[galaxy-dev] Gzipped input to functional tests with multiple=true
Hi all, I think I've found a bug in the Galaxy test framework :( With most file inputs, a gzipped input file works fine (Galaxy's upload code handles unzipping it). However, with multiple=true this seems to break (with the Twill backend, the API test framework is OK), e.g. param name=filenames type=data format=fastq,mira multiple=true required=true label=Read file(s) help=Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs). / Fails: param name=filenames value=SRR639755_mito_pairs_sample.fastq.gz ftype=fastqsanger / e.g. https://travis-ci.org/peterjc/pico_galaxy/builds/27426318 Excerpt from log: == FAIL: test_tool_00 (functional.test_toolbox.TestForTool_mira_4_0_de_novo) MIRA v4.0 de novo assember ( mira_4_0_de_novo ) Test-1 -- Traceback (most recent call last): File /home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py, line 108, in test_tool self.do_it( td ) File /home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/functional/test_toolbox.py, line 32, in do_it data_list = galaxy_interactor.run_tool( testdef, test_history ) File /home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/interactor.py, line 449, in run_tool self.twill_test_case.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) File /home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/twilltestcase.py, line 1789, in run_tool self.submit_form( **kwd ) File /home/travis/build/peterjc/pico_galaxy/galaxy-central-master/test/base/twilltestcase.py, line 1999, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'read_group_0|filenames' to value '['SRR639755_mito_pairs_sample.fastq.gz']' in form 'tool_form' threw exception: id=None name=None label='SRR639755_mito_pairs_sample.fastq.gz' control: SelectControl(read_group_0|filenames=[80]) If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the test tag set. This works, param name=filenames value=SRR639755_mito_pairs_sample.fastq ftype=fastqsanger / e.g. https://travis-ci.org/peterjc/pico_galaxy/builds/27426336 See: https://github.com/peterjc/pico_galaxy/commit/e6967767535ca29debcdc19d7f0502d73276b6a0 Regards, Peter ___ 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] galaxy-dev Digest, Vol 96, Issue 14
This is a new one for me. What configuration are you using for both your
'database_connection', and the 'amqp_internal_connection' in your
universe_wsgi.ini?
On Fri, Jun 13, 2014 at 12:29 AM, xlwang xlwang_0...@163.com wrote:
Hello,
when i run my galaxy instance type:
$ sh run.sh
I get some error like this:
Traceback (most recent call last):
File /export/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py, line
38, in app_factory
from galaxy.app import UniverseApplication
File /export/galaxy-dist/lib/galaxy/app.py, line 21, in module
from galaxy.queue_worker import GalaxyQueueWorker
File /export/galaxy-dist/lib/galaxy/queue_worker.py, line 10, in
module
import galaxy.queues
File /export/galaxy-dist/lib/galaxy/queues.py, line 17, in module
from kombu import Exchange, Queue
File
/export/galaxy-dist/eggs/kombu-3.0.13-py2.7.egg/kombu/__init__.py, line
67, in __getattr__
module = __import__(object_origins[name], None, None, [name])
File /export/galaxy-dist/eggs/kombu-3.0.13-py2.7.egg/kombu/entity.py,
line 10, in module
from .abstract import MaybeChannelBound
File
/export/galaxy-dist/eggs/kombu-3.0.13-py2.7.egg/kombu/abstract.py, line
12, in module
from .connection import maybe_channel
File
/export/galaxy-dist/eggs/kombu-3.0.13-py2.7.egg/kombu/connection.py, line
24, in module
from kombu import exceptions
File
/export/galaxy-dist/eggs/kombu-3.0.13-py2.7.egg/kombu/exceptions.py, line
12, in module
from amqp import ChannelError, ConnectionError, ResourceError
File /export/galaxy-dist/eggs/amqp-1.4.5-py2.7.egg/amqp/__init__.py,
line 32, in module
from .basic_message import Message # noqa
File
/export/galaxy-dist/eggs/amqp-1.4.5-py2.7.egg/amqp/basic_message.py, line
19, in module
from .serialization import GenericContent
File
/export/galaxy-dist/eggs/amqp-1.4.5-py2.7.egg/amqp/serialization.py, line
33, in module
from .five import int_types, long_t, string, string_t, items
File /export/galaxy-dist/eggs/amqp-1.4.5-py2.7.egg/amqp/five.py, line
171, in module
librt = ctypes.CDLL('librt.so.1', use_errno=True)
TypeError: __init__() got an unexpected keyword argument 'use_errno'
I have no idea why this happend. How can I fix it?
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Re: [galaxy-dev] multiple file selection for from_file
Hi Jun, You should be using Tool Data Tables instead of acting on .loc files directly. You can specify a data table to be built up from more than one file and multiple data tables to use various file configurations. ‘from_data_table’: https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#from_data_table see also https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables Thanks for using Galaxy, Dan On Jun 12, 2014, at 8:23 PM, Jun Fan j@qmul.ac.uk wrote: Hi all I gather that it is NOT allowed to assign multiple file to from_file attribute for options in select param as the expect value of from_file attribute is the name of A file. But would it be nice to allow this feature? For example, there are two loc file A and B, when I want to get the options from both files, instead of adding an extra file containing all options from two files, it will be more maintainable to use something like from_file = “A.loc, B.loc”, isn’t it? BTW, could anyone help me on this http://dev.list.galaxyproject.org/jobs-don-t-get-killed-when-histories-deleted-tc4664678.html? Best regards! Jun ___ 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] 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] Per-tool configuration
I am writing a tool that should be configurable by the server admin. I am considering adding a configuration file, but where should such a file be placed? Is the tool-data directory the right place? Is there another standard way for per-tool configuration? Jan ___ 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] Per-tool configuration
I would have different answers for your depending on what options are available to the server admin. What exactly about the tool is configurable - can you be more specific? -John On Fri, Jun 13, 2014 at 10:59 AM, Jan Kanis jan.c...@jankanis.nl wrote: I am writing a tool that should be configurable by the server admin. I am considering adding a configuration file, but where should such a file be placed? Is the tool-data directory the right place? Is there another standard way for per-tool configuration? Jan ___ 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/
[galaxy-dev] Proposed cd-hit tool dependency change in galaxy
Hi all, When installing and testing the cd-hit tool from jjohnson from the main galaxy toolshed into my local instance of galaxy, I encountered a problem where galaxy cannot find the cd-hit program. The error was: /bin/sh: 1: cd-hit-est: not found As I debugged the problem, I found that there is an bug in the tool dependency. It installs the cd-hit programs but never moves the programs into the configurable galaxy install directory. This could cause many problems in the situation where users don't have cd-hit already installed on their computer and must depend on the tool dependency to run the tool. I propose we add the following code to the tool dependency: action type=move_file sourcecd-hit/source destination$INSTALL_DIR/destination /action action type=move_file sourcecd-hit-est/source destination$INSTALL_DIR/destination /action After I made these changes, I pushed the changes into a new repo on my local toolshed, I managed to successfully install cd-hit into a local and dev-test instance of galaxy and the cd-hit tool ran successfully. Thanks for your understanding, Charles Qi ___ 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] troubleshooting Galaxy with LSF
The problem seems to be with DRMAA for Python. While it works fine on the OpenSuse 12.1 box, I'm getting a segfault on RH 6.4. Surprisingly, the job however gets submitted and run successfully. ___ 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] troubleshooting Galaxy with LSF
The problem seems to be with DRMAA for Python. While it works fine on the OpenSuse 12.1 box, I'm getting a segfault on RH 6.4. Surprisingly, the job however gets submitted and run successfully. ___ 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/
[galaxy-dev] Adding a reference genome
I installed a local instance of galaxy approximately a month ago (build 2014.04.14) and have since updated to latest_2014.06.02. It is running on 64-bit Ubuntu 12.04. I'm having an issue with the Data Manager to fetch reference genomes (data_manager_fetch_genome_all_fasta, Rev. 2ebc856bce29). It will successfully submit a job to the queue but it quickly has an error. I'm selecting UCSC as the source and bosTau7 as UCSC's DBKEY for source FASTA. The only error/warning I see in the server logs seems related to samtools:galaxy.tools.deps DEBUG 2014-06-12 20:07:30,952 Building dependency shell command for dependency 'samtools'galaxy.tools.deps WARNING 2014-06-12 20:07:30,952 Failed to resolve dependency on 'samtools', ignoring Samtools 0.1.19 seems to be installed through galaxy and I also installed samtools through apt-get. I installed the apt-get version after the first time trying this didn't work. In the list of jobs, it has an error state and the command line is the following:python /home/stephen/Work/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/2ebc856bce29/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py /home/stephen/Work/galaxy-dist/database/files/000/dataset_22.dat --dbkey_description 'unspecified (?)' I need to use the bosTau7 (or perhaps bosTau6) cow reference genomes and can't figure out any other ways to properly load them into galaxy. I'd like them available for everything on the server and would prefer this over using a custom reference genome. I may be missing something obvious because the command line doesn't seem to specify the genome I want but I can't type anything new into the DBKEY to assign data field. How can I get the fetch genome data manager to work or otherwise load the bosTau7 reference genome into galaxy? Thanks, Stephen ___ 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] Missing navigation pane
After multiple restarts of my computer and the galaxy server program, it seems to have come back so I guess that's solved. Still can't successfully fetch reference genomes using the data manager but I guess I should start a new question/thread for that. Gives some dependancy error about samtools but I'm not sure if that is the real issue stopping it. Anyway, thanks. Stephen Date: Tue, 10 Jun 2014 10:39:55 -0400 Subject: Re: [galaxy-dev] Missing navigation pane From: dannon.ba...@gmail.com To: sedwards...@hotmail.com CC: galaxy-...@bx.psu.edu Hey Stephen, Can you look in the server logs to see if there are any errors being reported? Or if there are any javascript errors in the browser window? You may also want to try clearing your browser cache. -Dannon On Tue, Jun 10, 2014 at 1:54 AM, Stephen E sedwards...@hotmail.com wrote: I installed a local instance of galaxy approximately a month ago (build 2014.04.14). I was having an issue with the Data Manager to fetch reference genomes and after checking to see if there was a newer version of galaxy, I decided to update and see if that fixed my problem. I ran hg pull and then hg update latest_2014.06.02. I tried to rerun galaxy but was instructed to run manage_db.sh so I did (sh manage_db.sh upgrade). When I ran galaxy after all this, it started but when opened in a web browser, the navagation pane at the top is missing (i.e. Analyze Data, Workflows, User, etc). There is a blue bar but nothing is on it. How do I get the missing navigation pane back? I can't do a lot of things without it (i.e. check help or change user settings). I can still get to the administrator section but only by appending /admin to the url. I need to know how to fix the new version or how to succesfully revert to a previous version without anything else breaking. ___ 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/
[galaxy-dev] Tools for managing installed toolshed tools?
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Asked this on IRC and was directed to send my request here in case anyone in the community knows: I'm looking to find out if anyone has already written tools to manage installed tools from the toolshed. E.g. something along the lines of apt-get for galaxy, where apt-get update would update toolshed status, apt-get upgrade to upgrade all tools, and apt-get install/remove would be available for removing and adding tools. If no one has this in the works, it has been added to the hackathon project list Cheers, Eric - -- Eric Rasche Programmer II Center for Phage Technology Texas AM University College Station, TX 77843 404-692-2048 tel:4046922048 e...@tamu.edu mailto:e...@tamu.edu -BEGIN PGP SIGNATURE- Version: GnuPG v2.0.22 (GNU/Linux) iQIcBAEBAgAGBQJTmyaxAAoJEMqDXdrsMcpVVYcQAIXAtmeWvH0XnIIO0bxEaym1 1EeWTcBvH3UzwpQ9ucHEegee3KN4E4FZ71yvfKQiFXTm5mKShxQ8ArlSxs08Q92K VAAYgySDgRD5QTbhjxmFGDu/18SOu0Br2vSNLCNIaiygRzIldjCMhKve0XAfY6qJ MQrb4/fiAW5skWhI51n2aSFOP2VENjPgJ/3KDfX6yRCYnvxNjcSQcmWo3z6j8AZI vEyqHDJOCWzzY1XE5oqYUC6RK80OPA9JLcwG7YHKRZgQ8uOONThfBBBPjhV++HS4 X7ZPPLd63ja6U/frNNSkCrBNlmN0xhzf1gxZygMbL72rdu/7fq4bqoO0aSpWX3/O Q9NaX891zRDExOAIGx1dRPQ55XgqOJZYDKru/ykwbbN6YZvh3wNnrLia8Y/Ilho5 zvqiBOh5PwK1fj3RPkiWgVY95yk5+MseXA469xi1QU3yUt8PVvSNInPbq0QrLNZo ZFkJ1U7UYsS6psUmnFdNBGM1NWUyf6KCW5EiFxxIcZ2C6pmKDx5jcRVinBR3GtLm jH+fK2vinqxn07x8h7Dq3NeBeqlB++obcsX74xaic9DwZKqiNu6oI9eGNv0cPI0Y OV1ZPMI/8kJZjZMNvpkMIAi+SaGvvM46kraaszqijmYYTa+jhw7Nenb40gkAV8Ud THpnh3a1IfVu76prCa7g =TnpX -END PGP SIGNATURE- ___ 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] Adding a reference genome
Hi Stephen, Can you provide the error message from the job? You can look at bug-report for the the output dataset created by the data manager for the “Data Manager History (automatically created)” history in your saved histories. Also any other relevant information from the log would be great as well. Thanks for using Galaxy, Dan On Jun 12, 2014, at 8:24 PM, Stephen E sedwards...@hotmail.com wrote: I installed a local instance of galaxy approximately a month ago (build 2014.04.14) and have since updated to latest_2014.06.02. It is running on 64-bit Ubuntu 12.04. I'm having an issue with the Data Manager to fetch reference genomes (data_manager_fetch_genome_all_fasta, Rev. 2ebc856bce29). It will successfully submit a job to the queue but it quickly has an error. I'm selecting UCSC as the source and bosTau7 as UCSC's DBKEY for source FASTA. The only error/warning I see in the server logs seems related to samtools: galaxy.tools.deps DEBUG 2014-06-12 20:07:30,952 Building dependency shell command for dependency 'samtools' galaxy.tools.deps WARNING 2014-06-12 20:07:30,952 Failed to resolve dependency on 'samtools', ignoring Samtools 0.1.19 seems to be installed through galaxy and I also installed samtools through apt-get. I installed the apt-get version after the first time trying this didn't work. In the list of jobs, it has an error state and the command line is the following: python /home/stephen/Work/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/2ebc856bce29/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py /home/stephen/Work/galaxy-dist/database/files/000/dataset_22.dat --dbkey_description 'unspecified (?)' I need to use the bosTau7 (or perhaps bosTau6) cow reference genomes and can't figure out any other ways to properly load them into galaxy. I'd like them available for everything on the server and would prefer this over using a custom reference genome. I may be missing something obvious because the command line doesn't seem to specify the genome I want but I can't type anything new into the DBKEY to assign data field. How can I get the fetch genome data manager to work or otherwise load the bosTau7 reference genome into galaxy? Thanks, Stephen ___ 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] troubleshooting Galaxy with LSF
Just for my curiosity, are you running a python environment isolated for galaxy or just using a system wide python environment? Regards, Iyad Kandalaft Microbial Biodiversity Bioinformatics Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada 960 Carling Ave.| 960 Ave. Carling Ottawa, ON| Ottawa (ON) K1A 0C6 E-mail Address / Adresse courriel iyad.kandal...@agr.gc.ca Telephone | Téléphone 613-759-1228 Facsimile | Télécopieur 613-759-1701 Teletypewriter | Téléimprimeur 613-773-2600 Government of Canada | Gouvernement du Canada From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of INKozin Sent: Thursday, June 12, 2014 11:35 AM To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] troubleshooting Galaxy with LSF The problem seems to be with DRMAA for Python. While it works fine on the OpenSuse 12.1 box, I'm getting a segfault on RH 6.4. Surprisingly, the job however gets submitted and run successfully. ___ 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/
