 43
>> 2650 Edegem
>> Belgium
>> Tel: +32 (0)3 275 97 56
>> E-mail: geert.vandewe...@ua.ac.be
>> http://ua.ac.be/cognitivegenetics
>> http://www.linkedin.com/pub/geert-vandeweyer/26/457/726
>> 
> 
> 
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