Run galaxy on a specific SGE queue
by Sarah Maman
Hi everyone,
Galaxy is set up on our cluster, and so far everything is working just
fine. However, we'd like to change the submission queue from the default to
a specific one.
To do so, we tryed to set on the universe_wsgi.ini file the
default_cluster_job_runner parameter as following:
default_cluster_job_runner = drmaa://-q test.q -l mem=8G -l h_vmem=10G/
When doing so, an error occured telling us the job has been rejected
because 2 queues were specified: the workq (default one) and the test.q.
Should be the queue setting this way ? What are we doing wrong ?
thanks for your help,
Sarah
--
Sarah Maman
INRA - LGC - SIGENAE
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel: +33(0)5.61.28.57.08
Fax: +33(0)5.61.28.57.53
8 years, 6 months
FW: order of menu items
by Stephanie LE GRAS
Dear all,
We have 2 different instances of Galaxy within our institute (a test and a production instance).
The thing is that the two tool menus are not in the same order and we don't understand why because we've got the same configuration files on both instance.
Test instance
[cid:1A999B49-4E2D-4B03-A0C8-0F3E7459F730]
Production instance:
[cid:31D3C34C-1FF2-4ED9-8A0D-DF73DEE548A7]
What could explain a difference in the order of the menu items?
The thing is that I would like to get the NGS tools all together.
Thank you in advance.
Stephanie
--
Stephanie Le Gras
Bioinformatics engineer
High throughput sequencing platform
IGBMC
1, rue Laurent Fries
67404 ILLKIRCH Cedex
France
Tel. : +33 (0)3 88 65 32 73
Tel. Solexa : +33 (0)3 88 65 32 97
8 years, 6 months
BWA installation
by מירב .
Hello all,
I am trying to install BWA , I used the command:
" bwa index -a bwtsw /global_data/hg18full.fa " and I got only 5 files
insted of 8
The missing files are
- rbwt
- rpac
- .rsa
I didn't recieve any error message while running.
thanks for your help
merav
8 years, 6 months
problem with current galaxy to submit job to drmaa/sge
by tin h
Hello galaxy-dev gurus,
I was trying to upgrade my galaxy server...
I removed the old galaxy-dist and ran
hg clone https://bitbucket.org/galaxy/galaxy-dist/
restored universe_wsgi.ini file and various tool-data config, and tried to
restart galaxy.
After some twiddling, I see the error message at the end of this email.
The strangest thing I see is this
/usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/wrappers.py
on my current system, drmaa-0.4b3-py2.6.egg is a file and not a
directory...
is the latest code that I just downloaded corrupted or something?
Much thanks in advance for your help in this matter.
-Tin
PS. Relevant entry in universe_wsgi.ini on cluster config:
start_job_runners = drmaa
default_cluster_job_runner = drmaa:///
galaxy.tools.genome_index DEBUG 2013-05-24 08:42:49,150 Loaded genome index
tool: __GENOME_INDEX__
galaxy.jobs.manager DEBUG 2013-05-24 08:42:49,153 Starting job handler
galaxy.jobs.runners DEBUG 2013-05-24 08:42:49,155 Starting 4 LocalRunner
workers
galaxy.jobs DEBUG 2013-05-24 08:42:49,156 Loaded job runner
'galaxy.jobs.runners.local:LocalJobRunner' as 'local'
Traceback (most recent call last):
File
"/usr/prog/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line
35, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/app.py", line 159, in
__init__
self.job_manager = manager.JobManager( self )
File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/manager.py", line 31,
in __init__
self.job_handler = handler.JobHandler( app )
File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 29,
in __init__
self.dispatcher = DefaultJobDispatcher( app )
File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/handler.py", line 543,
in __init__
self.job_runners = self.app.job_config.get_job_runner_plugins()
File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line
486, in get_job_runner_plugins
rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get(
'kwds', {} ) )
File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
line 75, in __init__
self.ds.initialize()
File
"/usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/__init__.py",
line 274, in initialize
_w.init(contactString)
File "
/usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/wrappers.py",
line 59, in init
return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer))
File
"/usr/prog/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/errors.py",
line 90, in error_check
raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value))
DrmCommunicationException: code 2: range_list containes no elements
8 years, 6 months
Re: [galaxy-dev] [galaxy-user] List of genomes
by Jennifer Jackson
Hello Yongde,
The list of genomes is gathered from many sources and is comprehensive
to facilitate external display functionality (at UCSC - main and
microbial-, Ensembl, Wormbase, etc.). When assigning a dataset in a
standard format to one of these sources, those available will appear as
links within the dataset's box.
Trackster (Galaxy's native visualization tool) is available to most
common data formats, even in the absence of an assigned database,
through the use of the Custom Reference Genome function (aka "Custom
Build"). We think this is a great advantage, in particular for cases
such as yours - since you don't have restrict yourself to external
applications that happen to host your genome. Click on the link here and
select "Trackster" to give it a test run:
The Custom Reference Genome function is also intended to be used for
smaller genomes such as this one when performing alignments and most
other jobs - no pre-indexing of the genome is necessary. Simply load the
genome in fasta format as a dataset and use it with tools, using a
"reference genome from the history". The rational is that these are
many, small, easily indexed during the course of job processing, and
provides immediate access to genomes that are either newly published, or
not widely used, or simply too numerous as a whole class for us to
practically process in full and keep current.
We have detailed help about how to use the Custom Reference Genome
method, including troubleshooting help should you need it, although in
practice you will likely find this to be fairly simple with 2-3
preparatory steps, depending on the source. Most if not all of these can
be done within Galaxy.
http://wiki.galaxyproject.org/Support#Custom_reference_genome
Hopefully this helps. If you do need more guidance, please let us know,
Best,
Jen
Galaxy team
On 4/29/13 9:01 AM, YBao wrote:
> Hi All,
>
> I was trying to map a set of data to a genome, Klebsiella pneumoniae
> subsp. Pneumoniae MGH 78578(31). While uploading the reads, I was able
> to find the reference genome as listed above. However, when I tried to
> map the data using wither bowtie or BWA, the pull down list did not
> include this genome. Can someone help or enlighten me as why it did
> not make into the list?
>
> Thanks
>
> Yongde
>
> --
> Yongde Bao
> DNA Sciences Core
> Dept. of Microbiology, Immunology,
> and Cancer Biology
> UVA
>
>
> ___________________________________________________________
> 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/
>
> To search Galaxy mailing lists use the unified search at:
>
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--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
8 years, 6 months
uploading large datasets into a new instance of Galaxy on a Mac Pro
by Elwood Linney
Hello,
I installed Galaxy on a new Mac Pro with 64gb of ram and a solid state
first drive and 3 , 2tb normal drives.
I can upload from my desktop a smaller file like a reference list or a
cuffdiff file but when I try to load a 16gb fastq file it just does not
load.
Given that I have my files on the same computer that has Galaxy, and given
that I am not well versed in unix, would anyone have a suggestion as to
ways I could easily upload these large files.
I would like to think I am just naive and that this has a simple solution.
Hopefully this is the correct list to pose this question.
Thank you for any help,
el linney
For those in the no, I did see this appear on the terminal after I tried to
upload the file through the browser mechanism for upload:
"Overflow Error: signed integer is greater than maximum"
8 years, 6 months
Storage question for Galaxy-Admins
by Raj Ayyampalayam
Hello,
I am trying to come up with a number for our local galaxy storage
requirements when we go live (This is an installation for research at
our university).
I checked out the survey that was done a while back for the
GalaxyAdmins. It seems that the bigger installations have allocated
about 200TB for their installation.
It would be of great help to me if I can get some feedback on storage
used by local galaxy installations.
If possible please use the following format:
Total capacity:
Used capacity:
Storage Technology:
Comments:
Thank you all very much.
-Raj
8 years, 6 months
"login to ftp server failed" or "Problem with ftp connexion to Galaxy"
by Danni Yu
To whom this may concern,
This is Danni Yu, a Galaxy user starting to use Galaxy since 2011. I was able to upload large files through ftp in 2011 and 2012. Now, I am facing the same problem as the other users (such as Barbara Sixt on May 27, 2013 and Fabrice Besnard on May 22, 2013). The error message is "530 login incorrect".
Ms. Jennifer Hillman-Jackson in Galaxy Support and Training team very kindly mentioned that "Please feel free to contact us for an update if this is still a problem by next Friday" on May 24, 2013.
Since it is already Friday but the problem still exists, I am hoping to learn whether a solution has been provided.
Thanks very much and Sincerely,
Danni
8 years, 6 months
