Re: [galaxy-dev] Announcing the UK Galaxy Community
Amazing! All the best from Germany! Bjoern 2014-08-14 15:21 GMT+02:00 graham etherington (TSL) graham.ethering...@sainsbury-laboratory.ac.uk: Dear UK Galaxy-devs, We're delighted to announce the launch of the UK Galaxy Community. Please visit the site and have a look around: http://galaxy-community.org.uk/ The aims of Galaxy-UK are: - To bring the Galaxy community in the United Kingdom closer together - Identify and address the needs of the community - Encourage interaction and collaboration. Galaxy-UK is also an information hub for events such as: - UK based Galaxy training courses - UK based talks involving Galaxy - Information on the location of UK Galaxy servers - Anything else that might be pertinent to bring the UK Galaxy users/admins together as a community We will be organising both online meetings and physical meetings, so keep an eye on the site for these events. Best wishes, The Galaxy-UK Team. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Announcing the UK Galaxy Community
I'm all in! :) 2014-08-14 17:11 GMT+02:00 Sebastian Schaaf sch...@ibe.med.uni-muenchen.de : Not to say 'exemplary' - really great :). @Björn: phone call within the next days? Cheers, Sebastian bjoern.gruen...@googlemail.com schrieb: Amazing! All the best from Germany! Bjoern 2014-08-14 15:21 GMT+02:00 graham etherington (TSL) graham.ethering...@sainsbury-laboratory.ac.uk: Dear UK Galaxy-devs, We're delighted to announce the launch of the UK Galaxy Community. Please visit the site and have a look around: http://galaxy-community.org.uk/ The aims of Galaxy-UK are: - To bring the Galaxy community in the United Kingdom closer together - Identify and address the needs of the community - Encourage interaction and collaboration. Galaxy-UK is also an information hub for events such as: - UK based Galaxy training courses - UK based talks involving Galaxy - Information on the location of UK Galaxy servers - Anything else that might be pertinent to bring the UK Galaxy users/admins together as a community We will be organising both online meetings and physical meetings, so keep an eye on the site for these events. Best wishes, The Galaxy-UK Team. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Sebastian Schaaf, M.Sc. Bioinformatics Faculty Coordinator NGS Infrastructure Chair of Biometry and Bioinformatics Department of Medical Informatics, Biometry and Epidemiology (IBE) University of Munich Marchioninistr. 15, K U1 (postal) Marchioninistr. 17, U 006 (office) D-81377 Munich (Germany) Tel: +49 89 2180-78178 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] TypeError with 'dict'
Hi,
Galaxy stores all information about a tool and it's parameters in a
database.
I suppose if something is wrong with your tool, under some circumstances,
it can't be stored in the database.
Cheers,
Bjoern
2014-08-12 9:23 GMT+02:00 Martin Christiansen
martinchristianse...@hotmail.com:
Hi Björn,
I'm using galaxy as a front-end to run a larger pipeline in the background.
Originally I implemented the pipeline which had the same wrapper and was
running fine.
I have now begun to break it down into steps where this is the first step.
The only thing I've changed is the output.
How would this cause an error in the python egg?
Martin
Date: Tue, 12 Aug 2014 09:06:51 +0200
From: bjoern.gruen...@gmail.com
To: martinchristianse...@hotmail.com; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] TypeError with 'dict'
Hi Martin,
please keep galaxy-dev in the CC list.
Am 12.08.2014 um 08:51 schrieb Martin Christiansen:
Hi Björn,
Most certainly. I have posted it below.
tool id=screen_reads name=Screen Reads
- add here a version number version=0.1
descriptionagainst hg19/description
command interpreter=bashscreen_reads.sh $Project.input
$Project.samples $Project $Samples /command
inputs
conditional name=Project
param name=input type=select label=Select project
option value=galaxy_test1galaxy_test1/option
option value=Untitled FolderUntitled Folder/option
- is the white space really needed? If so $Project.input will be two
words. Use ${Project.input} to convert it to onw argument
/param
when value=galaxy_test1
param name=samples type=select label=Select samples
display=checkboxes multiple=True
option value=147406386-700171390147406386-700171390/option
option value=158256496-700097688158256496-700097688/option
option value=158337416-700013715158337416-700013715/option
option value=158337416-700097837158337416-700097837/option
option value=158357646-700035237158357646-700035237/option
option value=158458797-700014562158458797-700014562/option
option value=158479027-700014724158479027-700014724/option
option value=158479027-700097196158479027-700097196/option
option value=158499257-700014837158499257-700014837/option
option value=158499257-700098561158499257-700098561/option
option value=158742018-700015181158742018-700015181/option
option value=158802708-700015245158802708-700015245/option
option value=158802708-700015250158802708-700015250/option
option value=158802708-700099803158802708-700099803/option
option value=158802708-700119165158802708-700119165/option
option value=158822939-700014954158822939-700014954/option
option value=158883629-700015113158883629-700015113/option
option value=158883629-700100227158883629-700100227/option
option value=158883629-700112812158883629-700112812/option
option value=158924089-700099307158924089-700099307/option
/param
/when
when value=Untitled Folder
param name=samples type=select label=Select samples
display=checkboxes multiple=True
- you don't have any option here.
/param
/when
/conditional
/inputs
outputs
data format=tabular name=Project label=Project
from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input/
data format=tabular name=Samples label=Samples
from_work_dir=/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples/
/outputs
- I'm not sure this will work. workdir is a special dir Galaxy creates
for you. It will be the working directory where your program get's
called. So assume your program creates foo.sam files. You can specify it
like from_work_dir='foo.sam'
The input handling looks also a little bit strange. You do not specify
any input file in Galaxy. That is not really Galaxy like :)
Cheers,
Bjoern
help
Reads screened against hg19.
/help
/tool
Best,
Martin
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Re: [galaxy-dev] Issues with dependencies for toolshed packages
Iry, are you seeing the same error with: https://toolshed.g2.bx.psu.edu/view/iuc/snpeff Cheers, Bjoern 2014-08-06 19:12 GMT+02:00 Iry Witham iry.wit...@jax.org: Hi Greg, That resolved the internal server error issue. Now I need to figure out the issue with the dependencies. I was unable to post the actual error message previously, but am doing so now. Here is the error I get for the dependency installation: Name Version Type Status Error snpEff http://galaxy2/admin_toolshed/manage_repository_tool_dependencies?repository_id=b1254334b8763c9coperation=browsetool_dependency_ids=81424a9b99396c5a 3.6 package Error File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 110, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( app, tool_shed_repository, tool_dependency, actions_dict ) File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 103, in install_and_build_package dir = tmp_dir File /usr/lib64/python2.6/contextlib.py, line 34, in __exit__ self.gen.throw(type, value, traceback) File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py, line 142, in _setenv yield File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py, line 68, in install_and_build_package initial_download=True ) File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py, line 32, in execute_step initial_download=initial_download ) File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py, line 397, in execute_step dir = td_common_util.url_download( work_dir, downloaded_filename, url, extract=True ) File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py, line 560, in url_download extraction_path = archive.extract( install_dir ) File /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py, line 60, in extract self.archive.extractall( os.path.join( path ) ) File /usr/lib64/python2.6/zipfile.py, line 940, in extractall self.extract(zipinfo, path, pwd) File /usr/lib64/python2.6/zipfile.py, line 928, in extract return self._extract_member(member, path, pwd) File /usr/lib64/python2.6/zipfile.py, line 965, in _extract_member target = file(targetpath, wb) [Errno 20] Not a directory: 'database/tmp/tmp-toolshed-mtdCAL19a/snpEff/snpEff.config' This current package is owned by jjohnson and is located in the test toolshed. Thanks, Iry From: Greg Von Kuster g...@bx.psu.edu Date: Wednesday, August 6, 2014 12:34 PM To: Iry Witham iry.wit...@jax.org Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Issues with dependencies for toolshed packages Hi Iry, Sorry for the inconvenience. The tool shed server was out of space - I've corrected the problem and have successfully installed repositories. Please try again and let us know if you encounter problems. Thanks! Greg Von Kuster On Aug 6, 2014, at 12:20 PM, Iry Witham iry.wit...@jax.org wrote: Hi Team, I have been trying to install package_snpEff_3_5 from the Galaxy main tool shed and package_snpEff_3_6 from the Galaxy test tool shed and have the same issue. Once the installer completes it shows that the dependency snpEff.x.x was not installed. When I try to install the dependency it reports that the directory /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/tmp/tmp-toolshed-mtdi48tQV/snpEff does not exist. I have checked to confirm that this is true and discovered that rather then a directory I find a null file named snpEff and the snpEff_v3.x_core.zip file. I checked my shedtool dependencies folder and the directory for these tools are empty. I have since uninstalled the package. I just tried again to install the snpEff tool and am getting the followig error message: Internal Server Error Galaxy was unable to successfully complete your request URL: http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413 Module galaxy.web.framework.middleware.error:*149* in __call__ http://galaxy2/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/repository_ids=76ad6cd032d7117echangeset_revisions=04d2a4f81413# app_iter *=* self*.*application*(*environ*,*sr_checker*)* Module paste.recursive:*84* in __call__
Re: [galaxy-dev] TestToolShed failure, Exception: History in error state.
Hi Peter, 2014-07-31 10:57 GMT+02:00 Peter Cock p.j.a.c...@googlemail.com: Hi Dave, You are right that on closer inspection I've mixed tool_dependencies.xml and repository_dependencies.xml *again*. Evidentially my mental model does not match Greg's here: (*) I need to define a tool installation recipe for something not in the Tool Shed -- write an install script called tool_dependencies.xml (*) I need to depend on a Python package by pointing at another repository in the Tool Shed -- repository_dependencies.xml I might be wrong, but I think that also goes to tool_dependencies.xml (*) I need to depend on a datatype package by pointing at another repository in the Tool Shed -- repository_dependencies.xml (*) I need to depend on a binary package by pointing at another repository in the Tool Shed -- repository_dependencies.xml ? No. You need tool_dependencies.xml for this too As far as I understood, everything that is referenced in the tool.xml under the requirement section, needs to be in a tool_dependencies.xml file. Any other dependency are from the repository (data_types, data_manager, workflows ...). Ciao, Bjoern But that aside, the test framework error here is completely unhelpful. Why is there no error message about missing a dependency? Was there an error from running my tool which was not shown? Thanks, Peter On Wed, Jul 30, 2014 at 6:07 PM, Dave Bouvier d...@bx.psu.edu wrote: Peter, I believe part of the problem is that the install and test framework is unable to resolve the dependency on blast+ 2.2.29 because it is defined as a repository dependency, not a tool dependency. I would recommend replacing the repository dependency in the blast_rbh repository with a tool dependency definition that references package_blast_plus_2_2_29. --Dave B. On 07/30/2014 05:27 AM, Peter Cock wrote: Hi all, I'm not sure when this started (having hardly looked at my Tool Shed test results since GCC2014), but I think this is a fairly recent problem with my BLAST RBH tests failing (which has held me back from posting this to the main Tool Shed). This could be some silly mistake in my tar-ball, but usually missing test files and the like get an explicit error. The tests are passing on my GitHub/TravisCI setup (using Twill and the API backend): e.g. https://travis-ci.org/peterjc/galaxy_blast/builds/30592097 Here is the current error (the same for the last few Test Tool Shed runs), https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh Traceback (most recent call last): File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 108, in test_tool self.do_it( td ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 35, in do_it self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py, line 69, in _verify_outputs galaxy_interactor.verify_output( history, output_data, output_testdef=output_testdef, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py, line 53, in verify_output self.wait_for_history( history_id, maxseconds ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py, line 107, in wait_for_history self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py, line 2453, in wait_for result = func() File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py, line 107, in lambda self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py, line 257, in __history_ready return self._state_ready( state, error_msg=History in error state. ) File /var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py, line 316, in _state_ready raise Exception( error_msg ) Exception: History in error state. Is a more detailed log available which might help debug this? Thanks, Peter As an aside, this looks like the Test Tool Shed is still using the Twill backend for the functional tests? ___ Please keep all replies on
Re: [galaxy-dev] Object-Store, setting filetypes crashes Galaxy
Hi Nate,
we encountered an addition bug related to the object-store:
Traceback (most recent call last):
File /usr/local/galaxy/galaxy-
dist/lib/galaxy/jobs/runners/__init__.py, line 153, in prepare_job
job_wrapper.prepare()
File /usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line
712, in prepare
self.command_line, self.extra_filenames = tool_evaluator.build()
File /usr/local/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py, line
348, in build
self.__build_command_line( )
File /usr/local/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py, line
364, in __build_command_line
command_line = fill_template( command, context=param_dict )
File /usr/local/galaxy/galaxy-dist/lib/galaxy/util/template.py, line 9,
in fill_template
return str( Template( source=template_text, searchList=[context] ) )
File
/usr/local/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py,
line 1004, in __str__
return getattr(self, mainMethName)()
File cheetah_DynamicallyCompiledCheetahTemplate_1402663002_65_42228.py,
line 94, in respond
File /usr/local/galaxy/galaxy-dist/lib/galaxy/tools/wrappers.py, line
203, in __getattr__
return getattr( self.dataset, key )
File /usr/local/galaxy/galaxy-dist/lib/galaxy/model/__init__.py, line
1493, in extra_files_path
return self.dataset.extra_files_path
File /usr/local/galaxy/galaxy-dist/lib/galaxy/model/__init__.py, line
1349, in extra_files_path
return self.object_store.get_filename( self, dir_only=True,
extra_dir=self._extra_files_path or dataset_%d_files % self.id )
File /usr/local/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py,
line 416, in get_filename
return self.__call_method('get_filename', obj, ObjectNotFound, True,
**kwargs)
File /usr/local/galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py,
line 436, in __call_method
% ( method, str( obj ), str( kwargs ) ) )
ObjectNotFound: objectstore, __call_method failed: get_filename on
galaxy.model.Dataset object at 0x7f7ee103fb90, kwargs: {'dir_only': True,
'extra_dir': 'dataset_118453_files'}
It should be reproducible with the latest Galaxy stable release and the
latest NCBI Blast+ wrappers if you are trying to generate a Blast+ database.
Thanks,
Bjoern
2014-06-12 16:50 GMT+02:00 Björn Grüning bjoern.gruen...@gmail.com:
Hi Nate,
yes that is fixing it for me!
Thanks!
Bjoern
Am 12.06.2014 16:26, schrieb Nate Coraor:
writeable (e.g. what you have new_files_path set to), that'd confirm it.
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[galaxy-dev] Object-Store, setting filetypes crashes Galaxy
Hi,
I have configured to use the hierarchical object store but as soon as I try
to reset the filetpye of a dataset Galaxy is crashing with:
galaxy.objectstore DEBUG 2014-06-12 14:39:21,180 Using preferred backend
'files3' for creation of MetadataFile 5963
132.230.153.57 - - [12/Jun/2014:14:39:20 +0200] POST
/datasets/966f24627ef70c12/edit HTTP/1.1 500 -
http://galaxy.uni-freiburg.de/datasets/966f24627ef70c12/edit; Mozilla/5.0
(X11; Linux x86_64; rv:29.0) Gecko/20100101 Fire
fox/29.0
Error - type 'exceptions.OSError': [Errno 2] No such file or directory:
'database/tmp/metadata_temp_file_1xnGcE'
URL: http://galaxy.uni-freiburg.de/datasets/966f24627ef70c12/edit
File
'/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__
app_iter = self.application(environ, sr_checker)
File
'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py',
line 84 in __call__
return self.application(environ, start_response)
File
'/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
132 in __call__
return self.handle_request( environ, start_response )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line
190 in handle_request
body = method( trans, **kwargs )
File
'/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py',
line 295 in edit
trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(
trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming =
{ 'input1':data }, overwrite = False ) #overwrite is False as per existi
ng behavior
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/actions/metadata.py',
line 18 in execute
overwrite, history, job_params )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/actions/metadata.py',
line 79 in execute_via_app
kwds = { 'overwrite' : overwrite } )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py', line
717 in setup_external_metadata
shutil.copy( dataset.metadata.get( meta_key, None ).file_name,
metadata_temp.file_name )
File '/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/metadata.py', line
575 in file_name
self._filename = abspath( tempfile.NamedTemporaryFile( dir =
self.tmp_dir, prefix = metadata_temp_file_ ).name )
File '/usr/local/python/2.7/lib/python2.7/tempfile.py', line 454 in
NamedTemporaryFile
(fd, name) = _mkstemp_inner(dir, prefix, suffix, flags)
File '/usr/local/python/2.7/lib/python2.7/tempfile.py', line 235 in
_mkstemp_inner
fd = _os.open(file, flags, 0600)
OSError: [Errno 2] No such file or directory:
'database/tmp/metadata_temp_file_1xnGcE'
I have attached my object_store_conf.xml file.
Thanks,
Bjoern
?xml version=1.0?
object_store type=hierarchical
backends
object_store type=distributed id=primary order=0
backends
backend id=files2 type=disk weight=1
files_dir path=/data/2/galaxy_db/files/
extra_dir type=temp path=/data/2/galaxy_db/tmp/
extra_dir type=job_work path=/data/2/galaxy_db/job_working_directory/
/backend
backend id=files3 type=disk weight=1
files_dir path=/data/3/galaxy_db/files/
extra_dir type=temp path=/data/3/galaxy_db/tmp/
extra_dir type=job_work path=/data/3/galaxy_db/job_working_directory/
/backend
/backends
/object_store
object_store type=disk id=secondary order=1
files_dir path=/data/0/galaxy_db/files/
extra_dir type=temp path=/data/0/galaxy_db/tmp/
extra_dir type=job_work path=/data/0/galaxy_db/job_working_directory/
/object_store
/backends
/object_store
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[galaxy-dev] Galaxy reports crashing with the latest stable release
Hi, I encountered the following bug during my testing of the latest stable release: Error - type 'exceptions.AttributeError': 'SpecifiedDateListGrid' object has no attribute 'info_text' URL: http://galaxy.uni-freiburg.de:9001/jobs/specified_date_handler?specified_date=2014-06-04 File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/exceptions/errormiddleware.py', line 144 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/reports/controllers/jobs.py', line 177 in specified_date_handler return self.specified_date_list_grid( trans, **kwd ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 296 in __call__ message = message, File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 1184 in fill_template def fill_template(self, filename, **kwargs): File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 1199 in fill_template_mako template_lookup = template_lookup or self.webapp.mako_template_lookup File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/usr/local/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ base.mako.py', line 66 in render_body __M_writer(unicode(next.body())) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ grid_base.mako.py', line 91 in render_body __M_writer(unicode(self.load())) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ grid_base.mako.py', line 120 in render_load __M_writer(unicode( h.to_json_string( self.get_grid_config( embedded=embedded, insert=insert ) ) )) File '/usr/local/galaxy/galaxy-dist/database/compiled_templates/reports/ grid_base.mako.py', line 193 in render_get_grid_config 'info_text' : grid.info_text, AttributeError: 'SpecifiedDateListGrid' object has no attribute 'info_text' Trello card is here: https://trello.com/c/EqQCAcIe Thanks, Bjoern ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] IGV display_application configuration failed with require_login=TRUE
Hi Vincent,
I think there was an error that was fixed recently. If you can, please try
yo upgrade or wait a few more days until the new galaxy-dist version is
released.
Bjoern
2014-02-04 navratil navra...@prabi.fr:
Dear galaxy-dev team,
We have configured a galaxy-dist server (stable release) behind an
Apache2 proxy (with mod_xsendfile) by following the galaxy wiki.
We would like to use the galaxy embeded user authentification with
require_login=True option instead of a remote_user configuration on the
proxy side.
With require_login = False it works but with require_login=True
configuration we fail to load .bam files into IGV (local) :
The IGV (Version 2.3.18) send this error:
*INFO [2014-02-04 16:05:56,660] [MessageUtils.java:60] [Thread-9] Error
loading
http://XX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam
http://XX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam:
An error occurred while accessing:
http://XX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam
http://XX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bambrInvalid
GZIP** header*
and the galaxy-server send this error_log:
**
*XX - - [04/Feb/2014:16:05:40 +0200] HEAD
/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam
HTTP/1.1 302 - - IGV Version 2.3.18 (20)09/05/2013 12:24 PM*
*XX - - [04/Feb/2014:16:05:40 +0200] HEAD /root HTTP/1.1 200 - -
IGV Version 2.3.18 (20)09/05/2013 12:24 PM*
**
*Exception happened during processing of request from ('127.0.0.1', 46142)*
*Traceback (most recent call last):*
* File
/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py,
line 1068, in process_request_in_thread*
*self.finish_request(request, client_address)*
* File /usr/lib/python2.7/SocketServer.py, line 334, in finish_request*
*self.RequestHandlerClass(request, client_address, self)*
* File /usr/lib/python2.7/SocketServer.py, line 651, in __init__*
*self.finish()*
* File /usr/lib/python2.7/SocketServer.py, line 710, in finish*
*self.wfile.close()*
* File /usr/lib/python2.7/socket.py, line 279, in close*
*self.flush()*
* File /usr/lib/python2.7/socket.py, line 303, in flush*
*self._sock.sendall(view[write_offset:write_offset+buffer_size])*
*error: [Errno 32] Broken pipe*
**
*XX - - [04/Feb/2014:16:05:40 +0200] GET
/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam
HTTP/1.1 302 - - IGV Version 2.3.18 (20)09/05/2013 12:24 PM*
*XX - - [04/Feb/2014:16:05:40 +0200] GET /root HTTP/1.1 200 - -
IGV Version 2.3.18 (20)09/05/2013 12:24 PM*
Any idea ?
Vincent
--
Vincent Navratil, PhD
IR UCBL - PRABI http://www.prabi.fr
Bâtiment Gregor Mendel
Université Claude Bernard - Lyon 1
16, rue Raphaël Dubois
69622 VILLEURBANNE CEDEX
Tel: +33 472432826
My 'ome' page http://vinavratil.free.fr
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Re: [galaxy-dev] Cheetah code issue
Hi, to access variables in a conditional you need to write something like that: $rangeorlist.rngstart $rangeorlist.rend $rangeorlist.stepsize Cheers, Bjoern 2014-02-04 Ketan Maheshwari ketancmaheshw...@gmail.com: Hi, While developing a tool, I am facing Cheetah code issue. I looked up the mailing list archive and found many similar issues reported earlier but could not debug this. Any tips in debugging is appreciated. File cheetah_DynamicallyCompiledCheetahTemplate_1391530084_29_71368.py, line 97, in respond NotFound: cannot find 'rngstart' Attached is the xml tool definition file. Best, Ketan ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] filter tag in output, multiple criteria
Hi,
something like that is also possible:
((
params['settingsType'] == custom and
params['unmapped_read_file'] is True
))
So I assume:
outtype == 0 or outtype == 2
will also work.
Cheers,
Bjoern
2014-01-31 Geert Vandeweyer geert.vandewey...@uantwerpen.be:
Hi,
Thanks for the quick suggestions.
The typo didn't exists in the original code, so that didn't solve it
unfortunately. I fixed it for now by using the negative filter (!=),
suggested by Peter.
Best,
Geert
On 01/31/2014 12:09 PM, Nicola Soranzo wrote:
Il 2014-01-31 11:52 Geert Vandeweyer ha scritto:
Hi,
I'm looking for the correct syntax to achieve the following:
data type=data format=txt name=loh label=${tool.name} result
on ${on_string} (loh)
filterouttype == 0 || outttype == 2 /filter
/data
data type=data format=txt name=cnv label=${tool.name} result
on ${on_string} (loh)
filterouttype == 1 || outttype == 2 /filter
/data
I tried the above, with and without parentheses, but it creates the
second dataset also when outtype == 0. Is this type of dual filtering
possible?
I don't know if this is the reason, but you seem to have a typo:
outttype == 2
should be
outtype == 2
Best,
Nicola
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--
Geert Vandeweyer, Ph.D.
Department of Medical Genetics
University of Antwerp
Prins Boudewijnlaan 43
2650 Edegem
Belgium
Tel: +32 (0)3 275 97 56
E-mail: geert.vandewe...@ua.ac.be
http://ua.ac.be/cognitivegenetics
http://www.linkedin.com/in/geertvandeweyer
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Re: [galaxy-dev] bowtie2 toolshed installation
Hi Alex, there is a difference in http://toolshed.g2.bx.psu.edu/view/devteam/package_bowtie2_2_1_0 and http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers The package_* is installing the binary for you and can be used by other programs as well. bowtie_wrappers contains the actual wrappers and is depending on package_*. To make it short. You need to install http://toolshed.g2.bx.psu.edu/view/devteam/bowtie_wrappers and both packages will be installed and you should see your wrapper. Ciao, Bjoern 2014-01-31 Alexander Kurze alexander.ku...@bioch.ox.ac.uk: Hi there, I have a local copy of galaxy and I am trying to install bowtie2 2.1.0 onto the system via the toolshed. However it just doesn't work. I always get a Server Error message. I have checked if the dependencies are installed and they are all installed in the toolshed depenencies folders. However, the actual repos only contains the tool_dependency.xml. (eg galaxy/shed_tools/ testtoolshed.g2.bx.psu.edu/repos/jjohnson/package_bowtie_2_1_0/38652b57e057/package_bowtie_2_1_0/tool_dependencies.xml ) I thought that there should be a bowtie2.xml file in the repos of package_bowtie_2_1_0 but there isn't... Also, looking at the shed_tool_config.xml I cannot see any entry for bowtie2. Is there a way to add bowtie2 manually? Best wishes, Alex ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] GATK2
I have no clue what is happening. Attached is my working *.loc flile.
See select-box is also filtered by the db-key of your dataset, but I think
you habe hg19 as dbkey, otherwise you would not see the hg19 in the select
box. There must be something wrong in you *.log file.
2014-01-30 Briand, Sheldon sheldon.bri...@ssc-spc.gc.ca:
We do see hg19 in the reference genome box. We are using revision
8bcc13094767 of the GATK2 wrapper. The only line in the .loc file is the
one listed in my first email. I've put that line in both tool-data and
tool-data/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767 loc files.
We didn't see the reference genome hg19 until the loc file for the repo was
populated.
Thanks!
-Sheldon
-Original Message-
From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
Sent: Thursday, January 30, 2014 1:33 PM
To: Briand, Sheldon
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] GATK2
Hi Sheldon,
The loc file is tabular. I put the 2bit file in the directory and had
no success. Here is the rather lengthy commandline:
#!/bin/sh
export GALAXY_SLOTS_CONFIGURED=1
if [ -n $SLURM_JOB_NUM_NODES ]; then
GALAXY_SLOTS=$SLURM_JOB_NUM_NODES
elif [ -n $NSLOTS ]; then
GALAXY_SLOTS=$NSLOTS
elif [ -f $PBS_NODEFILE ]; then
GALAXY_SLOTS=`wc -l $PBS_NODEFILE` else
GALAXY_SLOTS=1
unset GALAXY_SLOTS_CONFIGURED
fi
export GALAXY_SLOTS
GALAXY_LIB=/software/packages/galaxy/galaxy-dist/lib
if [ $GALAXY_LIB != None ]; then
if [ -n $PYTHONPATH ]; then
PYTHONPATH=$GALAXY_LIB:$PYTHONPATH
else
PYTHONPATH=$GALAXY_LIB
fi
export PYTHONPATH
fi
[ -f /home/galaxy/.bashrc ] . /home/galaxy/.bashrc cd
/software/packages/galaxy/galaxy-dist/database/job_working_directory/0
00/101
PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/samtoo
ls/0.1.19/iuc/gatk2/8bcc13094767; export PACKA GE_BASE; .
/software/packages/galaxy/galaxy-dist/dependancies/samtools/0.1.19/iuc
/gatk2/8bcc13094767/env.sh; PACKAGE
_BASE=/software/packages/galaxy/galaxy-dist/dependancies/environment_s
ettings/GATK2_PATH/iuc/gatk2/8bcc13094767; exp ort PACKAGE_BASE; .
/software/packages/galaxy/galaxy-dist/dependancies/environment_setting
s/GATK2_PATH/iuc/gatk2/8bc c13094767/env.sh;
PACKAGE_BASE=/software/packages/galaxy/galaxy-dist/dependancies/enviro
nment_settings/GATK2_SITE_OP TIONS/iuc/gatk2/8bcc13094767; export
PACKAGE_BASE; .
/software/packages/galaxy/galaxy-dist/dependancies/environment_
settings/GATK2_SITE_OPTIONS/iuc/gatk2/8bcc13094767/env.sh; python
/software/packages/galaxy/shed_tools/toolshed.g2.b
x.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py
--stdout /software/packages/galaxy/galaxy-dist/da
tabase/files/000/dataset_126.dat -d -I
/software/packages/galaxy/galaxy-dist/database/files/000/dataset_114.
dat bam gatk_input -d
/software/packages/galaxy/galaxy-dist/database/files/_metadata_files/000/meta
data_19.dat bam_index gatk_input -p ' java -jar
$GATK2_PATH/GenomeAnalysisTK.jar-T Rea
lignerTargetCreator -o
/software/packages/galaxy/galaxy-dist/database/files/000/dataset_125.dat
$GATK2_S
ITE_OPTIONS --num_cpu_threads_per_data_thread 1
--num_threads ${GALAXY_SLOTS:-4}
-R
- that is the error. Here needs to be your path to the fasta file. Can
you point to me to Tool Shed Version you are using and are you running the
latest revision? Do you see hg19 / hg18 in the select-box under
using-reference genome
Can you attach your gatk2_picard_index.loc?
Thanks,
Bjoern
'; return_code=$?; cd /software/packages/galaxy/galaxy-dist;
/software/packages/galaxy/galaxy-dist/set_metadata.sh
./database/files
/software/packages/galaxy/galaxy-dist/database/job_working_directory/0
00/101 . /software/packages/g alaxy/galaxy-dist/universe_wsgi.ini
/software/packages/galaxy/galaxy-dist/database/tmp/tmpfjJAKX
/software/packages/
galaxy/galaxy-dist/database/job_working_directory/000/101/galaxy.json
/software/packages/galaxy/galaxy-dist/database
/job_working_directory/000/101/metadata_in_HistoryDatasetAssociation_1
02_DXIvP5,/software/packages/galaxy/galaxy-dis
t/database/job_working_directory/000/101/metadata_kwds_HistoryDatasetA
ssociation_102_ifJAbu,/software/packages/galax
y/galaxy-dist/database/job_working_directory/000/101/metadata_out_Hist
oryDatasetAssociation_102_Ie2O0C,/software/pac
kages/galaxy/galaxy-dist/database/job_working_directory/000/101/metada
ta_results_HistoryDatasetAssociation_102_xLNtK
a,,/software/packages/galaxy/galaxy-dist/database/job_working_director
y/000/101/metadata_override_HistoryDatasetAsso
ciation_102__IZJ7Y
/software/packages/galaxy/galaxy-dist/database/job_working_directory/0
00/101/metadata_in_HistoryD
atasetAssociation_103_uoVLce,/software/packages/galaxy/galaxy-dist/dat
