Groovy tool for galaxy
by Anshul Tak
Hi,
I have a question regarding galaxy. Can I execute groovy scipts using
galaxy? I installed groovy in galaxy docker image and all the dependencies.
However, when I try to execute a tool which require groovy engine it
says "/export/galaxy-central/database/job_working_directory/000/2/tool_script.sh:
line 9: groovy: command not found"
So I understood the error that galaxy is not able to find groovy but
ideally it should take the groovy engine as it is installed.
Can you give me some pointers to solve this issue?
--
With Regards,
Anshul Tak
2 years, 2 months
Pulsar - running as real DRMAA user problems
by Poole, Richard
Hey John,
So I’ve been happily using Pulsar to send all my Galaxy server jobs to our cluster here at UCL for several months now (I love it!). I am now exploring the ‘run-as-real-user’ option for DRMAA submissions and have run into a problem. The files are correctly staged, correctly chowned, successfully submitted to the queue and the job runs. However, at job end (collection?) fails with the following error message in Pulsar:
Exception happened during processing of request from (‘*.*.*.*', 54321)
Traceback (most recent call last):
File "/opt/rocks/lib/python2.6/site-packages/Paste-2.0.1-py2.6.egg/paste/httpserver.py", line 1072, in process_request_in_thread
self.finish_request(request, client_address)
File "/opt/rocks/lib/python2.6/SocketServer.py", line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/opt/rocks/lib/python2.6/SocketServer.py", line 617, in __init__
self.handle()
File "/opt/rocks/lib/python2.6/site-packages/Paste-2.0.1-py2.6.egg/paste/httpserver.py", line 446, in handle
BaseHTTPRequestHandler.handle(self)
File "/opt/rocks/lib/python2.6/BaseHTTPServer.py", line 329, in handle
self.handle_one_request()
File "/opt/rocks/lib/python2.6/site-packages/Paste-2.0.1-py2.6.egg/paste/httpserver.py", line 441, in handle_one_request
self.wsgi_execute()
File "/opt/rocks/lib/python2.6/site-packages/Paste-2.0.1-py2.6.egg/paste/httpserver.py", line 291, in wsgi_execute
self.wsgi_start_response)
File "/cluster/galaxy/pulsar/pulsar/web/framework.py", line 39, in __call__
return controller(environ, start_response, **request_args)
File "/cluster/galaxy/pulsar/pulsar/web/framework.py", line 144, in controller_replacement
result = self.__execute_request(func, args, req, environ)
File "/cluster/galaxy/pulsar/pulsar/web/framework.py", line 124, in __execute_request
result = func(**args)
File "/cluster/galaxy/pulsar/pulsar/web/routes.py", line 82, in status
return status_dict(manager, job_id)
File "/cluster/galaxy/pulsar/pulsar/manager_endpoint_util.py", line 12, in status_dict
job_status = manager.get_status(job_id)
File "/cluster/galaxy/pulsar/pulsar/managers/stateful.py", line 95, in get_status
proxy_status, state_change = self.__proxy_status(job_directory, job_id)
File "/cluster/galaxy/pulsar/pulsar/managers/stateful.py", line 115, in __proxy_status
proxy_status = self._proxied_manager.get_status(job_id)
File "/cluster/galaxy/pulsar/pulsar/managers/queued_external_drmaa_original.py", line 62, in get_status
external_status = super(ExternalDrmaaQueueManager, self)._get_status_external(external_id)
File "/cluster/galaxy/pulsar/pulsar/managers/base/base_drmaa.py", line 31, in _get_status_external
drmaa_state = self.drmaa_session.job_status(external_id)
File "/cluster/galaxy/pulsar/pulsar/managers/util/drmaa/__init__.py", line 50, in job_status
return self.session.jobStatus(str(external_job_id))
File "build/bdist.linux-x86_64/egg/drmaa/session.py", line 518, in jobStatus
c(drmaa_job_ps, jobId, byref(status))
File "build/bdist.linux-x86_64/egg/drmaa/helpers.py", line 299, in c
return f(*(args + (error_buffer, sizeof(error_buffer))))
File "build/bdist.linux-x86_64/egg/drmaa/errors.py", line 151, in error_check
raise _ERRORS[code - 1](error_string)
InvalidJobException: code 18: The job specified by the 'jobid' does not exist.
With this corresponding error from my Galaxy server:
galaxy.tools.actions INFO 2016-10-13 18:47:51,851 Handled output (279.421 ms)
galaxy.tools.actions INFO 2016-10-13 18:47:52,093 Verified access to datasets (5.271 ms)
galaxy.tools.execute DEBUG 2016-10-13 18:47:52,118 Tool [toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4] created job [25008<http://toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.4]%...>] (560.404 ms)
galaxy.jobs DEBUG 2016-10-13 18:47:52,579 (25008) Working directory for job is: /Users/galaxy/galaxy-dist/database/job_working_directory/025/25008
galaxy.jobs.handler DEBUG 2016-10-13 18:47:52,591 (25008) Dispatching to pulsar runner
galaxy.jobs DEBUG 2016-10-13 18:47:52,677 (25008) Persisting job destination (destination id: hpc_low)
galaxy.jobs.runners DEBUG 2016-10-13 18:47:52,681 Job [25008] queued (90.231 ms)
galaxy.jobs.handler INFO 2016-10-13 18:47:52,699 (25008) Job dispatched
galaxy.tools.deps DEBUG 2016-10-13 18:47:53,138 Building dependency shell command for dependency 'samtools'
galaxy.jobs.runners.pulsar INFO 2016-10-13 18:47:53,233 Pulsar job submitted with job_id 25008
galaxy.jobs DEBUG 2016-10-13 18:47:53,257 (25008) Persisting job destination (destination id: hpc_low)
galaxy.datatypes.metadata DEBUG 2016-10-13 18:51:03,922 Cleaning up external metadata files
galaxy.jobs.runners.pulsar ERROR 2016-10-13 18:51:03,945 failure finishing job 25008
Traceback (most recent call last):
File "/Users/galaxy/galaxy-dist/lib/galaxy/jobs/runners/pulsar.py", line 386, in finish_job
run_results = client.full_status()
File "/Users/galaxy/galaxy-dist/lib/pulsar/client/client.py", line 132, in full_status
return self.raw_check_complete()
File "/Users/galaxy/galaxy-dist/lib/pulsar/client/decorators.py", line 28, in replacement
return func(*args, **kwargs)
File "/Users/galaxy/galaxy-dist/lib/pulsar/client/decorators.py", line 13, in replacement
response = func(*args, **kwargs)
File "/Users/galaxy/galaxy-dist/lib/pulsar/client/client.py", line 146, in raw_check_complete
check_complete_response = self._raw_execute("status", {"job_id": self.job_id})
File "/Users/galaxy/galaxy-dist/lib/pulsar/client/client.py", line 215, in _raw_execute
return self.job_manager_interface.execute(command, args, data, input_path, output_path)
File "/Users/galaxy/galaxy-dist/lib/pulsar/client/interface.py", line 96, in execute
response = self.transport.execute(url, method=method, data=data, input_path=input_path, output_path=output_path)
File "/Users/galaxy/galaxy-dist/lib/pulsar/client/transport/standard.py", line 34, in execute
response = self._url_open(request, data)
File "/Users/galaxy/galaxy-dist/lib/pulsar/client/transport/standard.py", line 20, in _url_open
return urlopen(request, data)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 154, in urlopen
return opener.open(url, data, timeout)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 437, in open
response = meth(req, response)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 550, in http_response
'http', request, response, code, msg, hdrs)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 475, in error
return self._call_chain(*args)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 409, in _call_chain
result = func(*args)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/urllib2.py", line 558, in http_error_default
raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 500: Internal Server Error
I am running 15.10 and Python 2.7.10 on my iMac for the server and the cluster submission node is running Pulsar 0.5.0 and Python 2.7.12
For these tests I run Pulsar in an interactive window so I have not set the sudoers file up, but rather enter sudo password when requested by Pulsar (at the first step of chowning the staging directory). Also have rewrites set up in Galaxy’s pulsar_actions.yml and I am using remote_scp for the file transfers rather than http - although I have also tried switching back to http (as I noticed caching, which I am also testing, does not work with scp transfers) but get an identical set of error messages.
As I say, I have no troubles using a regular queued_drmaa manager in pulsar. Any ideas what the problem may be?
Cheers,
Rich
Richard J Poole PhD
Wellcome Trust Fellow
Department of Cell and Developmental Biology
University College London
518 Rockefeller
21 University Street, London WC1E 6DE
Office (518 Rockefeller): +44 20 7679 6577 (int. 46577)
Lab (529 Rockefeller): +44 20 7679 6133 (int. 46133)
https://www.ucl.ac.uk/cdb/academics/poole
2 years, 6 months
Running jobs as real user and extra_file_path
by Louise-Amélie Schmitt
Hi everyone,
I just wanted to ask how the extra_file_path is handled in case of job
running as the real user since the file_path is only writable by the
galaxy user. Any clue?
Thanks,
L-A
2 years, 6 months
Testing updated NCBI BLAST+ wrappers for version 2.5.0
by Peter Cock
Hello all,
I have updated the NCBI BLAST+ wrappers on the Test Tool Shed,
the wrapper is now at v0.2.00:
https://testtoolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus/
The main changes is this now depends on BLAST+ 2.5.0, and that is
available via either BioConda or the Tool Shed:
https://toolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_5_0/
https://testtoolshed.g2.bx.psu.edu/view/iuc/package_blast_plus_2_5_0/
In order for the dependency to work smoothly on both BioConda
and the Tool Shed system, we have changed the package name
from "blast+" to just "blast". Given the NCBI stopped updated the
original "legacy" BLAST some time ago, when combined with the
version number this is no longer ambiguous.
Jumping from using BLAST+ 2.2.31 to using BLAST+ 2.5.0
required updating lots of the test files for NCBI changes, including
dropping the GI numbers in many outputs, expanding the percentage
identity field from 2dp to 3dp, and also changing how -parse_deflines
works with tabular output.
The wrappers (deliberately) do not yet offer any new functionality
added in the recent NCBI BLAST+ updates, in particular BLAST
XML v2 is not yet available as an output with a datatype in Galaxy.
At this point I would welcome feedback from those of you using the
BLAST+ wrappers - including if you were able to install this with the
dependencies from BioConda or the traditional Tool Shed packages.
Once I'm confident that this is all OK, I will update the main Tool Shed
(and think about adding new functionality in 2017).
Thank you all,
Peter
2 years, 7 months
SLURM configuration problem
by Leonor Palmeira
Dear all,
we have setup a Galaxy instance on a virtual machine, and we want to be
able to submit jobs to our HPC system (SLURM).
Currently, we do not understand how to define that jobs will be sent to
the HPC cluster.
We have set :
export $DRMAA_LIBRARY_PATH=/var/lib/libdrmaa.so
This is our config/job_conf.xml :
<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way
it is configured by default (if there is no explicit config). -->
<job_conf>
<plugins>
<plugin id="drmaa" type="runner"
load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" />
</plugins>
<handlers default="handlers">
<handler id="handler0" tags="handlers" />
<handler id="main" />
</handlers>
<destinations default="slurm">
<destination id="slurm" runner="drmaa">
<param id="nativeSpecification">-P all_5hrs</param>
</destination>
</destinations>
</job_conf>
And the output of "sh run.sh" :
galaxy.jobs.manager DEBUG 2017-02-07 15:50:39,962 Starting job handler
galaxy.jobs INFO 2017-02-07 15:50:39,962 Handler 'main' will load all
configured runner plugins
galaxy.jobs.runners.state_handler_factory DEBUG 2017-02-07 15:50:39,971
Loaded 'failure' state handler from module
galaxy.jobs.runners.state_handlers.resubmit
pulsar.managers.util.drmaa DEBUG 2017-02-07 15:50:39,975 Initializing
DRMAA session from thread MainThread
Traceback (most recent call last):
File
"/home/mass/GAL/APP/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line
55, in paste_app_factory
app = galaxy.app.UniverseApplication( global_conf=global_conf,
**kwargs )
File "/home/mass/GAL/APP/galaxy/lib/galaxy/app.py", line 170, in __init__
self.job_manager = manager.JobManager( self )
File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/manager.py", line 23,
in __init__
self.job_handler = handler.JobHandler( app )
File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/handler.py", line 32,
in __init__
self.dispatcher = DefaultJobDispatcher( app )
File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/handler.py", line 723,
in __init__
self.job_runners = self.app.job_config.get_job_runner_plugins(
self.app.config.server_name )
File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/__init__.py", line
687, in get_job_runner_plugins
rval[id] = runner_class( self.app, runner[ 'workers' ],
**runner.get( 'kwds', {} ) )
File "/home/mass/GAL/APP/galaxy/lib/galaxy/jobs/runners/drmaa.py",
line 88, in __init__
self.ds = DrmaaSessionFactory().get()
File
"/usr/local/lib/python2.7/dist-packages/pulsar/managers/util/drmaa/__init__.py",
line 31, in get
return DrmaaSession(session_constructor, **kwds)
File
"/usr/local/lib/python2.7/dist-packages/pulsar/managers/util/drmaa/__init__.py",
line 49, in __init__
DrmaaSession.session.initialize()
File "/usr/local/lib/python2.7/dist-packages/drmaa/session.py", line
257, in initialize
py_drmaa_init(contactString)
File "/usr/local/lib/python2.7/dist-packages/drmaa/wrappers.py", line
73, in py_drmaa_init
return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer))
File "/usr/local/lib/python2.7/dist-packages/drmaa/errors.py", line
151, in error_check
raise _ERRORS[code - 1](error_string)
InternalException: code 1: cell directory
"/usr/lib/gridengine-drmaa/default" doesn't exist
Could anyone point us in the right direction?
This would be greatly appreciated.
Best regards
Leonor
--
Leonor Palmeira | PhD
Associate Scientist
Department of Human Genetics
CHU de Liège | Domaine Universitaire du Sart-Tilman
4000 Liège | BELGIQUE
Tél: +32-4-366.91.41
Fax: +32-4-366.72.61
e-mail: lpalmeira(a)chu.ulg.ac.be
2 years, 7 months
BioBlend: getting a list of datasets in a folder
by D K
I'm trying to get a list of all the datasets in a folder using BioBlend. I
don't see a function for doing this in the API documentation. I can use
"show_folder" to get some information regarding the contents of a folder,
but not the dataset IDs themselves
This is as far as I've gotten:
s = gi.libraries.show_folder(LibID, folder_id = subfolderID)
>
print(s)
{u'parent_library_id': u'd413a19dec13d11e', u'update_time':
> u'2017-02-24T18:10:02.789955', u'description':
> u'170124_M02550_0174_000000000-AV8FJ', u'name':
> u'170124_M02550_0174_000000000-AV8FJ', u'deleted': False, u'item_count': 2,
> u'parent_id': u'Ff1b9846ab84237e7', u'genome_build': u'?', u'model_class':
> u'LibraryFolder', u'id': u'F84ffe6fca6c4fbda', u'library_path': [u'2017',
> u'170124_M02550_0174_000000000-AV8FJ']}
There are two items (item_count) as expected, how do I get the actual
dataset IDs?
Thanks!
2 years, 8 months
Newline characters for txt files
by Lawrence, Cris W
I have observed that when I upload a file with CRLF line endings into Galaxy and then later download it, the endings have changed to UNIX (LF only). I also observed that an uploaded file containing CR only line endings in Galaxy downloads to a file again with LF only line endings. These file types are txt. Just want to confirm - does Galaxy scrub line endings?
- Cris
2 years, 8 months
installation error on venv dependencies.xml
by Linda Bakker
Hi All,
I am having some problems with my tool dependencies to setup a python venv.
Dependencies.xml looks like this:
When i install my tool from the toolshed, it fails to install the venv
dependency with this error message:
I am not sure what the problem exactly seems to be. os.py should be a
default python package right or do i need to specify it in the
dependencies file?
Can someone point me in the right direction of what the problem might be.
Thanks!
with regards ,
Linda Bakker
--
Linda Bakker
Bioinformatics Research Assistant
Plant Research International, Wageningen UR
Building 107 (Radix), room W1.Fa.054
Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
tel: +31-317-480756
email: linda.bakker(a)wur.nl
2 years, 8 months
SAML Authentication
by Keith Suderman
Is anyone using SAML for authentication? There is a feature request for SAML support on GitHub ( https://github.com/galaxyproject/galaxy/issues/3146), but it doesn't look like any work has been done.
We need to add the ability for our users to authenticate with a SAML identity provider (IdP), in particular with InCommon/EduRoam/EduCause et al. Looking at the documentation there appears to be "the old way" (configuring Apache/Nginx to do the authentication) and "the new way" where Galaxy handles the authentication. Is it correct to assume that to use the new way I should implement an external authenticator, something like galaxy/auth/providers/saml.py and then some sort of magic to get a config/auth_conf.xml working?
I just want to make sure I am heading down the correct path before investing too much time.
- Keith
Keith Suderman
Research Associate
Department of Computer Science
Vassar College, Poughkeepsie NY
suderman(a)cs.vassar.edu
2 years, 8 months
ansible-galaxy-tools and venv
by Matthias Bernt
Dear galaxy developers,
Is it expected that the virtualenv in .venv/ does include the python
binary but does not include the python shared libraries?
Some more details:
I have installed galaxy on CentOS 6.8 which includes the required python
2.7 only via software collections. For the installation of galaxy I have
enabled the software collection by calling "source
/opt/rh/python27/enable" (which sets PATH, LD_LIBRARY_PATH, MANPATH,
XDG_DATA_DIRS, and PKG_CONFIG_PATH).
Currently I was trying to run the ansible role ansible-galaxy-tools from
https://github.com/galaxyproject/ansible-galaxy-tools which runs
"/home/galaxy/galaxy/.venv/bin/python manage_bootstrap_user.py ..."
and gives me
/home/galaxy/galaxy/.venv/bin/python: error while loading shared
libraries: libpython2.7.so.1.0: cannot open shared object file: No such
file or directory.
This python call would work if I again "source /opt/rh/python27/enable".
But then the venv python binary is used with the library of the system.
Intuitively I would expect that the library and binary belong together.
Cheers,
Matthias
--
-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.bernt(a)ufz.de, www.ufz.de
Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------
2 years, 8 months
