jquery / js / python programming for galaxy / bugs, ideally for AWS ec2
by carl crott
Good morning all,
So I'm looking to contribute I'm really interested in the power that amazon
integration can bring to these tools and I'm wondering if anyone happens to
know of bugs offhand or programming which specifically deals with AWS / EC2.
If anyone happens to know of simple things offhand feel free to shout at me!
-Carl
--
Carl Crott
Web Applications Engineer
www.black-glass.com
412-610-0600
11 years, 1 month
Can not clean my galaxy datasets
by Jennifer Jackson
On 12/19/11 6:15 AM, liram_vardi(a)agilent.com wrote:
> Hi Jennifer,
>
> Thank you again for the quick reply in my last issue.
>
> I have another Galaxy problem and I hope you will be able to assist.
> Because I am developing my Galaxy server while there are members in my group that are using this Galaxy instance in parallel,
> I am trying to create another Galaxy process (instance), which will be used only for testing...
>
> Therefore, I created a copy of Galaxy directory in other location (let say: /galaxy-dist_test)
> And changed the listening port in "universe_wsgi.ini" to another port (8081).
> Then, I tried to run both of Galaxy instances in parallel.
> (One is listening on port 8080 and the other is on 8081)
>
> The problem is occurred when I send a job for a run in one of the instance (let say: the one that run on 8080),
> Then, It cause to the another Instance (the one on port 8081) to collapse (And the history is disappeared...)
>
> What is the problem?
> How can I solve it?
> How can I create two different and self-contained galaxy servers on the same computer?
>
> I tried also to use the instructions :
> http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Sc...
> But it was not helpful to my problem...
>
> Thank you a lot!
> Liram
>
> -----Original Message-----
> From: Jennifer Jackson [mailto:jen@bx.psu.edu]
> Sent: Tuesday, November 29, 2011 4:42 PM
> To: VARDI,LIRAM (A-Labs,ex1)
> Cc: galaxy-dev(a)bx.psu.edu
> Subject: Re: [galaxy-dev] Can not clean my galaxy datasets
>
> Hello Liram,
>
> Perhaps the allow_user_dataset_purge option has not been set to True in universe_wsgi.ini?
>
> Please see this wiki for details:
> http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas
>
> Hopefully this helps, but please let us know if you need more assistance,
>
> Best,
>
> Jen
> Galaxy team
>
> On 11/29/11 5:44 AM, liram_vardi(a)agilent.com wrote:
>> Hello,
>>
>> My name is Liram Vardi and I'm using local Galaxy instance.
>>
>> Anyway, I can't clean my deleted datasets from my own locally disk.
>>
>> When I am trying to delete dataset, as was explained in
>> http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions,
>>
>> First, I used the "delete 'X' icon" near the dataset to delete the
>> dataset,
>>
>> Then, when I go to "Options -> Show Deleted Datasets", I can see my
>> "deleted dataset" on the list
>>
>> with the note: /"This dataset has been deleted. Click _here_ to
>> undelete it"//*but I don't get the also the option "or _here_ to
>> immediately remove it from disk."*/.
>>
>> Also, when I use the option "Options -> Purge Deleted Datasets", I'm
>> getting a message "0 datasets have been deleted permanently" and
>>
>> my deleted dataset still stays in the "Options -> Show Deleted Datasets"
>> menu list.
>>
>> I also tried to clear the history, but when I'm doing that, the "using
>> X Mb" tab on the upper right corner is still not reset.
>>
>> What is the problem?
>>
>> Thanks a lot for your help!
>>
>> Liram
>>
>>
>>
>> ___________________________________________________________
>> 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/
>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/wiki/Support
>
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
11 years, 1 month
Exiting a java application without errors
by graham etherington (TSL)
Hi,
I've created a java app tested it from the command line and put it in the
shared/jars folder. It runs for a while and then the history item turns
red. If I view the dataset output though, everything is as should be, i.e.
the expected output from the tool is seen.
If I click on the view error 'bug' this is what I see:
"Tool execution generated the following error message:
21-Dec-2011 17:08:14
org.biojava3.genome.parsers.gff.GFF3Reader read
INFO: Gff.read(): Reading
/home/galaxy/software/galaxy-central/database/files/012/dataset_12450.dat"
This is the output from org.biojava3.genome.parsers.gff and I have no way
of switching that off.
Can anyone suggest a way to handle this output so that it doesn't throw an
error. I need the output from this tool to use as input to other tools.
Many thanks,
Graham
Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601
11 years, 1 month
Re: [galaxy-dev] Itinerary for 10/24 UVa visit
by Greg Von Kuster
The tool shed does not handle displaying images included in tool configs like this, nor does it properly link to other files that within the tool's subdirectory hierarchy to which the tool config may point. This is because the files are contained within an hg repository's internal .i files, and the process of deciphering the relative pointer, opening and reading the file and displaying it correctly is non-trivial.
The tool shed displays most of the tool though, so the user looking at it is provided an overall general sense of what the tool does. Those developing tools that plan to host them on the tool shed should develop them as usual, not making decisions for the tool page based on what will or will not be correctly displayed in the tool shed.
At some point I may make some improvements in this area, but it is nowhere on my development plans at the current time.
On Dec 21, 2011, at 8:29 PM, James Taylor wrote:
> Hrmmmmm... Don't know if we have a solution in the Toolshed for this yet. Greg, thoughts? Thanks!
>
> -- jt
>
> (composed on my phone)
>
> On Dec 21, 2011, at 5:56 PM, Aaron Quinlan <aaronquinlan(a)gmail.com> wrote:
>
>> Okay, last question for the day. For some of the more complicated tools, I'd like to include a little PNG image as an example. I noticed that the gops XML files use references like:
>>
>> .. image:: ./static/operation_icons/gops_complement.gif
>>
>> However, I imagine you want something slightly different for Tool Shed tools. I couldn't find any docs on this - how should I setup my repository directory structure for using icons in the XML files?
>>
>> Sorry to bother...
>> arq
>>
>> On Dec 21, 2011, at 1:37 PM, James Taylor wrote:
>>
>>> Excellent!
>>>
>>> On Dec 21, 2011, at 1:31 PM, Aaron Quinlan wrote:
>>>
>>>> Works like a charm. Hoping to have a few tools up on the "shed" by the New Year. Speaking of, have a good one.
>>>>
>>>>
>>>> On Dec 21, 2011, at 12:58 PM, James Taylor wrote:
>>>>
>>>>> Aaron, right now Galaxy instances don't come with all the len files in the distribution, there is a cron script to generate them from UCSC tables.
>>>>>
>>>>> Frankly, that is gross, I'm thinking we should do that once ourselves, keep it version controlled, and let people rsync it down.
>>>>>
>>>>> But in the meantime, drop hg19.len in tool-data/shared/ucsc/chrom and you should be good to go.
>>>>>
>>>>> On Dec 21, 2011, at 12:51 PM, Aaron Quinlan wrote:
>>>>>
>>>>>> Hey James,
>>>>>>
>>>>>> I am putting the finishing touches on a first small release of bedtools on the tool shed. However, I am facing one likely trivial problem. GenomeCoverageBed, when accepting BED input, needs to know the chromosome sizes in order to do its work. On the command line, this done by passing it a chromSizes file as a -g option. However, I believe Galaxy can be told which genome one is dealing with for a given file. In turn, I imagine I can automatically point the tool to the correct chromSizes file without having the user explicitly say which file to use.
>>>>>>
>>>>>> I guessed that this is what complement.xml was doing with the -l ${chromInfo} $allchroms call.
>>>>>>
>>>>>> However, I can't get this to work. When I added ${chromInfo} as the -g option for genomeCoverageBed, it complained that it couldn't find hg19.len.
>>>>>>
>>>>>> Can you point me to a link for how to do this? I imagine I am missing something obvious.
>>>>>>
>>>>>> Best,
>>>>>> Aaron
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Dec 1, 2011, at 10:46 AM, James Taylor wrote:
>>>>>>
>>>>>>> On Nov 30, 2011, at 8:18 PM, Aaron Quinlan wrote:
>>>>>>>
>>>>>>>> So, I plan to just release XML configs and assume the user has installed the correct version until the fabric script support is present.
>>>>>>>
>>>>>>> This is definitely the way to go.
>>>>>>>
>>>>>>>> It'll happen. I hope things are going well.
>>>>>>>
>>>>>>> Okay, but do let me know if I can help.
>>>>>>>
>>>>>>> -- jt
>>>>>>>
>>>>>>> James Taylor, Assistant Professor, Biology / Computer Science, Emory University
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>
>
Greg Von Kuster
Galaxy Development Team
greg(a)bx.psu.edu
11 years, 1 month
Search the Galaxy!
by Dave Clements
Hello all,
I am happy to announce that Galaxy now has several Google Custom Searches
that make it much easier (really - way, way easier) to find answers to your
questions about Galaxy. They are available at
http://galaxyproject.org/search/.
*Name & URL *
* Description *
**
*Galaxy Web Search <http://galaxyproject.org/search/web>*
http://galaxyproject.org/search/web
Searches *everything:* Galaxy Main <http://wiki.g2.bx.psu.edu/Main>,
the mailing
list archives <http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>, the Galaxy
wiki <http://wiki.g2.bx.psu.edu/FrontPage>, Galaxy's source code at
Bitbucket <https://bitbucket.org/galaxy/galaxy-central/src/tip/>, and the Tool
Shed <http://wiki.g2.bx.psu.edu/Tool%20Shed>. The results are returned in a
unified list, and are also grouped into several categories.
*Galaxy Mailing List Search <http://galaxyproject.org/search/mailinglists>*
http://galaxyproject.org/search/mailinglists
Searches all the Galaxy mailing list
archives<http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>.
The results are returned in a unified list, and are also grouped by mailing
list.**
*UseGalaxy Search <http://galaxyproject.org/search/usegalaxy>*
http://galaxyproject.org/search/usegalaxy
Search for information about *using* Galaxy. Searches Galaxy
Main<http://wiki.g2.bx.psu.edu/Main>(
UseGalaxy.org <http://usegalaxy.org/>), the
wiki<http://wiki.g2.bx.psu.edu/Learn>(excluding the
Admin <http://wiki.g2.bx.psu.edu/Admin> pages), and the Galaxy-User and
Galaxy-Announce mailing list
archives<http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>.
*GetGalaxy Search <http://galaxyproject.org/search/getgalaxy>*
http://galaxyproject.org/search/getgalaxy
Search for information about installing, customizing, and developing
Galaxy. Searches the Galaxy Bitbucket (source)
site<https://bitbucket.org/galaxy/galaxy-central/src/tip/>,
the Tool Shed <http://toolshed.g2.bx.psu.edu/>, the
wiki<http://wiki.g2.bx.psu.edu/Admin>(excluding the
Learn <http://wiki.g2.bx.psu.edu/Learn> pages), and the Galaxy-Dev and
Galaxy-Announce mailing list
archives<http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>.
We strongly encourage you to give these try. Please send feedback and
suggestions to Galaxy Outreach <outreach(a)galaxyproject.org>.
Happy searching (and a Happy New Year!),
Dave Clements
--
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://galaxyproject.org/wiki/
11 years, 1 month
embedded code into Pages
by remy d1
Hi,
I would like to modify Pages a lot. For example, I would like to create a
galaxy Page with rss-reader written in PHP (or javascript) in it.
I found where content is stored for Pages, but not the script who read this
content.
Is there any possibility to integrate code into Galaxy Page which could be
executed ?
Thanks,
Regards.
11 years, 1 month
Re: [galaxy-dev] problems previewing certain files, downloading files and with login
by Alfonso Núñez Salgado
Hi,
I have found an old thread where Matthew Conte talks about problems
previewing certain files, downloading them.
Matthew Conte wrote:
I'm having several problems with my local galaxy install which may or
may not be related to one another.,,The first problem I'm having is with
the "Display data in browser" feature. Some files type formats
(fastqsanger, fasta) display fine. However, other file type formats
(png, svg, txt) simply do not display at all. I have debugging turned
on, but do not see any error within the browser or within the galaxy log
or web server log after clicking the "Display data in browser" eyeball
icon. It is simply a blank middle panel. I'm having several problems
with my local galaxy install which may or may not be related to one
another.,,The first problem I'm having is with the "Display data in
browser" feature. Some files type formats (fastqsanger, fasta) display
fine. However, other file type formats (png, svg, txt) simply do not
display at all. I have debugging turned on, but do not see any error
within the browser or within the galaxy log or web server log after
clicking the "Display data in browser" eyeball icon. It is simply a
blank middle panel.
http://gmod.827538.n3.nabble.com/problems-previewing-certain-files-downlo...
In my case all this happen without a proxy, (so) and I can login in
correctly but I still having problem previewing and downloading files.
hg summary
parent: 6298:b258de1e6cea tip
branch: default
11 years, 1 month
Post...
by Saadeh, Heba
Hello,
I would like to be added, in order to be able to post some comments...
Regards,
heba
---
Heba Saadeh
Ph.D. Student
Dept. of Medical and Molecular Genetics,
Medicine School,
King's College London,
Guy's Hospital, 8th floor Tower Wing,
London, SE1 9RT.
Office: +44(0)20 7188 3715
11 years, 1 month
Fwd: Galaxy issues
by David Matthews
Hi Guys,
Sorry to be a pain but this seems to be getting worse for us. Here are the latest tracebacks - any suggestions would be gratefully received!!
Cheers
David
> galaxy.jobs.runners.pbs ERROR 2011-12-13 19:57:57,689 Uncaught exception checking jobs
> Traceback (most recent call last):
> File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 338, in monitor
> self.check_watched_items()
> File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 351, in check_watched_items
> ( failures, statuses ) = self.check_all_jobs()
> File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 462, in check_all_jobs
> statuses.update( self.convert_statjob_to_bunches( jobs ) )
> File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", line 476, in convert_statjob_to_bunches
> statuses[ job.name ] = Bunch( **status )
> MemoryError
> Unhandled exception in thread started by
> Traceback (most recent call last):
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/threading.py", line 504, in __bootstrap
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/threading.py", line 580, in __bootstrap_inner
> MemoryError
> Unhandled exception in thread started by <bound method Thread.__bootstrap of <Thread(Thread-11, stopped 1111390528)>>
> Traceback (most recent call last):
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/threading.py", line 504, in __bootstrap
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/threading.py", line 545, in __bootstrap_inner
> MemoryError
> Unexpected exception in worker <function <lambda> at 0x883acf8>
> Traceback (most recent call last):
> File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 863, in worker_thread_callback
> File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1037, in <lambda>
> File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1056, in process_request_in_thread
> File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1044, in handle_error
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/SocketServer.py", line 334, in handle_error
> MemoryError
> Unhandled exception in thread started by <bound method Thread.__bootstrap of <Thread(Thread-10, stopped 1109289280)>>
> Traceback (most recent call last):
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/threading.py", line 504, in __bootstrap
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/threading.py", line 545, in __bootstrap_inner
> MemoryError
> ----------------------------------------
> Exception happened during processing of request from ('xxx.xxx.xxx.xxx', 44389)
> Traceback (most recent call last):
> File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/SocketServer.py", line 322, in finish_request
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/SocketServer.py", line 616, in __init__
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/SocketServer.py", line 657, in setup
> MemoryError
> ----------------------------------------
> ----------------------------------------
> Exception happened during processing of request from ('xxx.xxx.xx.xx', 60069)
> Unexpected exception in worker <function <lambda> at 0x883a2a8>Traceback (most recent call last):
>
> File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread
> Unhandled exception in thread started by <bound method Thread.__bootstrap of <Thread(worker 9, stopped 1130301760)>>
> Traceback (most recent call last):
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/threading.py", line 504, in __bootstrap
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/threading.py", line 545, in __bootstrap_inner
> MemoryError File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/SocketServer.py", line 322, in finish_request
>
> Unexpected exception in worker <function <lambda> at 0x8721410>
> Traceback (most recent call last):
> File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 863, in worker_thread_callback
> Unhandled exception in thread started by <bound method Thread.__bootstrap of <Thread(worker 0, stopped 1086265664)>>
> Traceback (most recent call last):
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/threading.py", line 504, in __bootstrap
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/threading.py", line 545, in __bootstrap_inner
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/traceback.py", line 242, in format_exc
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/traceback.py", line 142, in format_exception
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/traceback.py", line 76, in format_tb
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/traceback.py", line 101, in extract_tb
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/linecache.py", line 14, in getline
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/linecache.py", line 40, in getlines
> MemoryError
> ----------------------------------------
> Exception happened during processing of request from ('xxx.xxx.xx.xx', 60071)
> Traceback (most recent call last):
> File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread
> Unexpected exception in worker <function <lambda> at 0x8721410>
> Traceback (most recent call last):
> File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 863, in worker_thread_callback
> Unhandled exception in thread started by <bound method Thread.__bootstrap of <Thread(worker 6, stopped 1123998016)>>
> Traceback (most recent call last):
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/threading.py", line 504, in __bootstrap
> self.__bootstrap_inner()
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/threading.py", line 545, in __bootstrap_inner
> (self.name, _format_exc()))
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/traceback.py", line 242, in format_exc
> return ''.join(format_exception(etype, value, tb, limit))
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/traceback.py", line 142, in format_exception
> list = list + format_tb(tb, limit)
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/traceback.py", line 76, in format_tb
> return format_list(extract_tb(tb, limit))
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/traceback.py", line 101, in extract_tb
> line = linecache.getline(filename, lineno, f.f_globals)
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/linecache.py", line 14, in getline
> lines = getlines(filename, module_globals)
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/linecache.py", line 40, in getlines
> return updatecache(filename, module_globals)
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/linecache.py", line 131, in updatecache
> lines = fp.readlines()
> MemoryError
> ----------------------------------------
> Exception happened during processing of request from ('xxx.xxx.xxx.xxx', 44416)
> Traceback (most recent call last):
> File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread
> Unexpected exception in worker <function <lambda> at 0x8721410>
> Traceback (most recent call last):
> File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 863, in worker_thread_callback
> Unhandled exception in thread started by <bound method Thread.__bootstrap of <Thread(worker 7, stopped 1126099264)>>
> Traceback (most recent call last):
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/threading.py", line 504, in __bootstrap
> self.__bootstrap_inner()
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/threading.py", line 545, in __bootstrap_inner
> (self.name, _format_exc()))
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/traceback.py", line 242, in format_exc
> return ''.join(format_exception(etype, value, tb, limit))
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/traceback.py", line 142, in format_exception
> list = list + format_tb(tb, limit)
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/traceback.py", line 76, in format_tb
> return format_list(extract_tb(tb, limit))
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/traceback.py", line 101, in extract_tb
> line = linecache.getline(filename, lineno, f.f_globals)
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/linecache.py", line 14, in getline
> lines = getlines(filename, module_globals)
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/linecache.py", line 40, in getlines
> return updatecache(filename, module_globals)
> File "/gpfs/cluster/isys/galaxy/Galaxy/lib/python2.6/linecache.py", line 131, in updatecache
> lines = fp.readlines()
> MemoryError
> ----------------------------------------
>
> --
> -----------------------------------------------------------
> Callum Wright
> HPC Systems Administrator
> High Performance Computing
> University of Bristol
>
> Phone: 0117 331 4429
> email: c.wright(a)bristol.ac.uk
> web: www.acrc.bristol.ac.uk
> -----------------------------------------------------------
>
11 years, 1 month
[query] contribute a data library for standard inclusion in the public Galaxy?
by William Ray
My apologies for the noise - I'm just trying to figure out who to talk to here:
A colleague and I are developing a dataset that we believe will be of significant interest to the psychiatric genetics field. We believe that one of the biggest obstacles currently facing the field is the lack of a centralized, standardized repository for this data. We therefore would like, if possible, to make the data available through Galaxy as a standard library (we believe that the psychiatric genetics field, in particular, is more likely to respond positively to, and utilize, a standard universal component, rather than a private/shared component).
Is there someone we could talk to about this idea, and the required logistics to make it happen?
Many thanks for your time,
William Ray
Chris Bartlett
Nationwide Children's Hospital
The Ohio State University Biophysics Program
11 years, 1 month
