Re: [galaxy-dev] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7
Thanks Sajoshca, that did help, along with replacing datatypes_conf.xml with datatypes_conf.xml.sample and tool_conf.xml with tool_conf.xml.samples (some of the migrated tools were not removed from this file). All in all...it's working now. Best, Liisa From: Sajoscha Sauer To: Liisa Koski Cc: "galaxy-dev@lists.bx.psu.edu Dev" Date: 11/04/2014 03:12 AM Subject:Re: [galaxy-dev] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7 Hi Liisa, For us, it was only copying the directory ?galaxy-dist/static/scripts/packed/viz? from a fresh install to the installation we wanted to update. I hope that helps! Cheers, Sajoscha On Apr 10, 2014, at 5:57 PM, Liisa Koski wrote: Hello, I just updated to Feb.10 and also noticed that Trackster is not working. I too get the blank screen. Could you please tell me how to manually update the vis packed files? I do not know what these are. Thanks in advance, Liisa ___ 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] trackster is not working on the vrelease_2014.02.10--2--29ce93a13ac7
Hello, I just updated to Feb.10 and also noticed that Trackster is not working. I too get the blank screen. Could you please tell me how to manually update the vis packed files? I do not know what these are. Thanks in advance, Liisa ___ 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] example_watch_folder.py problem importing file
Hello, I am testing the example_watch_folder.py script on my local instance of Galaxy (Feb.10 distribution). I have set up a simple workflow with the Fasta-to-Tabular tool. It takes a single input fasta file. Works in Galaxy UI. I have created input and output folders and followed the steps here http://gmod.827538.n3.nabble.com/Trouble-Shooting-example-watch-folder-py-td4030355.html But when I run the script and put a simple fasta file in the input folder I get the following error in the logs: galaxy.jobs.runners.drmaa DEBUG 2014-04-10 11:11:03,127 (1899) command is: python galaxy_dist_dev/tools/data_source/upload.py galaxy_dist_dev galaxy_dist_dev/database/tmp/tmpK40iV3galaxy_dist_dev/database/tmp/tmpx_5QyU 3802:galaxy_dist_dev/database/job_working_directory/001/1899/dataset_3802_files:galaxy_dist_dev/database/files/003/dataset_3802.dat; return_code=$?; cd galaxy_dist_dev; galaxy_dist_dev/set_metadata.sh ./database/files galaxy_dist_dev/database/job_working_directory/001/1899 . galaxy_dist_dev/universe_wsgi.ini galaxy_dist_dev/database/tmp/tmpK40iV3 galaxy_dist_dev/database/job_working_directory/001/1899/galaxy.json; sh -c "exit $return_code" galaxy.jobs.runners.drmaa DEBUG 2014-04-10 11:11:03,127 (1899) native specification is: -V -q all.q -l hostname="hostname.ca" galaxy.jobs.runners.drmaa INFO 2014-04-10 11:11:03,133 (1899) queued as 678390 galaxy.jobs DEBUG 2014-04-10 11:11:03,180 (1899) Persisting job destination (destination id: name_hwew) galaxy.jobs.runners.drmaa DEBUG 2014-04-10 11:11:03,579 (1899/678390) state change: job is running 10.1.1.111 - - [10/Apr/2014:11:11:07 -0400] "POST /api/workflows?key=dd3916dfb37dffc08f070f1e3503015a HTTP/1.1" 200 - "-" "Python-urllib/2.6" galaxy.jobs.runners.drmaa DEBUG 2014-04-10 11:11:07,778 (1899/678390) state change: job finished normally galaxy.jobs DEBUG 2014-04-10 11:11:08,082 setting dataset state to ERROR galaxy.jobs DEBUG 2014-04-10 11:11:08,227 job 1899 ended galaxy.datatypes.metadata DEBUG 2014-04-10 11:11:08,227 Cleaning up external metadata files galaxy.jobs DEBUG 2014-04-10 11:11:08,652 (1900) Working directory for job is: galaxy_dist_dev/database/job_working_directory/001/1900 galaxy.datatypes.metadata DEBUG 2014-04-10 11:11:08,770 Cleaning up external metadata files galaxy.jobs.handler INFO 2014-04-10 11:11:08,795 (1900) Job unable to run: one or more inputs in error state 10.202.22.186 - - [10/Apr/2014:11:11:31 -0400] "GET /history/list HTTP/1.1" 200 - "http://galaxy.server.ca:8080/root"; "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:11.0) Gecko/20100101 Firefox/11.0" And in the dataset itself in the resulting Galaxy history UI WARNING:galaxy.datatypes.registry:Overriding conflicting datatype with extension 'asn1', using datatype from galaxy_dist_dev/database/tmp/tmpK40iV3. Yesterday, before I did the upgrade to Feb.10. The input files would import (as a green dataset in the History UI) put be empty and say 'no peak' Thanks in advance for any help, Liisa ___ 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] Empty history pane
Our use was using the lastest Firefox release. I asked him to try FireFox Portable and that seemed to do the trick. It was a problem with his Firefox install. Thanks for you help, Liisa From: Dannon Baker To: Liisa Koski Cc: Galaxy Dev Date: 13/03/2014 06:39 PM Subject:Re: [galaxy-dev] Empty history pane If it's possible, can you check (or ask the user to check) if there are any javascript errors if you open the browser console when experiencing this failure? On Thu, Mar 13, 2014 at 2:07 PM, Liisa Koski wrote: Hello, Our site maintains a local Galaxy installation (Nov.4th distributuion). One of our usrers has lost the ability to view anything in his history pane. He is able to run tools and view the list of 'Saved Histories' in the middle pane but the History pane itself stays empty. When I impersonate him I can see his history pane. Very weird. Any insight would be much appreciated. Thanks, Liisa ___ 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] Empty history pane
Thanks Dannon, I set java to open the console (I assume that's what you are referring to) but when going to galaxy it doesn't open. The console does open when i go to java.com and verify my version. i've also just removed and reinstalled java and rebooted machine. still no history pane :( From: Dannon Baker To: Liisa Koski Cc: Galaxy Dev Date: 13/03/2014 06:39 PM Subject:Re: [galaxy-dev] Empty history pane If it's possible, can you check (or ask the user to check) if there are any javascript errors if you open the browser console when experiencing this failure? On Thu, Mar 13, 2014 at 2:07 PM, Liisa Koski wrote: Hello, Our site maintains a local Galaxy installation (Nov.4th distributuion). One of our usrers has lost the ability to view anything in his history pane. He is able to run tools and view the list of 'Saved Histories' in the middle pane but the History pane itself stays empty. When I impersonate him I can see his history pane. Very weird. Any insight would be much appreciated. Thanks, Liisa ___ 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] Empty history pane
Hello, Our site maintains a local Galaxy installation (Nov.4th distributuion). One of our usrers has lost the ability to view anything in his history pane. He is able to run tools and view the list of 'Saved Histories' in the middle pane but the History pane itself stays empty. When I impersonate him I can see his history pane. Very weird. Any insight would be much appreciated. Thanks, Liisa___ 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] Galaxy Reports link - registed users per month - does not work
Hello,
First..I love the Galaxy Reports tool...thanks so much for this.
I did however come across an error when trying to few the Registered Users
per month link. It would be really nice to have this working :)
Thanks in advance,
Liisa
URL: http://domain:9001/users/registered_users_per_month
Module paste.exceptions.errormiddleware:144 in __call__
>> app_iter = self.application(environ, sr_checker)
Module paste.debug.prints:106 in __call__
>> environ, self.app)
Module paste.wsgilib:543 in intercept_output
>> app_iter = application(environ, replacement_start_response)
Module paste.lint:170 in lint_app
>> iterator = application(environ, start_response_wrapper)
Module paste.recursive:84 in __call__
>> return self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
>> return self.application(environ, start_response)
Module galaxy.web.framework.base:132 in __call__
>> return self.handle_request( environ, start_response )
Module galaxy.web.framework.base:190 in handle_request
>> body = method( trans, **kwargs )
Module galaxy.webapps.reports.controllers.users:29 in
registered_users_per_month
>> for row in q.execute():
Module sqlalchemy.sql.expression:2841 in execute
Module sqlalchemy.engine.base:2453 in _execute_clauseelement
Module sqlalchemy.engine.base:1584 in _execute_clauseelement
Module sqlalchemy.engine.base:1698 in _execute_context
Module sqlalchemy.engine.base:1691 in _execute_context
Module sqlalchemy.engine.default:331 in do_execute
Module MySQLdb.cursors:173 in execute
Module MySQLdb.connections:36 in defaulterrorhandler
OperationalError: (OperationalError) (1305, 'FUNCTION
galaxy_production.date_trunc does not exist') 'SELECT date_trunc(%s,
date(galaxy_user.create_time)) AS date, count(galaxy_user.id) AS num_users
\nFROM galaxy_user GROUP BY date_trunc(%s, date(galaxy_user.create_time))
ORDER BY date DESC' ('month', 'month')
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Re: [galaxy-dev] Visualizations broken after Aug. 12 update
Thank you Jeremy, It turned out the issue was our version of bedtools. We updated to 2.17.0 and no longer have the errors. Cheers, Liisa From: Jeremy Goecks To: Liisa Koski Cc: "galaxy-dev@lists.bx.psu.edu Galaxy-dev" Date: 05/10/2013 08:08 PM Subject:Re: [galaxy-dev] Visualizations broken after Aug. 12 update You'll need to do two things: (1) Install wigToBigWig and bedtools; see steps 2 and 3 here: http://wiki.galaxyproject.org/Visualization%20Setup (2) Update your datatypes_conf.xml file: If you haven't made changes to your datatypes_conf.xml file, you can just copy datatypes_conf.xml.sample to datatypes_conf.xml to get the needed converters. If you've made changes to datatypes_conf.xml, you'll need to manually add the needed converters. We recently transitioned all the *_to_summary_tree converters to *_to_bigwig, so you'll want to remove the summary_tree converters and replace them with the bigwig converters. Let us know if you have any problems/questions. Best, J. On Oct 3, 2013, at 1:33 PM, Liisa Koski wrote: Hello, We recently updated to the Aug.12 distribution. I u commented the visualizations_config_directory = config/visualizations in the universe file and when I restarted and tried to view past Trackster Visualizations none of my tracks load. I get the error displayed in the track itself: Cannot display dataset due to an error. View error. Try again. When I click on View error I get pop up with this for my gff3 track: Input error: Cannot split into blocks. Found interval with fewer than 12 columns. needLargeMem: trying to allocate 0 bytes (limit: 17179869184) With this for my BAM track: grep: /Galaxy/galaxy_dist/database/files/016/dataset_16392.dat: No such file or directory needLargeMem: trying to allocate 0 bytes (limit: 17179869184) All tracks in all published Visualizations are no longer loading. I do not see any errors in the log files. I have also updated my datatypes.conf file by copying over datatypes.conf.sample Any help would be much appreciated. Thanks in advance, Liisa ___ 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] Visualizations broken after Aug. 12 update
Hello, We recently updated to the Aug.12 distribution. I u commented the visualizations_config_directory = config/visualizations in the universe file and when I restarted and tried to view past Trackster Visualizations none of my tracks load. I get the error displayed in the track itself: Cannot display dataset due to an error. View error. Try again. When I click on View error I get pop up with this for my gff3 track: Input error: Cannot split into blocks. Found interval with fewer than 12 columns. needLargeMem: trying to allocate 0 bytes (limit: 17179869184) With this for my BAM track: grep: /Galaxy/galaxy_dist/database/files/016/dataset_16392.dat: No such file or directory needLargeMem: trying to allocate 0 bytes (limit: 17179869184) All tracks in all published Visualizations are no longer loading. I do not see any errors in the log files. I have also updated my datatypes.conf file by copying over datatypes.conf.sample Any help would be much appreciated. Thanks in advance, Liisa ___ 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] Can't specify workflow parameters for integer values
Hello,
I created a simple workflow with an input file and the 'Select first'
tool. I wanted the value to be a parameter ${value}. I am able to save the
workflow and see the little grey parameters box at the top of the workflow
editor.
When I try to run this workflow I get a yellow box at the top of the
window stating the following:
Problems were encountered when loading this workflow, likely due to tool
version changes. Missing parameter values have been replaced with default.
Please review the parameter values below.
I do not however see an error in paster.log
When I reopen the workflow in the editor I get a popup window saying
'Workflow loaded with changes'
Problems were encountered loading this workflow (possibly a result of tool
upgrades). Please review the following parameters and then save.
Step 2: Select first
Value no longer valid for 'Select first', replaced with default
I am running two instances of Galaxy (Jan. 11 distributuion) and this
occurs in both of my instances. Will other workflows as well. But it
appears to only occur for integer parameters...not text parameters.
Any help would be much appreciated.
Liisa
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[galaxy-dev] maximum recursion depth exceeded while calling a Python object
Hi, I'm running a local instance of Galaxy and no matter what tool I run I get the following error: Error executing tool: maximum recursion depth exceeded while calling a Python object In the log file: galaxy.tools ERROR 2013-01-25 14:06:54,375 Exception caught while attempting tool execution: Traceback (most recent call last): File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1776, in handle_input _, out_data = self.execute( trans, incoming=params, history=history ) File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 2103, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/Galaxy/galaxy_dist/lib/galaxy/tools/actions/__init__.py", line 203, in execute chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name File "/Galaxy/galaxy_dist/lib/galaxy/model/__init__.py", line 1161, in get_converted_dataset new_dataset = self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, set_output_history=False ).values()[0] File "/Galaxy/galaxy_dist/lib/galaxy/datatypes/data.py", line 467, in convert_dataset converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 2103, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/Galaxy/galaxy_dist/lib/galaxy/tools/actions/__init__.py", line 203, in execute chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name File "/Galaxy/galaxy_dist/lib/galaxy/model/__init__.py", line 1161, in get_converted_dataset new_dataset = self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, set_output_history=False ).values()[0] File "/Galaxy/galaxy_dist/lib/galaxy/datatypes/data.py", line 467, in convert_dataset converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 2103, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/Galaxy/galaxy_dist/lib/galaxy/tools/actions/__init__.py", line 203, in execute chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name File "/Galaxy/galaxy_dist/lib/galaxy/model/__init__.py", line 1161, in get_converted_dataset new_dataset = self.datatype.convert_dataset( trans, self, target_ext, return_output=True, visible=False, deps=deps, set_output_history=False ).values()[0] File "/Galaxy/galaxy_dist/lib/galaxy/datatypes/data.py", line 467, in convert_dataset converted_dataset = converter.execute( trans, incoming=params, set_output_hid=visible, set_output_history=set_output_history)[1] File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 2103, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) thousands of lines here...ending with... File "/Galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py", line 760, in _make_proxy selectable.columns.add(c) File "/Galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/expression.py", line 1668, in add self[column.key] = column File "/Galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/expression.py", line 1671, in __setitem__ if key in self: File "/Galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/sql/expression.py", line 1702, in __contains__ return util.OrderedProperties.__contains__(self, other) File "/Galaxy/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/util.py", line 652, in __contains__ return key in self._data RuntimeError: maximum recursion depth exceeded while calling a Python object Any help would be much appreciated, Thanks in advance, Liisa ___ 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/
Re: [galaxy-dev] Fw: Error when attempting to install new distributuion - TypeError: Invalid argument(s) 'server_side_cursors', 'max_overflow'
Yes that worked! Thanks,
Liisa
From: Jeremy Goecks
To: Liisa Koski
Cc:
Date: 23/01/2013 11:02 PM
Subject:Re: [galaxy-dev] Fw: Error when attempting to install new
distributuion - TypeError: Invalid argument(s) 'server_side_cursors',
'max_overflow'
My guess is that you'll need to comment out some database options in your
universe_wsgi.ini file that are valid for MySQL but not for SQLite.
Specifically, database_engine_option_max_overflow and perhaps other
options as well.
Best,
J.
On Jan 23, 2013, at 1:54 PM, Liisa Koski wrote:
Hello,
I am attempting to install a new galaxy-dist and am running into the
following error. I first tried it by using a mysql database but this error
also occurs when I use the default SQLite database.
Any help would be much appreciated.
Thanks in advance,
Liisa
[galaxy-dev]$ ./run.sh
Some eggs are out of date, attempting to fetch...
Fetched
http://eggs.galaxyproject.org/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.6-linux-x86_64-ucs4.egg
Fetch successful.
galaxy-dev/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
RuntimeWarning: __builtin__.file size changed, may indicate binary
incompatibility
from csamtools import *
python path is: galaxy-dev/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/boto-2.5.2-py2.6.egg,
galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/Fabric-1.4.2-py2.6.egg,
galaxy-dev/eggs/ssh-1.7.14-py2.6.egg,
galaxy-dev/eggs/Whoosh-0.3.18-py2.6.egg,
galaxy-dev/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/amqplib-0.6.1-py2.6.egg,
galaxy-dev/eggs/pexpect-2.4-py2.6.egg,
galaxy-dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
galaxy-dev/eggs/Babel-0.9.4-py2.6.egg,
galaxy-dev/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/Mako-0.4.1-py2.6.egg,
galaxy-dev/eggs/WebHelpers-0.2-py2.6.egg,
galaxy-dev/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/wchartype-0.1-py2.6.egg,
galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg,
galaxy-dev/eggs/docutils-0.7-py2.6.egg,
galaxy-dev/eggs/WebOb-0.8.5-py2.6.egg,
galaxy-dev/eggs/Routes-1.12.3-py2.6.egg,
galaxy-dev/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/PasteDeploy-1.3.3-py2.6.egg,
galaxy-dev/eggs/PasteScript-1.7.3-py2.6.egg,
galaxy-dev/eggs/Paste-1.6-py2.6.egg, galaxy-dev/lib,
/usr/lib64/python2.6/site-packages/distribute-0.6.12-py2.6.egg,
/usr/lib64/python2.6/site-packages/blist-1.3.4-py2.6-linux-x86_64.egg,
/usr/lib/python2.6/site-packages/nose-1.0.0-py2.6.egg,
/usr/lib/python2.6/site-packages/argparse-1.2.1-py2.6.egg,
/usr/lib/python2.6/site-packages/pip-1.2.1-py2.6.egg,
/usr/lib/python2.6/site-packages, /usr/lib64/python2.6/xml/etree,
/usr/lib64/python26.zip, /usr/lib64/python2.6,
/usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk,
/usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload,
/usr/lib64/python2.6/site-packages/PIL,
/usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg-info,
/usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg-info,
/usr/lib64/python2.6/site-packages
galaxy.tool_shed.tool_shed_registry DEBUG 2013-01-21 13:52:06,034 Loading
references to tool sheds from tool_sheds_conf.xml
galaxy.tool_shed.tool_shed_registry DEBUG 2013-01-21 13:52:06,034 Loaded
reference to tool shed: Galaxy main tool shed
galaxy.tool_shed.tool_shed_registry DEBUG 2013-01-21 13:52:06,034 Loaded
reference to tool shed: Galaxy test tool shed
galaxy.model.migrate.check DEBUG 2013-01-21 13:52:06,112 pysqlite>=2 egg
successfully loaded for sqlite dialect
Traceback (most recent call last):
File "galaxy-dev/lib/galaxy/webapps/galaxy/buildapp.py", line 36, in
app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "galaxy-dev/lib/galaxy/app.py", line 45, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
).get( '__file__', None ), self.config.database_engine_options, app=self )
File "galaxy-dev/lib/galaxy/model/migrate/check.py", line 46, in
create_or_verify_database
engine = create_engine( url, **engine_options )
File
"galaxy-dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/__init__.py",
line 223, in create_engine
return strategy.create(*args, **kwargs)
File
"galaxy-dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/strategies.py",
line 121, in create
engineclass.__name__))
TypeError: Invalid argument(s) 'server_side_cursors','max_overflow' sent
to create_engine(), using configuration
SQLi
[galaxy-dev] Fw: Error when attempting to install new distributuion - TypeError: Invalid argument(s) 'server_side_cursors', 'max_overflow'
Hello,
I am attempting to install a new galaxy-dist and am running into the
following error. I first tried it by using a mysql database but this error
also occurs when I use the default SQLite database.
Any help would be much appreciated.
Thanks in advance,
Liisa
[galaxy-dev]$ ./run.sh
Some eggs are out of date, attempting to fetch...
Fetched
http://eggs.galaxyproject.org/pysqlite/pysqlite-2.5.6_3.6.17_static-py2.6-linux-x86_64-ucs4.egg
Fetch successful.
galaxy-dev/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1:
RuntimeWarning: __builtin__.file size changed, may indicate binary
incompatibility
from csamtools import *
python path is: galaxy-dev/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/boto-2.5.2-py2.6.egg,
galaxy-dev/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/Fabric-1.4.2-py2.6.egg,
galaxy-dev/eggs/ssh-1.7.14-py2.6.egg,
galaxy-dev/eggs/Whoosh-0.3.18-py2.6.egg,
galaxy-dev/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/amqplib-0.6.1-py2.6.egg,
galaxy-dev/eggs/pexpect-2.4-py2.6.egg,
galaxy-dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,
galaxy-dev/eggs/Babel-0.9.4-py2.6.egg,
galaxy-dev/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/Mako-0.4.1-py2.6.egg,
galaxy-dev/eggs/WebHelpers-0.2-py2.6.egg,
galaxy-dev/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/wchartype-0.1-py2.6.egg,
galaxy-dev/eggs/elementtree-1.2.6_20050316-py2.6.egg,
galaxy-dev/eggs/docutils-0.7-py2.6.egg,
galaxy-dev/eggs/WebOb-0.8.5-py2.6.egg,
galaxy-dev/eggs/Routes-1.12.3-py2.6.egg,
galaxy-dev/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg,
galaxy-dev/eggs/PasteDeploy-1.3.3-py2.6.egg,
galaxy-dev/eggs/PasteScript-1.7.3-py2.6.egg,
galaxy-dev/eggs/Paste-1.6-py2.6.egg, galaxy-dev/lib,
/usr/lib64/python2.6/site-packages/distribute-0.6.12-py2.6.egg,
/usr/lib64/python2.6/site-packages/blist-1.3.4-py2.6-linux-x86_64.egg,
/usr/lib/python2.6/site-packages/nose-1.0.0-py2.6.egg,
/usr/lib/python2.6/site-packages/argparse-1.2.1-py2.6.egg,
/usr/lib/python2.6/site-packages/pip-1.2.1-py2.6.egg,
/usr/lib/python2.6/site-packages, /usr/lib64/python2.6/xml/etree,
/usr/lib64/python26.zip, /usr/lib64/python2.6,
/usr/lib64/python2.6/plat-linux2, /usr/lib64/python2.6/lib-tk,
/usr/lib64/python2.6/lib-old, /usr/lib64/python2.6/lib-dynload,
/usr/lib64/python2.6/site-packages/PIL,
/usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg-info,
/usr/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg-info,
/usr/lib64/python2.6/site-packages
galaxy.tool_shed.tool_shed_registry DEBUG 2013-01-21 13:52:06,034 Loading
references to tool sheds from tool_sheds_conf.xml
galaxy.tool_shed.tool_shed_registry DEBUG 2013-01-21 13:52:06,034 Loaded
reference to tool shed: Galaxy main tool shed
galaxy.tool_shed.tool_shed_registry DEBUG 2013-01-21 13:52:06,034 Loaded
reference to tool shed: Galaxy test tool shed
galaxy.model.migrate.check DEBUG 2013-01-21 13:52:06,112 pysqlite>=2 egg
successfully loaded for sqlite dialect
Traceback (most recent call last):
File "galaxy-dev/lib/galaxy/webapps/galaxy/buildapp.py", line 36, in
app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File "galaxy-dev/lib/galaxy/app.py", line 45, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {}
).get( '__file__', None ), self.config.database_engine_options, app=self )
File "galaxy-dev/lib/galaxy/model/migrate/check.py", line 46, in
create_or_verify_database
engine = create_engine( url, **engine_options )
File
"galaxy-dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/__init__.py",
line 223, in create_engine
return strategy.create(*args, **kwargs)
File
"galaxy-dev/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/strategies.py",
line 121, in create
engineclass.__name__))
TypeError: Invalid argument(s) 'server_side_cursors','max_overflow' sent
to create_engine(), using configuration
SQLiteDialect/SingletonThreadPool/TLEngine. Please check that the keyword
arguments are appropriate for this combination of components.___
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/
Re: [galaxy-dev] DRMAA runner weirdness
In our case someone had installed and started a second development instance of galaxy but used the same database as the first development instance. So the ids were mixed up and and causing some jobs to crash. Yuck! Thanks, Liisa From: Nate Coraor To: Liisa Koski Cc: kellr...@soe.ucsc.edu, "galaxy-dev@lists.bx.psu.edu" , galaxy-dev-boun...@lists.bx.psu.edu Date: 14/01/2013 10:48 AM Subject:Re: [galaxy-dev] DRMAA runner weirdness On Jan 11, 2013, at 9:32 AM, Liisa Koski wrote: > Hello, > Can you please post the link to this patch? I do not see it in the mail thread and I too have noticed some issues with the DRMAA job running since updating to the Oct. 23rd distribution. I don't know if it is related yet but I'd like to try the patch to see. I have two local instances of Galaxy (prod and dev). On my dev instance (which is fully up to date), when I run the same job multiple times, sometimes it finishes and sometimes it dies, this is independent of which node it runs on. My prod instance is still at the Oct. 03 distribution and does not experience this problem. So I am afraid to update our production instance. > > Thanks in advance, > Liisa Hi Liisa, Here's the one that Kyle is referring to: https://bitbucket.org/galaxy/galaxy-central/commits/c015b82b3944f967e2c859d5552c00e3e38a2da0 However, this patch should only fix the problem of the server segfaulting when deleting certain jobs (ones that have not yet been dispatched to the cluster). --nate > > > > > From:Kyle Ellrott > To:Nate Coraor > Cc:"galaxy-dev@lists.bx.psu.edu" > Date:10/01/2013 07:44 PM > Subject:Re: [galaxy-dev] DRMAA runner weirdness > Sent by:galaxy-dev-boun...@lists.bx.psu.edu > > > > I did a merge of galaxy-central that included the patch you posted today. The scheduling problem seems to have gone away. Although I'm still getting back 'Job output not returned from cluster' for errors. This seems odd, as the system previously would output stderr correctly. > > Kyle > > > On Thu, Jan 10, 2013 at 8:30 AM, Nate Coraor wrote: > On Jan 9, 2013, at 12:18 AM, Kyle Ellrott wrote: > > > I'm running a test Galaxy system on a cluster (merged galaxy-dist on Janurary 4th). And I've noticed some odd behavior from the DRMAA job runner. > > I'm running a multithread system, one web server, one job_manager, and three job_handlers. DRMAA is the default job runner (the command for tophat2 is drmaa://-V -l mem_total=7G -pe smp 2/), with SGE 6.2u5 being the engine underneath. > > > > My test involves trying to run three different Tophat2 jobs. The first two seem to start up (and get put on the SGE queue), but the third stays grey, with the job manager listing it in state 'new' with command line 'None'. It doesn't seem to leave this state. Both of the jobs that actually got onto the queue die (reasons unknown, but much to early, probably some tophat/bowtie problem), but one job is listed in error state with stderr as 'Job output not returned from cluster', while the other job (which is no longer in the SGE queue) is still listed as running. > > Hi Kyle, > > It sounds like there are bunch of issues here. Do you have any limits set as to the number of concurrent jobs allowed? If not, you may need to add a bit of debugging information to the manager or handler code to figure out why the 'new' job is not being dispatched for execution. > > For the 'error' job, more information about output collection should be available from the Galaxy server log. If you have general SGE problems this may not be Galaxy's fault. You do need to make sure that the stdout/stderr files are able to be properly copied back to the Galaxy server upon job completion. > > For the 'running' job, make sure you've got 'set_metadata_externally = True' in your Galaxy config. > > --nate > > > > > Any ideas? > > > > > > Kyle > > ___ > > 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/ > > ___ > 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/ ___ 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/
Re: [galaxy-dev] DRMAA runner weirdness
Hello, Can you please post the link to this patch? I do not see it in the mail thread and I too have noticed some issues with the DRMAA job running since updating to the Oct. 23rd distribution. I don't know if it is related yet but I'd like to try the patch to see. I have two local instances of Galaxy (prod and dev). On my dev instance (which is fully up to date), when I run the same job multiple times, sometimes it finishes and sometimes it dies, this is independent of which node it runs on. My prod instance is still at the Oct. 03 distribution and does not experience this problem. So I am afraid to update our production instance. Thanks in advance, Liisa From: Kyle Ellrott To: Nate Coraor Cc: "galaxy-dev@lists.bx.psu.edu" Date: 10/01/2013 07:44 PM Subject:Re: [galaxy-dev] DRMAA runner weirdness Sent by:galaxy-dev-boun...@lists.bx.psu.edu I did a merge of galaxy-central that included the patch you posted today. The scheduling problem seems to have gone away. Although I'm still getting back 'Job output not returned from cluster' for errors. This seems odd, as the system previously would output stderr correctly. Kyle On Thu, Jan 10, 2013 at 8:30 AM, Nate Coraor wrote: On Jan 9, 2013, at 12:18 AM, Kyle Ellrott wrote: > I'm running a test Galaxy system on a cluster (merged galaxy-dist on Janurary 4th). And I've noticed some odd behavior from the DRMAA job runner. > I'm running a multithread system, one web server, one job_manager, and three job_handlers. DRMAA is the default job runner (the command for tophat2 is drmaa://-V -l mem_total=7G -pe smp 2/), with SGE 6.2u5 being the engine underneath. > > My test involves trying to run three different Tophat2 jobs. The first two seem to start up (and get put on the SGE queue), but the third stays grey, with the job manager listing it in state 'new' with command line 'None'. It doesn't seem to leave this state. Both of the jobs that actually got onto the queue die (reasons unknown, but much to early, probably some tophat/bowtie problem), but one job is listed in error state with stderr as 'Job output not returned from cluster', while the other job (which is no longer in the SGE queue) is still listed as running. Hi Kyle, It sounds like there are bunch of issues here. Do you have any limits set as to the number of concurrent jobs allowed? If not, you may need to add a bit of debugging information to the manager or handler code to figure out why the 'new' job is not being dispatched for execution. For the 'error' job, more information about output collection should be available from the Galaxy server log. If you have general SGE problems this may not be Galaxy's fault. You do need to make sure that the stdout/stderr files are able to be properly copied back to the Galaxy server upon job completion. For the 'running' job, make sure you've got 'set_metadata_externally = True' in your Galaxy config. --nate > > Any ideas? > > > Kyle > ___ > 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] Can't edit galaxy workflow
Hi, Can you please send the entire link to access this changeset? I keep searching for 5013377e0bf7 but can not find it. Thanks in advance, Liisa From: Dannon Baker To: Sanjarbek Hudaiberdiev Cc: galaxy-...@bx.psu.edu Date: 13/11/2012 12:34 PM Subject:Re: [galaxy-dev] Can't edit galaxy workflow Sent by:galaxy-dev-boun...@lists.bx.psu.edu Sanjar, This is fixed as of 5013377e0bf7. This may not be in the next distribution, but will be in the one after that. Of course, you can manually pull the change from galaxy-central at any time. -Dannon On Nov 13, 2012, at 9:45 AM, Sanjarbek Hudaiberdiev wrote: > I tried to reply to similar posts, but couldn't figure out how to do it. So posting again: > > Galaxy giving this error when editing workflow, just after creating workflow from existing history: > > URL: http://localhost/galaxy/workflow/load_workflow?id=df7a1f0c02a5b08e&_=1352817462148 > Module weberror.evalexception.middleware:364 in respond > >> app_iter = self.application(environ, detect_start_response) > Module paste.debug.prints:98 in __call__ > >> environ, self.app) > Module paste.wsgilib:539 in intercept_output > >> app_iter = application(environ, replacement_start_response) > Module paste.recursive:80 in __call__ > >> return self.application(environ, start_response) > Module paste.httpexceptions:632 in __call__ > >> return self.application(environ, start_response) > Module galaxy.web.framework.base:160 in __call__ > >> body = method( trans, **kwargs ) > Module galaxy.web.framework:73 in decorator > >> return simplejson.dumps( func( self, trans, *args, **kwargs ) ) > Module galaxy.webapps.galaxy.controllers.workflow:733 in load_workflow > >> 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), > Module galaxy.workflow.modules:258 in get_tooltip > >> return self.tool.help.render( static_path=static_path ) > AttributeError: 'NoneType' object has no attribute 'render' > > Could anyone help me to solve this problem? > > Thanks, > Sanjar. > ___ > 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] Error when running cleanup_datasets.py
That did it! Thanks Nate! From: Nate Coraor To: Liisa Koski Cc: galaxy-dev@lists.bx.psu.edu Date: 12/11/2012 12:13 PM Subject:Re: [galaxy-dev] Error when running cleanup_datasets.py On Nov 8, 2012, at 8:55 PM, Liisa Koski wrote: > Hi Nate, > I'm back to trying to figure this out again as I am running out of disk space. I added the bit of code you suggested below, but I don't think it helped, I'm not so familiar with python. > > I'm now running Galaxy Reports and it tells me that I have 7479 datasets that were deleted but have not yet been purged. > > I get the error below when I run cleanup_datasets.py with both the -5 and -4 flag > > Marking as deleted: LibraryDatasetDatasetAssociation id 6907 (for dataset id 51991) > Deleting dataset id 51991 > Deleting library dataset id 7225 > Traceback (most recent call last): > File "scripts/cleanup_datasets/cleanup_datasets.py", line 526, in > if __name__ == "__main__": main() > File "scripts/cleanup_datasets/cleanup_datasets.py", line 124, in main > purge_folders( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry ) > File "scripts/cleanup_datasets/cleanup_datasets.py", line 247, in purge_folders > _purge_folder( folder, app, remove_from_disk, info_only = info_only ) > File "scripts/cleanup_datasets/cleanup_datasets.py", line 499, in _purge_folder > _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) > File "scripts/cleanup_datasets/cleanup_datasets.py", line 499, in _purge_folder > _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) > File "scripts/cleanup_datasets/cleanup_datasets.py", line 497, in _purge_folder > _purge_dataset_instance( ldda, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable > File "scripts/cleanup_datasets/cleanup_datasets.py", line 373, in _purge_dataset_instance > log.debug( '%s %s has None dataset' % ( type( dataset_instance ), dataset_instance.id ) ) > AttributeError: 'NoneType' object has no attribute 'id' Ah, I was looking at the wrong level. You have a library_dataset without an associated library_dataset_dataset_association. The following SQL should return it and any others: select id from library_dataset where library_dataset_dataset_association_id is null Although the output indicates that the offending library_dataset id should be 7225. The easiest way to solve this problem is probably to orphan the broken library dataset, e.g.: update library_dataset set folder_id = null where id=7225; --nate > > Thanks in advance for your help, > Liisa > > > > > > From: Nate Coraor > To:Liisa Koski > Cc:galaxy-dev@lists.bx.psu.edu > Date:02/10/2012 10:50 AM > Subject:Re: [galaxy-dev] Error when running cleanup_datasets.py > > > > On Oct 2, 2012, at 10:44 AM, Liisa Koski wrote: > > > Hi Nate, > > That select statement does not return anything :( > > Could you add a bit of debugging to the script to see what the id is of the dataset_instance that has a None dataset? > > if dataset_instance is None: >log.debug( '%s %s has None dataset' % ( type( dataset_instance ), dataset_instance.id ) ) > > Thanks, > --nate > > > > > Thanks, > > Liisa > > > > > > > > > > > > From:Nate Coraor > > To:Liisa Koski > > Cc:galaxy-dev@lists.bx.psu.edu > > Date:01/10/2012 01:01 PM > > Subject:Re: [galaxy-dev] Error when running cleanup_datasets.py > > > > > > > > On Sep 24, 2012, at 10:41 AM, Liisa Koski wrote: > > > > > Hello, > > > I am trying to run the cleanup scripts on my local installation but get stuck when trying to run the following: > > > > > > ./scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 10 -5 -r > > > > > > Deleting library dataset id 7225 > > > Traceback (most recent call last): > > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 524, in > > > if __name__ == "__main__": main() > > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 124, in main > > > purge_folders( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_ret
Re: [galaxy-dev] Error when running cleanup_datasets.py
Hi Nate, I'm back to trying to figure this out again as I am running out of disk space. I added the bit of code you suggested below, but I don't think it helped, I'm not so familiar with python. I'm now running Galaxy Reports and it tells me that I have 7479 datasets that were deleted but have not yet been purged. I get the error below when I run cleanup_datasets.py with both the -5 and -4 flag Marking as deleted: LibraryDatasetDatasetAssociation id 6907 (for dataset id 51991) Deleting dataset id 51991 Deleting library dataset id 7225 Traceback (most recent call last): File "scripts/cleanup_datasets/cleanup_datasets.py", line 526, in if __name__ == "__main__": main() File "scripts/cleanup_datasets/cleanup_datasets.py", line 124, in main purge_folders( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry ) File "scripts/cleanup_datasets/cleanup_datasets.py", line 247, in purge_folders _purge_folder( folder, app, remove_from_disk, info_only = info_only ) File "scripts/cleanup_datasets/cleanup_datasets.py", line 499, in _purge_folder _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) File "scripts/cleanup_datasets/cleanup_datasets.py", line 499, in _purge_folder _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) File "scripts/cleanup_datasets/cleanup_datasets.py", line 497, in _purge_folder _purge_dataset_instance( ldda, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable File "scripts/cleanup_datasets/cleanup_datasets.py", line 373, in _purge_dataset_instance log.debug( '%s %s has None dataset' % ( type( dataset_instance ), dataset_instance.id ) ) AttributeError: 'NoneType' object has no attribute 'id' Thanks in advance for your help, Liisa From: Nate Coraor To: Liisa Koski Cc: galaxy-dev@lists.bx.psu.edu Date: 02/10/2012 10:50 AM Subject:Re: [galaxy-dev] Error when running cleanup_datasets.py On Oct 2, 2012, at 10:44 AM, Liisa Koski wrote: > Hi Nate, > That select statement does not return anything :( Could you add a bit of debugging to the script to see what the id is of the dataset_instance that has a None dataset? if dataset_instance is None: log.debug( '%s %s has None dataset' % ( type( dataset_instance ), dataset_instance.id ) ) Thanks, --nate > > Thanks, > Liisa > > > > > > From:Nate Coraor > To:Liisa Koski > Cc:galaxy-dev@lists.bx.psu.edu > Date:01/10/2012 01:01 PM > Subject:Re: [galaxy-dev] Error when running cleanup_datasets.py > > > > On Sep 24, 2012, at 10:41 AM, Liisa Koski wrote: > > > Hello, > > I am trying to run the cleanup scripts on my local installation but get stuck when trying to run the following: > > > > ./scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 10 -5 -r > > > > Deleting library dataset id 7225 > > Traceback (most recent call last): > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 524, in > > if __name__ == "__main__": main() > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 124, in main > > purge_folders( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry ) > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 247, in purge_folders > > _purge_folder( folder, app, remove_from_disk, info_only = info_only ) > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 497, in _purge_folder > > _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 497, in _purge_folder > > _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 495, in _purge_folder > > _purge_dataset_instance( ldda, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable > > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 376, in _purge_dataset_instance > > ( dataset_instance.__class__.__name__, dataset_instance.id, dataset_instance.dataset.id ) > > AttributeError: 'NoneType' object has no attribute 'id' > > Hi Liisa, > > It'd
[galaxy-dev] How to get a shedtool to run locally
Hello, I've installed a tool to my local Galaxy installation via my local ToolShed. I would like to run this tool locally, and not have it submitted to the grid. I have tried two ids in the universe_wsgi.ini [galaxy:tool_runners] section. The tool id directly from the tool.xml file and the id from the shed_tool_conf.xml (same id found in the integrated_tool_panel.xml) tool = local:/// galaxy.server:9009/repos/user/tool/1.0 = local:/// My job still gets submitted to the grid. Any help would be much appreciated. Thanks, Liisa ___ 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/
Re: [galaxy-dev] Error when running cleanup_datasets.py
Hi Nate, That select statement does not return anything :( Thanks, Liisa From: Nate Coraor To: Liisa Koski Cc: galaxy-dev@lists.bx.psu.edu Date: 01/10/2012 01:01 PM Subject:Re: [galaxy-dev] Error when running cleanup_datasets.py On Sep 24, 2012, at 10:41 AM, Liisa Koski wrote: > Hello, > I am trying to run the cleanup scripts on my local installation but get stuck when trying to run the following: > > ./scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 10 -5 -r > > Deleting library dataset id 7225 > Traceback (most recent call last): > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 524, in > if __name__ == "__main__": main() > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 124, in main > purge_folders( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry ) > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 247, in purge_folders > _purge_folder( folder, app, remove_from_disk, info_only = info_only ) > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 497, in _purge_folder > _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 497, in _purge_folder > _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 495, in _purge_folder > _purge_dataset_instance( ldda, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable > File "./scripts/cleanup_datasets/cleanup_datasets.py", line 376, in _purge_dataset_instance > ( dataset_instance.__class__.__name__, dataset_instance.id, dataset_instance.dataset.id ) > AttributeError: 'NoneType' object has no attribute 'id' Hi Liisa, It'd appear that you have a library_dataset_dataset_association in your dataset that lacks an associated dataset. Does 'select id from library_dataset_dataset_association where dataset_id is null' in your database return anything? --nate > > > Any help would be much appreciated. > > Thanks, > Liisa > ___ > 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/ ___ 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/
[galaxy-dev] Can't create custom visualization
Hello,
I'm trying to create a custom visualization in Trackster. I am doing the
following steps. Visualization -> New Visualization -> Add a Custom Build
I get directed to the url below:
http://galaxy.ca:8080/user/dbkeys?use_panels=True
But the web page says:
Server Error
An error occurred. See the error logs for more information. (Turn debug on
to display exception reports here)
My paster.log file shows the following:
WSGI Variables
--
application:
paste.cookies: (,
'__utma=99541067.1404064366.1320847925.1320847925.1320857512.2;
galaxysession=c6ca0ddb55be603a67ec94afb2c9a07cafdf91af0226f4689d096411ea1bc0c1004977df81ecca90;
galaxycommunitysession=eb142648ac45b770e95464ae1d51cc6457899dd48ca7f3e61a826ece0a2b5d2a65f4ac4aabb6e5e9;
toolshedgalaxyurl="http://martin.dnalandmarks.ca:8080/";;
galaxyreportssession=c6ca0ddb55be603a922aa045b4afae662fca8487217f2ea25e5b488dcf5d52aefac5347681c8bf98')
paste.expected_exceptions: []
paste.httpexceptions:
paste.httpserver.thread_pool:
paste.parsed_querystring: ([('use_panels', 'True')], 'use_panels=True')
paste.recursive.forward:
paste.recursive.include:
paste.recursive.include_app_iter:
paste.recursive.script_name: ''
paste.throw_errors: True
webob._parsed_query_vars: (MultiDict([('use_panels', 'True')]),
'use_panels=True')
wsgi process: 'Multithreaded'
Any help would be much appreciated.
Thanks,
Liisa
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Re: [galaxy-dev] problem installing blast_datatypes manually
Thanks Peter, It was in fact the snffier type. I changed it to I am using the July07 distribution. The reason I installed the datatypes manually is because when I did it via the directions with the toolshed all my workflows that used blast tools were broken. They could no longer find the blast tools. So I immediately removed the toolshed installation and tried to set up as before. With the blast wrappers back in the tools/ncbi_blast_plus directory. Now my workflows are functional again. Thanks for your help, Liisa From: Peter Cock To: "galaxy-dev@lists.bx.psu.edu" Cc: Liisa Koski Date: 26/09/2012 04:33 AM Subject:Re: [galaxy-dev] problem installing blast_datatypes manually On Tue, Sep 25, 2012 at 8:39 PM, Peter Cock wrote: > On Tuesday, September 25, 2012, Liisa Koski wrote: >> >> Hello, >> I followed the instructions below to manually install the blast_datatypes: >> >> Manual Installation >> === >> >> Normally you would install this via the Galaxy ToolShed, which would move >> the provided blast.py file into a suitable location and process the >> datatypes_conf.xml entry to be combined with your local configuration. >> >> However, if you really want to this should work for a manual install. Add >> the following line to the datatypes_conf.xml file in the Galaxy main >> folder: >> >>> mimetype="application/xml" display_in_upload="true"/> >> >> Also create the file lib/galaxy/datatypes/blast.py by moving, copying or >> linking the blast.py file provided in this tar-ball. Finally add 'import blast' >> near >> the start of file lib/galaxy/datatypes/registry.py (after the other import >> lines). >> >> = >> >> I restarted my local Galaxy instance but still get this error. >> >> WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype >> 'galaxy.datatypes.xml:BlastXml' to sniff_order: 'module' object has no >> attribute 'BlastXml' >> >> >> Any help would be much appreciated. >> Thanks, >> Liisa > > > The error message sounds like your XML file is using the old location of the > BlastXml class (it used to be in an xml.py file, now it is in blast.py > instead). Can you grep the XML file for Blast? (Use -I for case insensitive) > > Sadly right now our Galaxy server is offline (suspected disk failure), so I > may not be able to double check what is on our machine. I'll try to have a > look at work tomorrow though. My guess is you have this, with an out of date sniffer line from when BLAST+ was part of the main distribution: And you should have: $ grep -i blast datatypes_conf.xml Or, if you leave out the sniffer: $ grep -i blast datatypes_conf.xml The sniffer is important to allow the user to upload BLAST XML files and have them automatically recognised as such. I see that I had not mentioned that in the tool's README file, an oversight I will fix in the next upload to the tool shed: https://bitbucket.org/peterjc/galaxy-central/changeset/5cefd5d5536ea9bc11021c4c1e0b8937175e4ba1 > (Out of interest, was there a reason you didn't use the automatic install > from the ToolShed?) I should probably have also checked - are you running a recent version of Galaxy where the NCBI BLAST+ wrappers have been removed from the core distribution? 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/
[galaxy-dev] problem installing blast_datatypes manually
Hello, I followed the instructions below to manually install the blast_datatypes: Manual Installation === Normally you would install this via the Galaxy ToolShed, which would move the provided blast.py file into a suitable location and process the datatypes_conf.xml entry to be combined with your local configuration. However, if you really want to this should work for a manual install. Add the following line to the datatypes_conf.xml file in the Galaxy main folder: Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking the blast.py file provided in this tar-ball. Finally add 'import blast' near the start of file lib/galaxy/datatypes/registry.py (after the other import lines). = I restarted my local Galaxy instance but still get this error. WARNING:galaxy.datatypes.registry:Error appending sniffer for datatype 'galaxy.datatypes.xml:BlastXml' to sniff_order: 'module' object has no attribute 'BlastXml' Any help would be much appreciated. Thanks, Liisa ___ 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/
[galaxy-dev] Can't edit Galaxy Workflow _ElementInterface instance has no attribute 'render'
Hello, After updating to the Sept. 07 distribution I am having problems editing an existing workflow. Server error URL: http:galaxy_url/workflow/load_workflow?id=ba751ee0539fff04&_=1348501448807 Module paste.exceptions.errormiddleware:143 in __call__ >> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ >> environ, self.app) Module paste.wsgilib:539 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ >> body = method( trans, **kwargs ) Module galaxy.web.framework:69 in decorator >> return simplejson.dumps( func( self, trans, *args, **kwargs ) ) Module galaxy.web.controllers.workflow:735 in load_workflow >> 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), Module galaxy.workflow.modules:262 in get_tooltip >> return self.tool.help.render( static_path=static_path ) AttributeError: _ElementInterface instance has no attribute 'render' Any help would be much appreciated. Thanks in advance, Liisa ___ 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/
[galaxy-dev] Error when running cleanup_datasets.py
Hello, I am trying to run the cleanup scripts on my local installation but get stuck when trying to run the following: ./scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 10 -5 -r Deleting library dataset id 7225 Traceback (most recent call last): File "./scripts/cleanup_datasets/cleanup_datasets.py", line 524, in if __name__ == "__main__": main() File "./scripts/cleanup_datasets/cleanup_datasets.py", line 124, in main purge_folders( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 247, in purge_folders _purge_folder( folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 497, in _purge_folder _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 497, in _purge_folder _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 495, in _purge_folder _purge_dataset_instance( ldda, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable File "./scripts/cleanup_datasets/cleanup_datasets.py", line 376, in _purge_dataset_instance ( dataset_instance.__class__.__name__, dataset_instance.id, dataset_instance.dataset.id ) AttributeError: 'NoneType' object has no attribute 'id' Any help would be much appreciated. Thanks, Liisa ___ 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/
[galaxy-dev] Error in db upgrade when updating to May11 distribution
Hello, I get an error when trying to upgrade my mysql db with sh manage_db.sh upgrade from version 94->95 (see below). Will cause problems with my installation? sh manage_db.sh upgrade 93 -> 94... Migration script to create "handler" column in job table. done 94 -> 95... Migration script to create table for tracking history_dataset_association subsets. (OperationalError) (1059, "Identifier name 'ix_history_dataset_association_subset_history_dataset_association_id' is too long") u'CREATE INDEX ix_history_dataset_association_subset_history_dataset_association_id ON history_dataset_association_subset (history_dataset_association_id)' () done 95 -> 96... Migration script to add column to openid table for provider. Remove any OpenID entries with nonunique GenomeSpace Identifier done 96 -> 97... Migration script to add the ctx_rev column to the tool_shed_repository table. done Thanks in advance, Liisa___ 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/
[galaxy-dev] Problems saving a cloned workflow
Hello, I cloned a workflow on my local Galaxy installation, renamed it, made some edits and pressed save. It has been saving now for about 3 hours. It only has 12 steps. Any suggestions? Thanks in advance, Liisa ___ 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/
[galaxy-dev] Error running set_dataset_sizes.py
Hello, I'm seeing some discrepancies in total user usage versus what my histories actually total so I wanted to run set_dataset_sizes.py and set_user_disk_usage.py I am getting the following error. ./set_dataset_sizes.py Loading Galaxy model... Processing 77915 datasets... Completed 0% Traceback (most recent call last): File "./set_dataset_sizes.py", line 43, in dataset.set_total_size() File "lib/galaxy/model/__init__.py", line 703, in set_total_size if self.object_store.exists(self, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True): AttributeError: 'NoneType' object has no attribute 'exists' Any help would be much appreciated. Thanks, Liisa ___ 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/
Re: [galaxy-dev] Can't clone workflows
Hi Dannon, Yes...the tags have piled up. I will apply this fix and try to remove some of the existing tags. Thanks for your suggestion. Liisa From: Dannon Baker To: Liisa Koski Cc: galaxy-dev@lists.bx.psu.edu Date: 21/03/2012 09:08 AM Subject:Re: [galaxy-dev] Can't clone workflows Liisa, I'm not able to reproduce this locally with a fresh galaxy-dist. Is there anything unique about your workflows or configuration here? And, this might be a long shot, but do you frequently use tags with your workflows? There was an issue that I've fixed with this recently that would cause a significant hang when cloning. -Dannon On Feb 29, 2012, at 4:03 PM, Liisa Koski wrote: > Hello, > I have lost the ability to clone workflows in my local installation of Galaxy (the latest galaxy-dist). When I try...it just hangs...and hangs... > > Any help would be much appreciated. > > Thanks, > Liisa > > ___ > 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/ > ___ 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/
[galaxy-dev] Can't clone workflows
Hello, I have lost the ability to clone workflows in my local installation of Galaxy (the latest galaxy-dist). When I try...it just hangs...and hangs... Any help would be much appreciated. Thanks, Liisa ___ 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/
Re: [galaxy-dev] Error Setting BAM Metadata
Yes it isand my galaxy is up to date. Thanks, Liisa From: Nate Coraor To: Liisa Koski Cc: galaxy-dev@lists.bx.psu.edu Date: 01/30/2012 03:07 PM Subject: Re: [galaxy-dev] Error Setting BAM Metadata On Jan 25, 2012, at 2:43 PM, Liisa Koski wrote: > Hello, > I am trying to upload BAM files (by pasting a URL) to my history(or DataLibrary) and get the following error. These are bam files which I had previously uploaded with no problems. > > Traceback (most recent call last): > File "/doolittle/Galaxy/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 126, in run_job >job_wrapper.finish( stdout, stderr ) > File "/doolittle/Galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 618, in finish >dataset.set_meta( overwrite = False ) > File "/doolittle/Galaxy/galaxy_dist/lib/galaxy/model/__init__.py", line 874, in set_meta >return self.datatype.set_meta( self, **kwd ) > File "/doolittle/Galaxy/galaxy_dist/lib/galaxy/datatypes/binary.py", line 179, in set_meta >raise Exception, "Error Setting BAM Metadata: %s" % stderr > Exception: Error Setting BAM Metadata: [bam_header_read] EOF marker is absent. The input is probably truncated. > [bam_header_read] invalid BAM binary header (this is not a BAM file) > > I ran bamtools on the unix command line to see if there was anything wrong with the file(s) but nothing. I tried uploading different bam files from other projects and get the same error. > > I did do an update to the latest release yesterday...if that helps? Hi Liisa, Is this a regular upload via a browser? --nate > > Thanks in advance, > Liisa > ___ > 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/ > ___ 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/
[galaxy-dev] Error executing tool: 'fasta'
Hi, I have tried running (on my local instance) a number of tools (fasta_to_tabular, tandem_repeat_finder, others) on my fasta file but keep getting the error Error executing tool: 'fasta' after file execution. In the log file I see this 10.1.1.119 - - [27/Jan/2012:15:47:15 -0400] "GET /tool_runner?tool_id=fasta2tab HTTP/1.1" 200 - " http://domain:8080/root/tool_menu"; "Mozilla/5.0 (Windows NT 5.2; WOW64; rv:6.0) Gecko/20100101 Firefox/6.0" galaxy.tools ERROR 2012-01-27 15:47:17,647 Exception caught while attempting tool execution: Traceback (most recent call last): File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1184, in handle_input _, out_data = self.execute( trans, incoming=params, history=history ) File "/Galaxy/galaxy_dist/lib/galaxy/tools/__init__.py", line 1503, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/Galaxy/galaxy_dist/lib/galaxy/tools/actions/__init__.py", line 199, in execute build_fasta_dataset = trans.app.model.HistoryDatasetAssociation.get( custom_build_dict[ 'fasta' ] ) KeyError: 'fasta' The fasta file is ok because I have a development installation and the tools work fine there. So there is something wrong with my production installation. I did a diff between the files galaxy_dist/lib/galaxy/tools/__init__.py and lib/galaxy/tools/actions/__init__.py but they are the same. Any help would be much appreciated. Thanks, Liisa___ 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/
[galaxy-dev] Error Setting BAM Metadata
Hello, I am trying to upload BAM files (by pasting a URL) to my history(or DataLibrary) and get the following error. These are bam files which I had previously uploaded with no problems. Traceback (most recent call last): File "/doolittle/Galaxy/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 126, in run_job job_wrapper.finish( stdout, stderr ) File "/doolittle/Galaxy/galaxy_dist/lib/galaxy/jobs/__init__.py", line 618, in finish dataset.set_meta( overwrite = False ) File "/doolittle/Galaxy/galaxy_dist/lib/galaxy/model/__init__.py", line 874, in set_meta return self.datatype.set_meta( self, **kwd ) File "/doolittle/Galaxy/galaxy_dist/lib/galaxy/datatypes/binary.py", line 179, in set_meta raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file) I ran bamtools on the unix command line to see if there was anything wrong with the file(s) but nothing. I tried uploading different bam files from other projects and get the same error. I did do an update to the latest release yesterday...if that helps? Thanks in advance, Liisa ___ 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/
[galaxy-dev] Problem uploading files from filesystem paths
Hi, I'm trying to upload data to Data Libraries from filesystems paths as Admin. I get the following error. Any ideas? Thanks in advance, Liisa Traceback (most recent call last): File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 394, in __main__() File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 386, in __main__ add_file( dataset, registry, js Job Standard Error Traceback (most recent call last): File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 394, in __main__() File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 386, in __main__ add_file( dataset, registry, json_file, output_path ) File "/data/Galaxy/galaxy-dist/tools/data_source/upload.py", line 300, in add_file if datatype.dataset_content_needs_grooming( dataset.path ): File "/data/Galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File "/data/Galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py", line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib64/python2.6/subprocess.py", line 633, in __init__ errread, errwrite) File "/usr/lib64/python2.6/subprocess.py", line 1139, in _execute_child raise child_exception OSError: [Errno 13] Permission denied ___ 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/
Re: [galaxy-dev] Divide FASTQ file into paired and unpaired reads (version 0.0.4) - naming suffix not recognized
Hi Peter, Thanks! The fix worked with the new Illumina format. Your help is much appreciated :) Cheers, Liisa Liisa Koski Bioinformatics Programmer From: Peter Cock To: Liisa Koski Cc: galaxy-dev Date: 2011-12-12 03:47 Subject: Re: [galaxy-dev] Divide FASTQ file into paired and unpaired reads (version 0.0.4) - naming suffix not recognized On Friday, December 9, 2011, Peter Cock wrote: > On Fri, Dec 9, 2011 at 5:05 PM, Liisa Koski wrote: >> >> Thanks Peter! That would be great! Let me know when you want me to test it :) >> Cheers, >> Liisa > > The revised code is here on bitbucket (on the branch "tools"), you'll > need fastq_paired_unpaired.py and fastq_paired_unpaired.xml v0.0.5: Try this (looks like I had the wrong link on Friday), sorry: https://bitbucket.org/peterjc/galaxy-central/src/a25f7920a1e5/tools/fastq 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/
Re: [galaxy-dev] Divide FASTQ file into paired and unpaired reads (version 0.0.4) - naming suffix not recognized
Thanks Peter! That would be great! Let me know when you want me to test it :) Cheers, Liisa Liisa Koski Bioinformatics Programmer Phone: 450-358-2621 x104, E-Mail: liisa.ko...@dnalandmarks.ca Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec CANADA DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science company Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at supp...@dnalandmarks.ca.Confidentialité: L'information contenue dans ce courriel est confidentielle et peut être assujettie aux règles concernant le secret professionel. L'information contenue dans ce courriel est autorisée uniquement pour l'individu ou l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, copier, distribuer ou utiliser le contenu de ce message. Si ce courriel est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes copies de votre système nous informer à supp...@dnalandmarks.ca. From: Peter Cock To: Liisa Koski Cc: galaxy-dev Date: 2011-12-09 11:55 Subject: Re: [galaxy-dev] Divide FASTQ file into paired and unpaired reads (version 0.0.4) - naming suffix not recognized On Fri, Dec 9, 2011 at 4:49 PM, Liisa Koski wrote: > Hi , > Looks like the tool Divide FASTQ file into paired and unpaired reads is not > recognizing my paired-end naming suffix > > @HWI-ST916:79:D04M5ACXX:1:1101:1:100326 1:N:0:TGNCCA > @HWI-ST916:79:D04M5ACXX:1:1101:1:100326 2:N:0:TGNCCA > > Is there a patch for this or another tool/way I can divide this fastq file? > > Thanks in advance, > Liisa That's a new Illumina FASTQ file isn't it, where they went and changed the read naming? That annoyed quite a few people... Presumably you're talking about my tool of that name on the Galaxy Tool Shed? I can take a look at this now if you agree to test it ;) 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/
[galaxy-dev] Divide FASTQ file into paired and unpaired reads (version 0.0.4) - naming suffix not recognized
Hi , Looks like the tool Divide FASTQ file into paired and unpaired reads is not recognizing my paired-end naming suffix @HWI-ST916:79:D04M5ACXX:1:1101:1:100326 1:N:0:TGNCCA @HWI-ST916:79:D04M5ACXX:1:1101:1:100326 2:N:0:TGNCCA Is there a patch for this or another tool/way I can divide this fastq file? Thanks in advance, Liisa ___ 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/
Re: [galaxy-dev] Can't view data files from published histories, only imported histories
Thanks Jeremy, that changeset fixed the issue :) Cheers, Liisa From: Jeremy Goecks To: Liisa Koski Cc: Date: 2011-11-30 18:07 Subject: Re: [galaxy-dev] Can't view data files from published histories, only imported histories Liisa, Updating FastQC won't solve this issue. You'll need to manually update galaxy-dist with this changeset to see the graphs: https://bitbucket.org/galaxy/galaxy-central/changeset/c8493a61bbea Otherwise, you can wait until the next galaxy-dist to get this changeset. Best, J. On Nov 30, 2011, at 2:39 PM, Liisa Koski wrote: Hi Jeremy, I updated to the latest galaxy-dist release and can now see the boxplots (png) files from published histories. I can see the FASTQC (html) reports too but the individual graphs within the report are missing. I will update fastqc itself and see if that makes a difference. Thanks, Liisa Liisa Koski Bioinformatics Programmer Phone: 518-309-3079, E-Mail: liisa.ko...@dnalandmarks.ca Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec CANADA DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science company Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at supp...@dnalandmarks.ca.Confidentialité: L'information contenue dans ce courriel est confidentielle et peut être assujettie aux règles concernant le secret professionel. L'information contenue dans ce courriel est autorisée uniquement pour l'individu ou l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, copier, distribuer ou utiliser le contenu de ce message. Si ce courriel est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes copies de votre système nous informer à supp...@dnalandmarks.ca. From: Jeremy Goecks To: Liisa Koski Cc: Date: 2011-11-28 14:46 Subject: Re: [galaxy-dev] Can't view data files from published histories, only imported histories Liisa, I'm not able to reproduce your issue on our public server. For instance, here's a history that includes both FastQC output and a boxplot; both display correctly: http://main.g2.bx.psu.edu/u/jeremy/h/unnamed-history-2 (Note that I just committed a fix to galaxy-central so that the images in the FastQC output show up correctly.) Some questions that might help us figure out the problem: *can you reproduce your problem on a public Galaxy instance, such as main or test? *is your Galaxy instance up to date? *is there something unusual about the datasets that you're using, e.g. are they imported on non-standard in some way? J. On Nov 28, 2011, at 1:35 PM, Liisa Koski wrote: Hi Jeremy, I'm trying to view boxplots (png) and FastQC (html) output. I can view other output types like tabular in the published histories, but not png or html. Thanks, Liisa Liisa Koski Bioinformatics Programmer Phone: 518-309-3079, E-Mail: liisa.ko...@dnalandmarks.ca Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec CANADA DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science company Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at supp...@dnalandmarks.ca.Confidentialité: L'information contenue dans ce courriel est confidentielle et peut être assujettie aux règles concernant le secret professionel. L'information contenue dans ce courriel est autorisée uniquement pour l'individu ou l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, copier, distribuer ou utiliser le contenu de ce message. Si ce courriel est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes copies de votre système nous informer à supp...@dnalandmarks.ca. From: Jeremy Goecks To: Liisa Koski Cc: Date: 2011-11-28 13:23 Subject: Re: [galaxy-dev] Can't view data files
Re: [galaxy-dev] Can't view data files from published histories, only imported histories
Hi Jeremy, I updated to the latest galaxy-dist release and can now see the boxplots (png) files from published histories. I can see the FASTQC (html) reports too but the individual graphs within the report are missing. I will update fastqc itself and see if that makes a difference. Thanks, Liisa Liisa Koski Bioinformatics Programmer Phone: 518-309-3079, E-Mail: liisa.ko...@dnalandmarks.ca Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec CANADA DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science company Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at supp...@dnalandmarks.ca.Confidentialité: L'information contenue dans ce courriel est confidentielle et peut être assujettie aux règles concernant le secret professionel. L'information contenue dans ce courriel est autorisée uniquement pour l'individu ou l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, copier, distribuer ou utiliser le contenu de ce message. Si ce courriel est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes copies de votre système nous informer à supp...@dnalandmarks.ca. From: Jeremy Goecks To: Liisa Koski Cc: Date: 2011-11-28 14:46 Subject: Re: [galaxy-dev] Can't view data files from published histories, only imported histories Liisa, I'm not able to reproduce your issue on our public server. For instance, here's a history that includes both FastQC output and a boxplot; both display correctly: http://main.g2.bx.psu.edu/u/jeremy/h/unnamed-history-2 (Note that I just committed a fix to galaxy-central so that the images in the FastQC output show up correctly.) Some questions that might help us figure out the problem: *can you reproduce your problem on a public Galaxy instance, such as main or test? *is your Galaxy instance up to date? *is there something unusual about the datasets that you're using, e.g. are they imported on non-standard in some way? J. On Nov 28, 2011, at 1:35 PM, Liisa Koski wrote: Hi Jeremy, I'm trying to view boxplots (png) and FastQC (html) output. I can view other output types like tabular in the published histories, but not png or html. Thanks, Liisa Liisa Koski Bioinformatics Programmer Phone: 518-309-3079, E-Mail: liisa.ko...@dnalandmarks.ca Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec CANADA DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science company Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at supp...@dnalandmarks.ca.Confidentialité: L'information contenue dans ce courriel est confidentielle et peut être assujettie aux règles concernant le secret professionel. L'information contenue dans ce courriel est autorisée uniquement pour l'individu ou l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, copier, distribuer ou utiliser le contenu de ce message. Si ce courriel est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes copies de votre système nous informer à supp...@dnalandmarks.ca. From: Jeremy Goecks To: Liisa Koski Cc: Date: 2011-11-28 13:23 Subject: Re: [galaxy-dev] Can't view data files from published histories, only imported histories Liisa, This functionality works fine in some instances, e.g. for this history: http://main.g2.bx.psu.edu/u/cartman/h/repeats I'd guess that it's related to the particular dataset type. What type of dataset are you trying to view when you see this error? Can you view any datasets from the history? Thanks, J. On Nov 28, 2011, at 1:11 PM, Liisa Koski wrote: Hi, I found a weird bug. I am trying to view data files by clicking on the 'eye' icon from a published history on my local galaxy installation. When I click on th
Re: [galaxy-dev] Lost my Data Libraries when I updated to the lastest galaxy-dist release?
Sorry! They are back! I was looking at the wrong installation :( Thanks, Liisa From: Greg Von Kuster To: Liisa Koski Cc: galaxy-dev Date: 2011-11-30 13:45 Subject: Re: [galaxy-dev] Lost my Data Libraries when I updated to the lastest galaxy-dist release? Lisa, What release did you update from? Did you have any access restrictions on the data libraries? If so, are you logged in as a user that has those access privileges? Simply updating you Galaxy code base should not have caused this issue for you. On Nov 30, 2011, at 1:38 PM, Liisa Koski wrote: Hi, I lost my Data Libraries when I updated to the latest galaxy-dist release :( What would be the best way to go about getting them back? Thanks in advance, Liisa ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ 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/
[galaxy-dev] Lost my Data Libraries when I updated to the lastest galaxy-dist release?
Hi, I lost my Data Libraries when I updated to the latest galaxy-dist release :( What would be the best way to go about getting them back? Thanks in advance, Liisa ___ 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/
Re: [galaxy-dev] Can't view data files from published histories, only imported histories
Hi Jeremy, I'm trying to view boxplots (png) and FastQC (html) output. I can view other output types like tabular in the published histories, but not png or html. Thanks, Liisa Liisa Koski Bioinformatics Programmer Phone: 518-309-3079, E-Mail: liisa.ko...@dnalandmarks.ca Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec CANADA DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science company Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at supp...@dnalandmarks.ca.Confidentialité: L'information contenue dans ce courriel est confidentielle et peut être assujettie aux règles concernant le secret professionel. L'information contenue dans ce courriel est autorisée uniquement pour l'individu ou l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, copier, distribuer ou utiliser le contenu de ce message. Si ce courriel est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes copies de votre système nous informer à supp...@dnalandmarks.ca. From: Jeremy Goecks To: Liisa Koski Cc: Date: 2011-11-28 13:23 Subject: Re: [galaxy-dev] Can't view data files from published histories, only imported histories Liisa, This functionality works fine in some instances, e.g. for this history: http://main.g2.bx.psu.edu/u/cartman/h/repeats I'd guess that it's related to the particular dataset type. What type of dataset are you trying to view when you see this error? Can you view any datasets from the history? Thanks, J. On Nov 28, 2011, at 1:11 PM, Liisa Koski wrote: Hi, I found a weird bug. I am trying to view data files by clicking on the 'eye' icon from a published history on my local galaxy installation. When I click on the eye I get a 'Server Error' and in the log file I get the following. Error - : global name 'data' is not defined URL: http://domain:8080/u/user/d/8bdb720fee635874 File 'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File 'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File 'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File 'galaxy_dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File 'galaxy_dist/lib/galaxy/web/controllers/dataset.py', line 693 in display_by_username_and_slug trans.response.set_content_type( data.get_mime() ) NameError: global name 'data' is not defined If I import the history into my own history pane I can click on the eye and see the data with no errors. Any ideas how I can see the data from the published histories? Thanks, Liisa Liisa Koski Bioinformatics Programmer ___ 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/ ___ 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/
[galaxy-dev] Can't view data files from published histories, only imported histories
Hi, I found a weird bug. I am trying to view data files by clicking on the 'eye' icon from a published history on my local galaxy installation. When I click on the eye I get a 'Server Error' and in the log file I get the following. Error - : global name 'data' is not defined URL: http://domain:8080/u/user/d/8bdb720fee635874 File 'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File 'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File 'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File 'galaxy_dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File 'galaxy_dist/lib/galaxy/web/controllers/dataset.py', line 693 in display_by_username_and_slug trans.response.set_content_type( data.get_mime() ) NameError: global name 'data' is not defined If I import the history into my own history pane I can click on the eye and see the data with no errors. Any ideas how I can see the data from the published histories? Thanks, Liisa Liisa Koski Bioinformatics Programmer ___ 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/
[galaxy-dev] Compatible MACS version?
Hi, I'm trying to use macs in my local Galaxy instance but am having difficulties. I have macs 1.4.0rc2 20110214 (Valentine) installed. I get macs: error: no such option: --lambdaset I checked documentation for Galaxy Dependencies but no version is mentioned for macs ( https://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies). Thanks in advance for the help, Liisa ___ 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/
[galaxy-dev] Import Library Datasets into Histories - automatically imports into current AND new history - Bug?
Hello, I noticed a change in the newest version. When importing Library Datasets into Histories...if you enter a New History name for the destination Galaxy will import into the new AND current history. So it is getting imported into two histories. Is this a bug? It would really be nice to only import a dataset into a new history like before. Thanks, Liisa ___ 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/
[galaxy-dev] BioMart -> Galaxy returns html
Hi, I'm trying to grab data from my local custom BioMart and export it to my local Galaxy installation. I did this by changing the address in the biomart.xml file http://mydomain/biomart/martview"; check_values="false" method="get" target="_top"> go to BioMart Central $GALAXY_URL The file it returns is html. When I change the data type to tabular and click on the eye I see the following... Request Error (invalid_request) Your request could not be processed. Request could not be handled http://domain.com/scripts/proxy_exception_2.pl"; method="post"> assistance from the internet support group. Any help would be much appreciated. Thanks, Liisa___ 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/
[galaxy-dev] Can I run workflow on certain nodes of the cluster?
Is it possible to run a specific workflow only on certain nodes of the cluster? Either using the API or by setting something in the config files? Thanks, Liisa ___ 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/
[galaxy-dev] Workflow steps stuck in job queue - since cleanup_datasets.py
Hi, Yesterday I ran the cleanup_datasets.py scripts as follows.. Deleting Userless Histories python cleanup_datasets.py universe_wsgi.ini -d 10 -1 Purging Deleted Histories python cleanup_datasets.py universe_wsgi.ini -d 10 -2 -r Purging Deleted Datasets python cleanup_datasets.py universe_wsgi.ini -d 10 -3 -r Purging Library Folders python cleanup_datasets.py universe_wsgi.ini -d 10 -5 -r Purging Libraries python cleanup_datasets.py universe_wsgi.ini -d 10 -4 -r Deleting Datasets / Purging Dataset Instances python cleanup_datasets.py universe_wsgi.ini -d 10 -6 -r This morning I noticed a number of workflows were either stuck at a certain step (ie..job running) or the step was grey (waiting in queue) but our cluster has free nodes. If I start a new workflow...it completes fine...just the 19 histories that were running yesterday are stuck. Did I do something wrong with the cleanup. Is there a way to restart these stuck histories without having to restart the entire workflow? Thanks in advance, Liisa ___ 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/
[galaxy-dev] sqlalchemy Timeout Error
Hi, We are running many NGS workflows at the same time on our local instance of Galaxy. They are crashing with the following error Error - : QueuePool limit of size 5 overflow 10 reached, connection timed out, timeout 30 In the universe_wsgi.ini we made the following adjustments: # If the server logs errors about not having enough database pool connections, # you will want to increase these values, or consider running more Galaxy # processes. database_engine_option_pool_size = 50 # this used to be 5 database_engine_option_max_overflow = 100 # this used to be 100 Those numbers were pulled out of a hat so I wanted to make sure what we were doing was correct. Is there a limit on the values? It doesn't appear to be crashing anymore but I still want to make sure. Thanks, Liisa___ 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/
[galaxy-dev] update probelm...
Hi I just tried to update my local installation of Galaxy but accidentally hit Ctr-C when it asked me a question added 285 changesets with 649 changes to 354 files local changed static/scripts/packed/jquery.jstore.js which remote deleted use (c)hanged version or (d)elete? interrupted! When I tried to do the update again...it says 'no changes found' But...after restarting my instance...I see that the changes did not get implemented. Is there a way to force this? Thanks in advance, Liisa___ 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/
Re: [galaxy-dev] Can't save BAM file from Galaxy
Thanks Nate! I set 'debug = False'and now I have no problem downloading my BAM/SAM files. Cheers, Liisa From: Nate Coraor To: Liisa Koski Cc: galaxy-...@bx.psu.edu Date: 2011-03-22 12:06 Subject: Re: [galaxy-dev] Can't save BAM file from Galaxy Liisa Koski wrote: > Hello, > I have a local instance of galaxy and after successfully running an NGS > analysis I am trying to save my BAM file to my local machine. When I click > on the save icon my Galaxy instance crashes with the following error. This > also happens when I try to save the SAM file. It does not happen when I > try to save a txt file. > > python: ./Modules/cStringIO.c:419: O_cwrite: Assertion `oself->pos + l < > 2147483647' failed. > ./run.sh: line 48: 19187 Aborted python > ./scripts/paster.py serve universe_wsgi.ini $@ > > Something to do with base positions? Hi Liisa, I'm not completely certain, but it may just be the debugging modules that are enabled by default trying to load the entire bam/sam file into memory before sending it. Try restarting your Galaxy server after setting 'debug = False' in universe_wsgi.ini and see if this makes a difference. --nate > > Thanks in advance for any help, > Liisa > > ___ > 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/ ___ 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/
[galaxy-dev] Can't save BAM file from Galaxy
Hello, I have a local instance of galaxy and after successfully running an NGS analysis I am trying to save my BAM file to my local machine. When I click on the save icon my Galaxy instance crashes with the following error. This also happens when I try to save the SAM file. It does not happen when I try to save a txt file. python: ./Modules/cStringIO.c:419: O_cwrite: Assertion `oself->pos + l < 2147483647' failed. ./run.sh: line 48: 19187 Aborted python ./scripts/paster.py serve universe_wsgi.ini $@ Something to do with base positions? Thanks in advance for any help, Liisa ___ 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/
Re: [galaxy-dev] Send data to GBrowse
I have figured out how to send data from my local Galaxy to my local GBrowse. Thanks for the help! Now I would also like to go in the other direction and send data from GBrowse to Galaxy. galaxy incoming = http://localhost/cgi-bin/gbrowse When I export data to Galaxy I get the main page of galaxy but do not see any data. The url in my browser is http://localhost:8080/?URL=http://localhost/cgi-bin/gbrowse Any ideas as to why I can't see the actual data? Shoudn't the url contain ref;start;end;type? Thanks for your help, Liisa From: Nicki Gray To: Liisa Koski Cc: "galaxy-dev@lists.bx.psu.edu" Date: 2011-02-10 11:40 Subject: Re: [galaxy-dev] Send data to GBrowse Hi Liisa When setting this up on our own local instance to get bigwig files to display in Gbrowse we edited: 1. universe_wsgi.ini 2. tool-data/shared/gbrowse/gbrowse_build_sites.txt 3. datatypes_conf.xml so that it includes 4. and in display_applications/gbrowse/ make sure you have the relevant xml files eg gbrowse_wig.xml, gbrowse_bigwig.xml Nicki Gray MRC Molecular Haematology Unit On 7 Feb 2011, at 19:03, Liisa Koski wrote: Hi, I have just installed Galaxy and am trying to configure it to allow display of data on my local installation of GBrowse. I have edited tool-data/shared/gbrowse/gbrowse_build_sites.txt (species http://domain.ca/cgi-bin/gbrowse/species species) As well as universe_wsgi.ini (gbrowse_display_sites = species) However I do not see a link in history items after I stop and start the server. Is there something else I'm missing? Thanks in advance for your help, Liisa ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Send data to GBrowse
Hi, I have just installed Galaxy and am trying to configure it to allow display of data on my local installation of GBrowse. I have edited tool-data/shared/gbrowse/gbrowse_build_sites.txt (species http://domain.ca/cgi-bin/gbrowse/species species) As well as universe_wsgi.ini (gbrowse_display_sites = species) However I do not see a link in history items after I stop and start the server. Is there something else I'm missing? Thanks in advance for your help, Liisa___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
