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- 10008 discussions
Hi Team,
I have a new instance of galaxy cloudman running on AWS and when I go to run some of the tools I have installed like SAM-to-BAM it requires a reference genome, but none is available. This is SAM-to-BAM version 1.1.4. This is the first tool I have found this to be an issue so far. Is there a loc file that needs modification? I will need to add several references.
Thanks,
Iry
The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
1
0
Hi,
I am developing a tool for STAR (https://code.google.com/p/rna-star/) and I realize I may be reinventing another wheel. Has anyone else created a tool for STAR? There's nothing else in the toolsheds for it yet.
David
--------------------
David Hoover, PhD
Helix Systems Staff
SCB/DCSS/CIT/NIH
301-435-2986
http://helix.nih.gov
5
11
On a local instance of Galaxy, I get this error when attempting to
reset my password:
Failed to reset password: (501, '5.1.7 Bad sender address syntax',
'galaxy-no-reply(a)10.32.16.121')
I am told my mail server requires the from address to either have a
domain name, or the IP address to be in brackets (e.g.,
[10.32.16.121]). Is there an option to configure the from address
format, or override the address?
If there are no configuration options, what files would I need to
modify to add brackets? The domain name is not an option.
Cheers,
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
evan(a)msi.umn.edu
boll0107(a)umn.edu
2
1
When I run a workflow and multiple steps fail, does Galaxy have the
option to send a digest of all problems, or does each failed step
result in another email? Or maybe only the first failed task results
in an email alert?
I'm trying not to get spammed when a workflow fails.
Cheers,
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
evan(a)msi.umn.edu
boll0107(a)umn.edu
2
1
Is there an API endpoint for sending the error report for a failed
step in a history? I would like to run a workflow via API and email
the first error that occurs.
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
evan(a)msi.umn.edu
boll0107(a)umn.edu
2
1
Hi,
I have configured a new galaxy-project site with SLURM (version 14). I have one server with a Galaxy-Project instance, one node with SLURM server and two SLURM worker nodes. I have compile SLURM-DRMAA from source codes. When I run “drmaa-run /bin/hostname” it’s work. But, when I try to run the server I got the next error:
Traceback (most recent call last):
File "/home/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 39, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "/home/galaxy-dist/lib/galaxy/app.py", line 141, in __init__
self.job_manager = manager.JobManager( self )
File "/home/galaxy-dist/lib/galaxy/jobs/manager.py", line 23, in __init__
self.job_handler = handler.JobHandler( app )
File "/home/galaxy-dist/lib/galaxy/jobs/handler.py", line 32, in __init__
self.dispatcher = DefaultJobDispatcher( app )
File "/home/galaxy-dist/lib/galaxy/jobs/handler.py", line 704, in __init__
self.job_runners = self.app.job_config.get_job_runner_plugins( self.app.config.server_name )
File "/home/galaxy-dist/lib/galaxy/jobs/__init__.py", line 621, in get_job_runner_plugins
rval[id] = runner_class( self.app, runner[ 'workers' ], **runner.get( 'kwds', {} ) )
File "/home/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 81, in __init__
self.ds.initialize()
File "/home/galaxy-dist/eggs/drmaa-0.7.6-py2.6.egg/drmaa/session.py", line 257, in initialize
py_drmaa_init(contactString)
File "/home/galaxy-dist/eggs/drmaa-0.7.6-py2.6.egg/drmaa/wrappers.py", line 73, in py_drmaa_init
return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer))
File "/home/galaxy-dist/eggs/drmaa-0.7.6-py2.6.egg/drmaa/errors.py", line 151, in error_check
raise _ERRORS[code - 1](error_string)
AlreadyActiveSessionException: code 11: DRMAA session already exist.
[root@galaxy-project galaxy-dist]#
This is my “job_conf.xml”:
<job_conf>
<plugins workers="4">
<plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
<plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
<plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" />
<plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner">
<param id="drmaa_library_path">/usr/local/lib/libdrmaa.so</param>
</plugin>
</plugins>
<handlers>
<handler id="main"/>
</handlers>
<destinations default="drmaa_slurm">
<destination id="local" runner="local"/>
<destination id="multicore_local" runner="local">
<param id="local_slots">4</param>
<param id="embed_metadata_in_job">True</param>
<job_metrics />
</destination>
<destination id="docker_local" runner="local">
<param id="docker_enabled">true</param>
</destination>
<destination id="drmaa_slurm" runner="drmaa">
<param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param>
<param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param>
<param id="galaxy_external_chown_script">scripts/external_chown_script.py</param>
</destination>
<destination id="direct_slurm" runner="slurm">
<param id="nativeSpecification">--time=00:01:00</param>
</destination>
</destinations>
<resources default="default">
<group id="default"></group>
<group id="memoryonly">memory</group>
<group id="all">processors,memory,time,project</group>
</resources>
<tools>
<tool id="foo" handler="trackster_handler">
<param id="source">trackster</param>
</tool>
<tool id="bar" destination="dynamic"/>
<tool id="longbar" destination="dynamic" resources="all" />
<tool id="baz" handler="special_handlers" destination="bigmem"/>
</tools>
<limits>
<limit type="registered_user_concurrent_jobs">2</limit>
<limit type="anonymous_user_concurrent_jobs">1</limit>
<limit type="destination_user_concurrent_jobs" id="local">1</limit>
<limit type="destination_user_concurrent_jobs" tag="mycluster">2</limit>
<limit type="destination_user_concurrent_jobs" tag="longjobs">1</limit>
<limit type="destination_total_concurrent_jobs" id="local">16</limit>
<limit type="destination_total_concurrent_jobs" tag="longjobs">100</limit>
<limit type="walltime">24:00:00</limit>
<limit type="output_size">10GB</limit>
</limits>
</job_conf>
Can you help me? I am newbie with “Galaxy Project” administration.
THANKS IN ADVANCE!!!!
Alfonso Pardo Diaz
System Administrator / Researcher
c/ Sola nº 1; 10200 Trujillo, ESPAÑA
Tel: +34 927 65 93 17 Fax: +34 927 32 32 37
[CETA-Ciemat logo]<http://www.ceta-ciemat.es/>
----------------------------
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----------------------------
1
1
Hi,
I am attempting to upload 94 .vcf files (only about 20 kb each).
However, the Files have been gray (file waiting to run) for a few
hours.
Then, I received the following message: An error occurred while
getting updates from the server. Please contact a Galaxy administrator
if problem persists. With a link "details" that included the message
below.
Thank you for any information that you may be able to offer. I am
using the "main" usegalaxy.org
Best,
Katie Collins
User name: Khofer
E-mail : khofer(a)buffalo.edu
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2
1
We are having issues with using Galaxy in Internet Explorer 11 (these work fine in Chrome & Firefox).
1. The jobs queued and history doesn't display unless you refresh the browser window. Clicking the history reload icon doesn't work.
2. If I click to edit something in the history, the tabs aren't clickable. Attributes are displayed but I can't click on Convert Format, Datatype, or Permissions.
Anyone else having this problem? I apologize if this information is documented somewhere but I was unable to find it.
Thank you for your assistance,
Dori
**********************************
Dori Sajdak
Senior Systems Administrator
State University of NY at Buffalo
Center for Computational Research
701 Ellicott St
Buffalo, NY 14203
Phone: (716) 881-8934
Fax: (716) 849-6656
Web: http://ccr.buffalo.edu
**********************************
5
10
24 Sep '14
Hi all,
I'm not sure how do this post-action act . I've been make some test
and it's very confused for me.
First, can this post-action be used on output which are used on other
steps of the workflow ? if yes, I suppose that galaxy wait for end of
use of this output before deleting.
Second, must I higlight the snowfalke of this output to permit its
deletion or must I keep the snowflake in grey ?
I post this question in galaxy-dev because I've added this
post-action on several outputs in my workflow and it has had no effect
on my outputs. And when I open the .ga file which describe my
workflow, I've seen just one of this post-action in one output.
Thanks.
Julie
2
6
Hi all,
I have notice that the run.sh script is creating automatically all missing configuration and location files to make sure Galaxy can work properly at first launch. However, the script is not taking care of the actual settings of an existing universe_wsgi.ini file. As a result, if the universe_wsgi.ini file says that job_conf.xml is located at foo/bar location, the run.sh will create a job_conf.xml file at the root of the galaxy source code anyway.
I'm thinking of improving the run.sh behavior to respect file path declared in an existing universe_wsgi.ini file in order not to create unused config or location files. I have currently started to implement this behavior in a small Python script (more handy than pure sh).
What do you think about this concern ? Should I go for a pull request at any point ?
Regards,
--
Julien
@julozi
2
3