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September 2014
- 59 participants
- 76 discussions
Question about Terms and Conditions for public galaxy server under development
by audrey michel 29 Sep '14
by audrey michel 29 Sep '14
29 Sep '14
Hi,
We are developing a galaxy server for public usage and we would like to
know if we should use the same terms and conditions as you provide for
Galaxy main when we publicly launch our server:
https://usegalaxy.org/static/terms.html
If so, could you let us know if we can use the exact same text or if we
need to replace "The Pennsylvania State University" with our University
name?
If we can't use the text in the link above, could you provide
recommendations?
Kind Regards,
Audrey Michel
2
1
...have been committed to toolshed:
https://toolshed.g2.bx.psu.edu/view/devteam/bwa_0_7_10
and github:
https://github.com/nekrut/bwa-mem
any feedback (especially in the form of github pull requests) is
appreciated.
One of the main changes is that these tools have no helper python scripts
(all magic happens within the tool xml) and they produce BAM output.
a.
--
Anton Nekrutenko
Professor of Biochemistry
and Molecular Biology
*http://nekrut.bx.psu.edu <http://nekrut.bx.psu.edu>*
(814) 826-3051
1
0
Hi all,
In a tool that I am writting I want to pass an input parameter value
(string) into the output file's metadata. Meaning that one of the tool
parameters is a barcode signature, 'NNWTGXN' for example. I want that
attribute to be stored somehow in the output file in order to be read by a
subsequent tool without the user having to set that parameter again.
The files I'll be working with are in FASTQ, BAM and tabular format.
Is it possible?
Bests,
Nikos
3
2
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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