[galaxy-dev] Help with Galaxy server migration
Dear all, I'm trying to migrate our local Galaxy server from a standalone server running on CentOS 5 to a setup that runs Galaxy in a Docker container (bgruening/galaxy-stable). Due to Docker and the setup of the container, almost all data, tools, configs etc. have to move to a different place. Since our old server is pretty cluttered up anyway, I would like to move just user data (logins, histories, datasets ...), but none of the tool installations, tool data or configs. My plan was to start with a fresh and clean new Galaxy installation, transfer the datasets and the database and then reinstall all tools through the toolshed (of course there are many more small odds and ends that need fixing). The problem is that after transfering the database, I always get an error when going to Manage installed tool shed repositories (see end of the mail). I tried just overwriting the pg_data directory (PostgreSQL versions are identical) and also exporting to sql (pg_dump) and importing in the new DB. Both times I made sure to run manage_db.sh upgrade afterwards. The error stays the same. I can't make much sense of the error message, my only guess is that it looks for something that's not there. However, I really don't want to transfer the tool directories and tool configurations, because that will get messy and difficult, since many paths need to be adjusted. There's a high chance for error and this way I also carry over the clutter. So is there a way to remove all tool installation information from the database, before I transfer it? Can this even be disentangled from the histories and datasets? Any help or other ideas on how to do this migration are highly appreciated! Thanks, Sarah 10.1.5.190 - - [16/Oct/2014:09:54:35 +] GET /admin_toolshed/browse_repositories HTTP/1.1 500 - http://deep2:8080/admin/index; Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0 Error - type 'exceptions.UnicodeDecodeError': 'ascii' codec can't decode byte 0xe2 in position 393: ordinal not in range(128) URL: http://deep2:8080/admin_toolshed/browse_repositories File 'lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/galaxy-central/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/galaxy-central/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File 'lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File 'lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File 'lib/galaxy/web/framework/decorators.py', line 87 in decorator return func( self, trans, *args, **kwargs ) File 'lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 167 in browse_repositories return self.installed_repository_grid( trans, **kwd ) File 'lib/galaxy/web/framework/helpers/grids.py', line 306 in __call__ kwargs=kwargs ) File 'lib/galaxy/web/framework/webapp.py', line 771 in fill_template return self.fill_template_mako( filename, **kwargs ) File 'lib/galaxy/web/framework/webapp.py', line 786 in fill_template_mako return template.render( **data ) File '/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/galaxy-central/eggs/Mako-0.4.1-py2.7.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/galaxy-central/database/compiled_templates/base.mako.py', line 66 in render_body __M_writer(unicode(next.body())) File '/galaxy-central/database/compiled_templates/grid_base.mako.py', line 91 in render_body __M_writer(unicode(self.load())) File '/galaxy-central/database/compiled_templates/grid_base.mako.py', line 120 in render_load __M_writer(unicode( h.dumps( self.get_grid_config( embedded=embedded, insert=insert ) ) )) File '/galaxy-central/database/compiled_templates/grid_base.mako.py', line 303 in render_get_grid_config value = column.get_value( trans, grid, item ) File 'lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py', line 106 in get_value return suc.get_tool_shed_repository_status_label( trans.app, tool_shed_repository ) File 'lib/tool_shed/util/shed_util_common.py', line 829 in get_tool_shed_repository_status_label elif tool_shed_repository.tool_dependencies_being_installed: File 'lib/galaxy/model/tool_shed_install/__init__.py', line 408 in tool_dependencies_being_installed for tool_dependency in
Re: [galaxy-dev] Help with Galaxy server migration
Dear John, thank you very much your help and the warnings! I'm testing it with a second database and so far it seems to work :-). I was also suspecting the encoding to be the issue, that's why I did it through pg_dump and specified the encoding of the new server for the dump. The error stayed the same and so far I have just seen it in the context of toolshed operations. I don't know what else I could do to ensure proper encoding. Best regards, Sarah - Original Message - From: John Chilton jmchil...@gmail.com To: Sarah Diehl di...@ie-freiburg.mpg.de Cc: galaxy-dev@lists.bx.psu.edu List galaxy-dev@lists.bx.psu.edu Sent: Thursday, October 16, 2014 3:17:39 PM Subject: Re: [galaxy-dev] Help with Galaxy server migration Hmm hopefully someone more knowledgeable about the tool shed than me responds also but I had a couple quick thoughts. The first is a warning - workflows may break. At very least workflows that depend on the previous instance having gone through tool migrations instead of tool install. My understanding is tool migrations cause links to the older versions of the tools to be created so workflows continue to operate - just installing the same version of the tool again doesn't set this up. Also - in theory if you resinstall the same versions of tools tool re-runs and stuff should still work - but I am not confident and I have not tested it myself - so if that functionality is important to you, you test it out before throwing out the old configuration. Next - I am a little bit concerned about this error. It would seem to point to some sort of encoding problem with the way the database was transferred - different table encodings or something? I don't really know anything about encoding and postgres though. That said I am not surprised there are problems with the tool shed. There are all sorts of implicit dependencies between what is on disk and what is in the database. If you really do want to start fresh I would clear out all of the tool shed tables before continuing. These tables including - tool_shed_repository,repository_repository_dependency_association, repository_dependency, tool_dependency, tool_version, tool_version_association, migrate_tools. Rather than truncating the existing tables - you could also just have Galaxy target a completely separate database for tool shed install stuff by creating a new postgres database, setting install_database_connection in your galaxy ini file (either universe_wsgi.ini or galaxy.ini depending on what version of Bjoern's docker image you are targetting) - or in the newest version of that Dockerfile you can just make sure your docker run includes a -e GALAXY_CONFIG_INSTALL_DATABASE_CONNECTION=postgresconnectionstring. You will also want to make sure that database gets populated - I think either of the following would work ./create_db.sh install ./migrate_db.sh install upgrade Sorry I have not definitive answers - but hopefully this is helpful. Good luck with the migration. You should let the list know how the Docker container thing goes for a production server. -John On Thu, Oct 16, 2014 at 8:36 AM, Sarah Diehl di...@ie-freiburg.mpg.de wrote: Dear all, I'm trying to migrate our local Galaxy server from a standalone server running on CentOS 5 to a setup that runs Galaxy in a Docker container (bgruening/galaxy-stable). Due to Docker and the setup of the container, almost all data, tools, configs etc. have to move to a different place. Since our old server is pretty cluttered up anyway, I would like to move just user data (logins, histories, datasets ...), but none of the tool installations, tool data or configs. My plan was to start with a fresh and clean new Galaxy installation, transfer the datasets and the database and then reinstall all tools through the toolshed (of course there are many more small odds and ends that need fixing). The problem is that after transfering the database, I always get an error when going to Manage installed tool shed repositories (see end of the mail). I tried just overwriting the pg_data directory (PostgreSQL versions are identical) and also exporting to sql (pg_dump) and importing in the new DB. Both times I made sure to run manage_db.sh upgrade afterwards. The error stays the same. I can't make much sense of the error message, my only guess is that it looks for something that's not there. However, I really don't want to transfer the tool directories and tool configurations, because that will get messy and difficult, since many paths need to be adjusted. There's a high chance for error and this way I also carry over the clutter. So is there a way to remove all tool installation information from the database, before I transfer it? Can this even be disentangled from the histories and datasets? Any help or other ideas on how to do this migration are highly appreciated! Thanks, Sarah 10.1.5.190 - - [16/Oct/2014:09:54:35 +] GET
[galaxy-dev] sorting of files in data libraries
Hi everyone, I uploaded a bunch of files to the Galaxy data libraries with the option Upload files from filesystem paths and Link to files without copying to Galaxy. Afterwards I edited the names that are displayed in Galaxy. However, now the files are not alphabetically sorted anymore. I tried moving them around, but the order stayed the same. Is this on purpose and is there a way to change it? Thanks, Sarah ___ 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] user information form
Hi everyone, is anybody using the user information form feature (https://wiki.galaxyproject.org/Admin/Config/User%20Information)? For me it does not seem to be working. I created a form as explained on the wiki page, but nothing changed in the user registration. It just causes an internal server error when I go to Manage your information. Best regards, Sarah ___ 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] Error when installing package_galaxy_utils
Hi Nate, thanks for all your help! I attached the full installation log file. Best regards, Sarah - Original Message - From: Nate Coraor n...@bx.psu.edu To: Sarah Diehl di...@ie-freiburg.mpg.de Cc: galaxy-dev@lists.bx.psu.edu List galaxy-dev@lists.bx.psu.edu Sent: Tuesday, February 25, 2014 3:57:36 PM Subject: Re: [galaxy-dev] Error when installing package_galaxy_utils Hi Sarah, Could you include the installation stdout as well? The dependency installation log separates stdout and stderr into two sections, there might be more detail about exactly where it's failing in the stdout. --nate On Fri, Feb 21, 2014 at 4:21 AM, Sarah Diehl di...@ie-freiburg.mpg.de wrote: Hi Nate, I tried it multiple times and always got the same error. I did successfully install other tools before and after that. I didn't notice any issues with the filesystem. Is there a way to find out what exactly the installation tries to do at that point? Thanks, Sarah - Original Message - From: Nate Coraor n...@bx.psu.edu To: Sarah Diehl di...@ie-freiburg.mpg.de Cc: galaxy-dev@lists.bx.psu.edu List galaxy-dev@lists.bx.psu.edu Sent: Friday, February 21, 2014 5:10:46 AM Subject: Re: [galaxy-dev] Error when installing package_galaxy_utils Hi Sarah, This looks a lot like a transient filesystem error. If you attempt to reinstall the repository, do you get the same error? --nate On Thu, Feb 20, 2014 at 10:48 AM, Sarah Diehl di...@ie-freiburg.mpg.de wrote: Hi everyone, I just updated our local Galaxy installation to the latest dist version and also did the tool migration steps (./scripts/migrate_tools/0009_tools.sh). However, the package galaxy_utils gave me an error and I don't have the slightest idea what happened. So any help to figure out the issue is greatly appreciated! Thanks, Sarah # export PYTHONPATH=$PYTHONPATH:/galaxy/galaxy_data/tools/galaxy_sequence_utils/1.0.0/devteam/package_galaxy_utils_1_0/0643676ad5f7/lib/python python setup.py install --home /galaxy/galaxy_data/tools/galaxy_seq uence_utils/1.0.0/devteam/package_galaxy_utils_1_0/0643676ad5f7 STDERR Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.38.tar.gz Extracting in /tmp/tmpo9Zxdz Now working in /tmp/tmpo9Zxdz/distribute-0.6.38 Building a Distribute egg in /galaxy/galaxy_server/database/tmp/tmp-toolshed-mtd00x35_/galaxy_sequence_utils-1.0.0 /galaxy/galaxy_server/database/tmp/tmp-toolshed-mtd00x35_/galaxy_sequence_utils-1.0.0/distribute-0.6.38-py2.7.egg error: site.py: Resource temporarily unavailable # ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ # export PYTHONPATH=$PYTHONPATH:/galaxy/galaxy_data/tools/galaxy_sequence_utils/1.0.0/devteam/package_galaxy_utils_1_0/0643676ad5f7/lib/python python setup.py install --home /galaxy/galaxy_data/tools/galaxy_sequence_utils/1.0.0/devteam/package_galaxy_utils_1_0/0643676ad5f7 STDOUT running install running bdist_egg running egg_info creating lib/galaxy_sequence_utils.egg-info writing lib/galaxy_sequence_utils.egg-info/PKG-INFO writing top-level names to lib/galaxy_sequence_utils.egg-info/top_level.txt writing dependency_links to lib/galaxy_sequence_utils.egg-info/dependency_links.txt writing manifest file 'lib/galaxy_sequence_utils.egg-info/SOURCES.txt' reading manifest file 'lib/galaxy_sequence_utils.egg-info/SOURCES.txt' writing manifest file 'lib/galaxy_sequence_utils.egg-info/SOURCES.txt' installing library code to build/bdist.linux-x86_64/egg running install_lib running build_py creating build creating build/lib creating build/lib/galaxy_utils copying lib/galaxy_utils/__init__.py - build/lib/galaxy_utils creating build/lib/galaxy_utils/sequence copying lib/galaxy_utils/sequence/__init__.py - build/lib/galaxy_utils/sequence copying lib/galaxy_utils/sequence/fasta.py - build/lib/galaxy_utils/sequence copying lib/galaxy_utils/sequence/fastq.py - build/lib/galaxy_utils/sequence copying lib/galaxy_utils/sequence/sequence.py - build/lib/galaxy_utils/sequence copying lib/galaxy_utils/sequence/transform.py - build/lib/galaxy_utils/sequence copying lib/galaxy_utils/sequence/vcf.py - build/lib/galaxy_utils/sequence creating build/bdist.linux-x86_64 creating build/bdist.linux-x86_64/egg creating build/bdist.linux-x86_64/egg/galaxy_utils copying build/lib/galaxy_utils/__init__.py - build/bdist.linux-x86_64/egg/galaxy_utils creating build/bdist.linux-x86_64/egg/galaxy_utils/sequence copying build/lib/galaxy_utils/sequence/__init__.py - build/bdist.linux-x86_64
[galaxy-dev] Error when installing package_galaxy_utils
Hi everyone, I just updated our local Galaxy installation to the latest dist version and also did the tool migration steps (./scripts/migrate_tools/0009_tools.sh). However, the package galaxy_utils gave me an error and I don't have the slightest idea what happened. So any help to figure out the issue is greatly appreciated! Thanks, Sarah # export PYTHONPATH=$PYTHONPATH:/galaxy/galaxy_data/tools/galaxy_sequence_utils/1.0.0/devteam/package_galaxy_utils_1_0/0643676ad5f7/lib/python python setup.py install --home /galaxy/galaxy_data/tools/galaxy_seq uence_utils/1.0.0/devteam/package_galaxy_utils_1_0/0643676ad5f7 STDERR Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.38.tar.gz Extracting in /tmp/tmpo9Zxdz Now working in /tmp/tmpo9Zxdz/distribute-0.6.38 Building a Distribute egg in /galaxy/galaxy_server/database/tmp/tmp-toolshed-mtd00x35_/galaxy_sequence_utils-1.0.0 /galaxy/galaxy_server/database/tmp/tmp-toolshed-mtd00x35_/galaxy_sequence_utils-1.0.0/distribute-0.6.38-py2.7.egg error: site.py: Resource temporarily unavailable # ___ 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] job_conf.xml output_size limit
Hi everyone, in my job_conf.xml I defined the following limit limit type=output_size536870912000/limit Galaxy seems to correctly identify the number as 500 GB, since I got the error: Job output file grew too large (greater than 500.0 GB), please try different inputs or parameters The problem is that the output file of the job is just a few GB (verified by rerunning the command manually). So Galaxy is wrongly stopping the job after just a few seconds, although the actual output size was fine. I disabled the limit for now, but I really want it in place. I just put it because I had a user generating output files of over 4 TB that filled up our storage (quotas only catch them when they are finished, but the user had two concurrent jobs running, both creating such huge files). Any help is appreciated! Thanks! Sarah ___ 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] Tabular data not displaying in main panel
Hello everyone, any news on this bug? I have the same issue here, with the error TypeError: column_types is undefined @ http://galaxy.immunbio.mpg.de/static/scripts/mvc/data.js:188 The suggested fix works for me, but the resulting formating isn't nice. Best regards, Sarah - Original Message - From: Ian Misner imis...@umd.edu To: galaxy-dev@lists.bx.psu.edu Sent: Friday, October 4, 2013 1:17:54 PM Subject: Re: [galaxy-dev] Tabular data not displaying in main panel Hello All, I'm having the same issue with tabular data not displaying,but I'm afraid I'm much newer to running a local galaxy instance. Apparently switching to https://bitbucket.org/galaxy/galaxy-central/src/a477486bf18eafdd14dd7ba1e91e17f1b05e8121/scripts/functional_tests.py?at=stable but frankly I don't know how to do that. Any help would be appreciated. Here is my current branch information changeset: 10421:a477486bf18e branch: stable tag: tip user:Nate Coraor n...@bx.psu.edu date:Thu Sep 26 11:02:58 2013 -0400 summary: Bugfix for tool-to-destination mapping, tool ids are lowercased but the mapping id was not lowercased. changeset: 10411:c42567f43aa7 user:greg date:Mon Aug 19 13:19:56 2013 -0400 summary: Filter invalid objects when generating the list of repository_dependencies objects that are associated with a tool shed repository installed into Galaxy. Cheers Ian ___ 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] deleted datasets inconsistent
Hi all, it seems my clean-up enthusiasm caused some inconsistencies with datasets' deleted status. I encounter the following phenomenon: datasets appear totally fine in the data libraries, but once they are loaded into a history, they appear as deleted there. I dug through the database and found out that the following query returns all datasets in the libraries that were uploaded before my clean-up: SELECT * FROM library_dataset_dataset_association INNER JOIN library_dataset ON library_dataset_dataset_association.library_dataset_id = library_dataset.id WHERE library_dataset_dataset_association.deleted = TRUE AND library_dataset.deleted = FALSE; When I set both deleted to false, only datasets that were added after the clean-up appear. Do I break something, if I reset library_dataset_dataset_association.deleted to FALSE for the inconsistent datasets? I tried it for one dataset and that seems to have fixed the problem. Is this some bug in the clean-up scripts? I guess that actually they should have been removed completely. Best regards, Sarah ___ 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] purging datasets doesn't free up disk space
Hello, our Galaxy server is running low on disk space, so I asked all users to (permanently) delete old histories and datasets. One specific user alone managed to reduce his space usage by 2 TB. That's at least what the Galaxy server says. Afterwards I additionally ran the following scripts: delete_userless_histories.sh -d 1 -r -f purge_histories.sh -d 1 -r -f purge_libraries.sh -d 1 -r -f purge_folders.sh -d 1 -r -f python cleanup_datasets.py universe_wsgi.ini -d 200 -6 -r -f purge_datasets.sh -d 1 -r -f Purging the histories took very long (about a day) and the log of deleted histories is huge. Purging the datasets also took some time. However, my disk usage is still the same as before. It wasn't reduced at all. Did I miss some important step or some waiting time? Any help would be appreciated. Thanks, Sarah ___ 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] purging datasets doesn't free up disk space
Hi Hans, thanks for your help. I didn't realize the sh scripts came with their own options. I just misunderstood that in the documentation. It seems to have worked though, the log file says: # 2013-02-28 11:56:20 - Handling stuff older than 1 days ... Purged 10097 datasets Freed disk space: 9515493164336 Elapsed time: 5669.43398285 So the freed disk space should be around 9 TB, right? Best regards, Sarah - Original Message - From: Hans-Rudolf Hotz h...@fmi.ch To: Sarah Diehl di...@ie-freiburg.mpg.de Cc: galaxy-dev@lists.bx.psu.edu List galaxy-dev@lists.bx.psu.edu Sent: Thursday, February 28, 2013 4:18:49 PM Subject: Re: [galaxy-dev] purging datasets doesn't free up disk space Hi Sarah May be the histories and/or datasets are shared with users who did not delete them? Also, have you looked at the log files? What is written in the log files for the purge_datasets.sh step? Do you have lines like: Removing disk, file ***/database/files/008/dataset_8271.dat and at the very end, something like: Purged 82 datasets Freed disk space: 647719608 Elapsed time: 1.51890397072 And I am confused with the way you call the scripts. This might be explained by different galaxy versions, however: delete_userless_histories.sh is in my case a wrapper executing 'cleanup_datasets.py' with the options: -d 90 -1. I do not provide the options when I call it. and the same is true for all the other scripts Regards, Hans-Rudolf On 02/28/2013 01:51 PM, Sarah Diehl wrote: Hello, our Galaxy server is running low on disk space, so I asked all users to (permanently) delete old histories and datasets. One specific user alone managed to reduce his space usage by 2 TB. That's at least what the Galaxy server says. Afterwards I additionally ran the following scripts: delete_userless_histories.sh -d 1 -r -f purge_histories.sh -d 1 -r -f purge_libraries.sh -d 1 -r -f purge_folders.sh -d 1 -r -f python cleanup_datasets.py universe_wsgi.ini -d 200 -6 -r -f purge_datasets.sh -d 1 -r -f Purging the histories took very long (about a day) and the log of deleted histories is huge. Purging the datasets also took some time. However, my disk usage is still the same as before. It wasn't reduced at all. Did I miss some important step or some waiting time? Any help would be appreciated. Thanks, Sarah ___ 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] purging datasets doesn't free up disk space
Ok, sorry for having bothered you again with my stupidness... I actually have a test instance of galaxy on the same server with the database directory hard-linked. After I deleted that one the space was free *d'oh*. - Original Message - From: Sarah Diehl di...@ie-freiburg.mpg.de To: Hans-Rudolf Hotz h...@fmi.ch, galaxy-dev@lists.bx.psu.edu List galaxy-dev@lists.bx.psu.edu Sent: Thursday, February 28, 2013 5:07:58 PM Subject: Re: [galaxy-dev] purging datasets doesn't free up disk space Hi Hans, thanks for your help. I didn't realize the sh scripts came with their own options. I just misunderstood that in the documentation. It seems to have worked though, the log file says: # 2013-02-28 11:56:20 - Handling stuff older than 1 days ... Purged 10097 datasets Freed disk space: 9515493164336 Elapsed time: 5669.43398285 So the freed disk space should be around 9 TB, right? Best regards, Sarah - Original Message - From: Hans-Rudolf Hotz h...@fmi.ch To: Sarah Diehl di...@ie-freiburg.mpg.de Cc: galaxy-dev@lists.bx.psu.edu List galaxy-dev@lists.bx.psu.edu Sent: Thursday, February 28, 2013 4:18:49 PM Subject: Re: [galaxy-dev] purging datasets doesn't free up disk space Hi Sarah May be the histories and/or datasets are shared with users who did not delete them? Also, have you looked at the log files? What is written in the log files for the purge_datasets.sh step? Do you have lines like: Removing disk, file ***/database/files/008/dataset_8271.dat and at the very end, something like: Purged 82 datasets Freed disk space: 647719608 Elapsed time: 1.51890397072 And I am confused with the way you call the scripts. This might be explained by different galaxy versions, however: delete_userless_histories.sh is in my case a wrapper executing 'cleanup_datasets.py' with the options: -d 90 -1. I do not provide the options when I call it. and the same is true for all the other scripts Regards, Hans-Rudolf On 02/28/2013 01:51 PM, Sarah Diehl wrote: Hello, our Galaxy server is running low on disk space, so I asked all users to (permanently) delete old histories and datasets. One specific user alone managed to reduce his space usage by 2 TB. That's at least what the Galaxy server says. Afterwards I additionally ran the following scripts: delete_userless_histories.sh -d 1 -r -f purge_histories.sh -d 1 -r -f purge_libraries.sh -d 1 -r -f purge_folders.sh -d 1 -r -f python cleanup_datasets.py universe_wsgi.ini -d 200 -6 -r -f purge_datasets.sh -d 1 -r -f Purging the histories took very long (about a day) and the log of deleted histories is huge. Purging the datasets also took some time. However, my disk usage is still the same as before. It wasn't reduced at all. Did I miss some important step or some waiting time? Any help would be appreciated. Thanks, Sarah ___ 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] Datasets linked into Galaxy do not work
Hi Nate, I found the problem :-). I looked for xsendfile errors in the apache log and that told me that the apache user doesn't seem to have access to the linked datasets, while the galaxy user has. Thanks for pointing me to the interaction between Galaxy and apache. Best regards, Sarah - Ursprüngliche Mail - Von: Nate Coraor n...@bx.psu.edu An: Sarah Diehl di...@ie-freiburg.mpg.de CC: galaxy-dev@lists.bx.psu.edu List galaxy-dev@lists.bx.psu.edu Gesendet: Dienstag, 19. Februar 2013 17:59:24 Betreff: Re: [galaxy-dev] Datasets linked into Galaxy do not work On Feb 14, 2013, at 4:38 AM, Sarah Diehl wrote: Hi Nate, copied datasets do work and I run Galaxy from the server root. Hi Sarah, I'm having trouble replicating this issue. Could you send along (privately) the relevant portions of your proxy server configuration, and universe_wsgi.ini? Thanks, --nate Thanks, Sarah - Original Message - From: Nate Coraor n...@bx.psu.edu To: Sarah Diehl di...@ie-freiburg.mpg.de Cc: galaxy-dev@lists.bx.psu.edu List galaxy-dev@lists.bx.psu.edu Sent: Wednesday, February 13, 2013 8:22:10 PM Subject: Re: [galaxy-dev] Datasets linked into Galaxy do not work On Feb 12, 2013, at 11:17 AM, Sarah Diehl wrote: Hi all, I have problems with datasets that were linked into Galaxy data libraries (as Admin: Add datasets, select Upload files from filesystem paths and Link to files without copying to Galaxy). Those files cannot be looked at, downloaded or viewed in a genome browser. Errors in the browser are: The requested URL /datasets/126e6c4f4c2d468e/display/ was not found on this server. The requested URL /library_common/download_dataset_from_folder was not found on this server. An error occurred while accessing: http://galaxy.immunbio.mpg.de/display_application/7108f175b5be4900/igv_bam/local_default/d85d47a3ee6ecd54/data/galaxy_7108f175b5be4900.bam Read error; BinaryCodec in readmode; streamed file (filename not available) I don't see any errors in the log files. We do this kind of linking a lot and everything worked fine in the past. I need to use this feature and need it to work, due to hard disk space and data duplication. Hi Sarah, Do display applications work correctly for datasets that were uploaded to a library and copied in to Galaxy rather than linked? Do you run Galaxy from the server root (http://galaxy.immunbio.mpg.de/) or some path underneath the root? Thanks, --nate Any help is appreciated. Best regards, Sarah ___ 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] Datasets linked into Galaxy do not work
Hi Nate, copied datasets do work and I run Galaxy from the server root. Thanks, Sarah - Original Message - From: Nate Coraor n...@bx.psu.edu To: Sarah Diehl di...@ie-freiburg.mpg.de Cc: galaxy-dev@lists.bx.psu.edu List galaxy-dev@lists.bx.psu.edu Sent: Wednesday, February 13, 2013 8:22:10 PM Subject: Re: [galaxy-dev] Datasets linked into Galaxy do not work On Feb 12, 2013, at 11:17 AM, Sarah Diehl wrote: Hi all, I have problems with datasets that were linked into Galaxy data libraries (as Admin: Add datasets, select Upload files from filesystem paths and Link to files without copying to Galaxy). Those files cannot be looked at, downloaded or viewed in a genome browser. Errors in the browser are: The requested URL /datasets/126e6c4f4c2d468e/display/ was not found on this server. The requested URL /library_common/download_dataset_from_folder was not found on this server. An error occurred while accessing: http://galaxy.immunbio.mpg.de/display_application/7108f175b5be4900/igv_bam/local_default/d85d47a3ee6ecd54/data/galaxy_7108f175b5be4900.bam Read error; BinaryCodec in readmode; streamed file (filename not available) I don't see any errors in the log files. We do this kind of linking a lot and everything worked fine in the past. I need to use this feature and need it to work, due to hard disk space and data duplication. Hi Sarah, Do display applications work correctly for datasets that were uploaded to a library and copied in to Galaxy rather than linked? Do you run Galaxy from the server root (http://galaxy.immunbio.mpg.de/) or some path underneath the root? Thanks, --nate Any help is appreciated. Best regards, Sarah ___ 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] Datasets linked into Galaxy do not work
Hi all, I have problems with datasets that were linked into Galaxy data libraries (as Admin: Add datasets, select Upload files from filesystem paths and Link to files without copying to Galaxy). Those files cannot be looked at, downloaded or viewed in a genome browser. Errors in the browser are: The requested URL /datasets/126e6c4f4c2d468e/display/ was not found on this server. The requested URL /library_common/download_dataset_from_folder was not found on this server. An error occurred while accessing: http://galaxy.immunbio.mpg.de/display_application/7108f175b5be4900/igv_bam/local_default/d85d47a3ee6ecd54/data/galaxy_7108f175b5be4900.bam Read error; BinaryCodec in readmode; streamed file (filename not available) I don't see any errors in the log files. We do this kind of linking a lot and everything worked fine in the past. I need to use this feature and need it to work, due to hard disk space and data duplication. Any help is appreciated. Best regards, Sarah ___ 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 with upload file tool on file uploaded through FTP server
Hi everyone, my local installation of Galaxy has an issue with using the Upload File tool on data that was uploaded to the ftp server. The ftp upload itself works fine: -rwxrwxrwx. 1 65533 65533 4804 2012-08-16 13:52 28S_rRNA.fa but there seems to be some issue with Galaxy moving it and I have no clue where the problem is. The final dataset /galaxy/galaxy_server/database/files/024/dataset_24020.dat is present as a file, but empty: -rw-rw-r--. 1 galaxy galaxy0 2012-08-16 13:53 dataset_24020.dat I'm grateful for any hints. Best regards, Sarah - Forwarded Message - From: di...@immunbio.mpg.de To: di...@immunbio.mpg.de, di...@immunbio.mpg.de Sent: Thursday, August 16, 2012 1:55:04 PM Subject: Galaxy tool error report from di...@immunbio.mpg.de GALAXY TOOL ERROR REPORT This error report was sent from the Galaxy instance hosted on the server xxx - This is in reference to dataset id 24020 from history id 1393 - You should be able to view the history containing the related history item 115: 28S_rRNA.fa by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link. xxx - The user 'di...@immunbio.mpg.de' provided the following information: - job id: 20566 tool id: upload1 - job command line: python /galaxy/galaxy_server/tools/data_source/upload.py /galaxy/galaxy_server /galaxy/galaxy_server/database/tmp/tmpw_TcHa /galaxy/galaxy_server/database/tmp/tmpKwHCcx 24020:/galaxy/galaxy_server/database/job_working_directory/020/20566/dataset_24020_files:/galaxy/galaxy_server/database/files/024/dataset_24020.dat - job stderr: Traceback (most recent call last): File /galaxy/galaxy_server/tools/data_source/upload.py, line 403, in module __main__() File /galaxy/galaxy_server/tools/data_source/upload.py, line 392, in __main__ add_file( dataset, registry, json_file, output_path ) File /galaxy/galaxy_server/tools/data_source/upload.py, line 289, in add_file line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) File /galaxy/galaxy_server/lib/galaxy/datatypes/sniff.py, line 98, in convert_newlines shutil.move( temp_name, fname ) File /usr/local/lib/python2.7/shutil.py, line 299, in move copy2(src, real_dst) File /usr/local/lib/python2.7/shutil.py, line 129, in copy2 copystat(src, dst) File /usr/local/lib/python2.7/shutil.py, line 98, in copystat os.utime(dst, (st.st_atime, st.st_mtime)) OSError: [Errno 1] Operation not permitted: '/galaxy/galaxy_server/database/ftp/di...@immunbio.mpg.de/28S_rRNA.fa' - job stdout: - job info: None - job traceback: None - (This is an automated message). ___ 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] Problem with upload file tool on file uploaded through FTP server
So, I fixed the problem myself ;-). For whatever reason the files need to be owned by the galaxy user. I achieved that by setting SQLDefaultUID 501 SQLDefaultGID 501 in the proftpd.conf. 501 is the UID and GID of the galaxy user and group. - Original Message - From: Sarah Diehl di...@immunbio.mpg.de To: galaxy-dev@lists.bx.psu.edu List galaxy-dev@lists.bx.psu.edu Sent: Thursday, August 16, 2012 2:24:53 PM Subject: [galaxy-dev] Problem with upload file tool on file uploaded through FTP server Hi everyone, my local installation of Galaxy has an issue with using the Upload File tool on data that was uploaded to the ftp server. The ftp upload itself works fine: -rwxrwxrwx. 1 65533 65533 4804 2012-08-16 13:52 28S_rRNA.fa but there seems to be some issue with Galaxy moving it and I have no clue where the problem is. The final dataset /galaxy/galaxy_server/database/files/024/dataset_24020.dat is present as a file, but empty: -rw-rw-r--. 1 galaxy galaxy0 2012-08-16 13:53 dataset_24020.dat I'm grateful for any hints. Best regards, Sarah - Forwarded Message - From: di...@immunbio.mpg.de To: di...@immunbio.mpg.de, di...@immunbio.mpg.de Sent: Thursday, August 16, 2012 1:55:04 PM Subject: Galaxy tool error report from di...@immunbio.mpg.de GALAXY TOOL ERROR REPORT This error report was sent from the Galaxy instance hosted on the server xxx - This is in reference to dataset id 24020 from history id 1393 - You should be able to view the history containing the related history item 115: 28S_rRNA.fa by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link. xxx - The user 'di...@immunbio.mpg.de' provided the following information: - job id: 20566 tool id: upload1 - job command line: python /galaxy/galaxy_server/tools/data_source/upload.py /galaxy/galaxy_server /galaxy/galaxy_server/database/tmp/tmpw_TcHa /galaxy/galaxy_server/database/tmp/tmpKwHCcx 24020:/galaxy/galaxy_server/database/job_working_directory/020/20566/dataset_24020_files:/galaxy/galaxy_server/database/files/024/dataset_24020.dat - job stderr: Traceback (most recent call last): File /galaxy/galaxy_server/tools/data_source/upload.py, line 403, in module __main__() File /galaxy/galaxy_server/tools/data_source/upload.py, line 392, in __main__ add_file( dataset, registry, json_file, output_path ) File /galaxy/galaxy_server/tools/data_source/upload.py, line 289, in add_file line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) File /galaxy/galaxy_server/lib/galaxy/datatypes/sniff.py, line 98, in convert_newlines shutil.move( temp_name, fname ) File /usr/local/lib/python2.7/shutil.py, line 299, in move copy2(src, real_dst) File /usr/local/lib/python2.7/shutil.py, line 129, in copy2 copystat(src, dst) File /usr/local/lib/python2.7/shutil.py, line 98, in copystat os.utime(dst, (st.st_atime, st.st_mtime)) OSError: [Errno 1] Operation not permitted: '/galaxy/galaxy_server/database/ftp/di...@immunbio.mpg.de/28S_rRNA.fa' - job stdout: - job info: None - job traceback: None - (This is an automated message). ___ 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] GATK Unified Genotyper Error
Hello all, one of my users encounters a strange error with the GATK tool Unified Genotyper. At the end of the message you see the original error report. The problem there was that the reference genome is missing. The tool was run as a part of a bigger workflow, but I double checked the workflow and the correct genome is specified there. All other GATK tools work, so there should be no error with the setup of the locally cached references. When I use the rerun button in Galaxy to repeat this step (without changing anything), everything works fine. Best regards, Sarah - Forwarded Message - From: di...@immunbio.mpg.de To: di...@immunbio.mpg.de, barenb...@immunbio.mpg.de Sent: Friday, August 10, 2012 10:08:12 AM Subject: Galaxy tool error report from barenb...@immunbio.mpg.de GALAXY TOOL ERROR REPORT - job id: 20471 tool id: gatk_unified_genotyper - job command line: python /galaxy/galaxy_server/tools/gatk/gatk_wrapper.py --max_jvm_heap_fraction 1--stdout /galaxy/galaxy_server/database/files/023/dataset_23795.dat-d -I /galaxy/galaxy_server/database/files/023/dataset_23792.dat bam gatk_input_0-d /galaxy/galaxy_server/database/files/_metadata_files/001/metadata_1060.dat bam_index gatk_input_0 -p 'java -jar /galaxy/galaxy_server/tool-data/shared/jars/gatk/GenomeAnalysisTK.jar -T UnifiedGenotyper --num_threads 4 --out /galaxy/galaxy_server/database/files/023/dataset_23793.dat --metrics_file /galaxy/galaxy_server/database/files/023/dataset_23794.dat -R --genotype_likelihoods_model BOTH --standard_min_confidence_threshold_for_calling 30.0 --standard_min_confidence_threshold_for_emitting 30.0' -d --dbsnp:dbsnp,%(file_type)s /galaxy/galaxy_data/gatk/b37/dbsnp_135.b37.vcf vcf input_dbsnp_0 - job stderr: # ERROR -- # ERROR A USER ERROR has occurred (version 1.6-13-g91f02df): # ERROR The invalid arguments or inputs must be corrected before the GATK can proceed # ERROR Please do not post this error to the GATK forum # ERROR # ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. # ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki # ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa # ERROR # ERROR MESSAGE: The fasta file you specified (/tmp/tmp-gatk-eEVeYq) does not exist. # ERROR -- - job stdout: - job info: None - job traceback: None - (This is an automated message). ___ 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] Task Manager: This Galaxy instance is not the job manager.
Hi, I think this bug is already fixed in the latest galaxy-central. I upgraded to the latest version last week or so and now it works fine again. Best, Sarah - Original Message - From: Rémy Dernat remy...@gmail.com To: Edward Kirton eskir...@lbl.gov Cc: galaxy-dev@lists.bx.psu.edu Sent: Friday, June 8, 2012 9:14:14 AM Subject: Re: [galaxy-dev] Task Manager: This Galaxy instance is not the job manager. Hi, Same issue here with multi servers. When I connect to the job manager instance, I have This Galaxy instance is not the job manager. If using multiple servers, please directly access the job manager instance to manage jobs. On the web server instance : Server Error URL: http://162.38.181.30:8000/galaxy/admin/jobs 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 : 184 in decorator return func ( self , trans , * args , ** kwargs ) Module galaxy.web.base.controller : 2428 in jobs job_lock = trans . app . job_manager . job_queue . job_lock ) AttributeError: 'NoopQueue' object has no attribute 'job_lock' extra data full traceback URL: http://162.38.181.30:8000/galaxy/admin/jobs 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 : 184 in decorator return func ( self , trans , * args , ** kwargs ) Module galaxy.web.base.controller : 2428 in jobs job_lock = trans . app . job_manager . job_queue . job_lock ) AttributeError: 'NoopQueue' object has no attribute 'job_lock' Regards, Rem 2012/6/7 Edward Kirton eskir...@lbl.gov yes, i've had the same error ever since the last galaxy-dist release. i previously had multiple servers and switched to the one manager, two handlers. rewrite rules didn't need to be changed. On Thu, May 24, 2012 at 8:14 AM, Sarah Diehl di...@immunbio.mpg.de wrote: Hi all, I have a similar, maybe related problem. I'm running a configuration as described at http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling . I have three webservers, one manager and two handlers. Everything is behind an Apache and the rewrite rules are set accordingly. When I try to access Manage Jobs, I also get the error This Galaxy instance is not the job manager. If using multiple servers, please directly access the job manager instance to manage jobs.. I have set the rewrite rule for admin/jobs to point to the manager server. When I access the manager directly from localhost I get the same error, while all other servers (web and handler) throw a server error: 127.0.0.1 - - [24/May/2012:15:37:50 +0200] GET /admin/jobs HTTP/1.1 500 - - Mozilla/5.0 (X11; Linux x86_64; rv:10.0.4) Gecko/20120424 Firefox/10.0.4 Error - type 'exceptions.AttributeError': 'NoopQueue' object has no attribute 'job_lock' URL: http://localhost:8080/admin/jobs File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 184 in decorator return func( self, trans, *args, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/base/controller.py', line 2428 in jobs job_lock = trans.app.job_manager.job_queue.job_lock ) AttributeError: 'NoopQueue' object has no attribute 'job_lock' Before the update everything worked fine (I also ran multiple servers then). Best regards, Sarah On 05/16/2012 10:27 PM, Dave Lin wrote
[galaxy-dev] strange issues with tool list
Hi all, currently I face some strange behaviour of the tool panel in Galaxy if I add top-level label tags to the tool_conf.xml. The problem is that the labels stay forever, even if I remove them again from the tool_conf.xml and they also appear three section earlier than where I put them. I tried to remove all tool configs except the one tool_conf.xml. I used just the unchanged tool_conf.xml.main, which added more labels that now stay, and I emptied the tmp directory. Nothing helped. Any help is very much appreciated. Best regards, Sarah ___ 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] strange issues with tool list
Thanks for pointing that out. I missed that there's now a seperate file to organize everything. However, it still seems to have some problems when installing tools from the shed. I just replaced some of my old manual installations of tools with an automatic installation from the shed, but some of the tools don't show up in the list or disappear after I install the next one. After deleting the integrated_tool_panel.xml again and restarting it seems to be fine for now. On 05/24/2012 02:57 PM, Greg Von Kuster wrote: Hello Sarah, This section of the Galaxy tool shed wiki should provide the information you need. Let me know if you bump into any additional questions. http://wiki.g2.bx.psu.edu/Tool%20Shed#Managing_the_layout_of_your_Galaxy_tool_panel Thanks! Greg Von Kuster On May 24, 2012, at 8:15 AM, Sarah Diehl wrote: Hi all, currently I face some strange behaviour of the tool panel in Galaxy if I add top-level label tags to the tool_conf.xml. The problem is that the labels stay forever, even if I remove them again from the tool_conf.xml and they also appear three section earlier than where I put them. I tried to remove all tool configs except the one tool_conf.xml. I used just the unchanged tool_conf.xml.main, which added more labels that now stay, and I emptied the tmp directory. Nothing helped. Any help is very much appreciated. Best regards, Sarah ___ 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] Task Manager: This Galaxy instance is not the job manager.
Hi all, I have a similar, maybe related problem. I'm running a configuration as described at http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling. I have three webservers, one manager and two handlers. Everything is behind an Apache and the rewrite rules are set accordingly. When I try to access Manage Jobs, I also get the error This Galaxy instance is not the job manager. If using multiple servers, please directly access the job manager instance to manage jobs.. I have set the rewrite rule for admin/jobs to point to the manager server. When I access the manager directly from localhost I get the same error, while all other servers (web and handler) throw a server error: 127.0.0.1 - - [24/May/2012:15:37:50 +0200] GET /admin/jobs HTTP/1.1 500 - - Mozilla/5.0 (X11; Linux x86_64; rv:10.0.4) Gecko/20120424 Firefox/10.0.4 Error - type 'exceptions.AttributeError': 'NoopQueue' object has no attribute 'job_lock' URL: http://localhost:8080/admin/jobs File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 184 in decorator return func( self, trans, *args, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/base/controller.py', line 2428 in jobs job_lock = trans.app.job_manager.job_queue.job_lock ) AttributeError: 'NoopQueue' object has no attribute 'job_lock' Before the update everything worked fine (I also ran multiple servers then). Best regards, Sarah On 05/16/2012 10:27 PM, Dave Lin wrote: Dear Galaxy Team, I've been getting the following error for some time when I try to access the Manage Jobs Task. This Galaxy instance is not the job manager. If using multiple servers, please directly access the job manager instance to manage jobs. For debugging purposes, I'm only running the single master instance. I'm using CloudMan/Amazon EC2. I traced the code and suspect it might have something to do with an Amazon IP Address/hostname discrepancy, but am not sure how to go about fixing this. On a related note, if I can't access this page, what is the best way to clear/cancel jobs via the command line? Thanks in advance, Dave Thanks, Dave ___ 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] AttributeError: 'module' object has no attribute 'FakeSocket'
Hi all, today I updated my test server to the newest galaxy-central version. However, when I start it, I get the following error: Traceback (most recent call last): File ./scripts/paster.py, line 34, in module command.run() File /galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py, line 84, in run invoke(command, command_name, options, args[1:]) File /galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py, line 123, in invoke exit_code = runner.run(args) File /galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py, line 218, in run result = self.command() File /galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py, line 276, in command relative_to=base, global_conf=vars) File /galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py, line 313, in loadapp **kw) File /galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File /galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 224, in loadobj global_conf=global_conf) File /galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 248, in loadcontext global_conf=global_conf) File /galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File /galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 413, in get_context section) File /galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 458, in _context_from_explicit value = import_string(found_expr) File /galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 18, in import_string return pkg_resources.EntryPoint.parse(x=+s).load(False) File /galaxy/galaxy_test/lib/pkg_resources.py, line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File /galaxy/galaxy_test/lib/galaxy/web/buildapp.py, line 19, in module from galaxy import config, jobs, util, tools File /galaxy/galaxy_test/lib/galaxy/tools/__init__.py, line 33, in module from galaxy.util.shed_util import * File /galaxy/galaxy_test/lib/galaxy/util/shed_util.py, line 14, in module from mercurial import ui, commands File /galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/commands.py, line 12, in module import hg, scmutil, util, revlog, extensions, copies, error, bookmarks File /galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/hg.py, line 12, in module import localrepo, bundlerepo, httprepo, sshrepo, statichttprepo, bookmarks File /galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httprepo.py, line 11, in module import changegroup, statichttprepo, error, httpconnection, url, util, wireproto File /galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/statichttprepo.py, line 11, in module import changelog, byterange, url, error File /galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/url.py, line 13, in module import httpconnection as httpconnectionmod File /galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpconnection.py, line 16, in module from mercurial import httpclient File /galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/__init__.py, line 48, in module import socketutil File /galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/socketutil.py, line 82, in module class FakeSocket(httplib.FakeSocket): AttributeError: 'module' object has no attribute 'FakeSocket' Any help appreciated. Thanks. Sarah ___ 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] AttributeError: 'module' object has no attribute 'FakeSocket'
Thanks Peter! It's very likely that I have the exact same problem, because I also have CentOS and needed to compile Python. On 05/22/2012 05:04 PM, Peter Cock wrote: On Tue, May 22, 2012 at 3:30 PM, Sarah Diehldi...@immunbio.mpg.de wrote: Hi all, today I updated my test server to the newest galaxy-central version. However, when I start it, I get the following error: Traceback (most recent call last): File ./scripts/paster.py, line 34, inmodule command.run() File /galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py, line 84, in run invoke(command, command_name, options, args[1:]) File /galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py, line 123, in invoke exit_code = runner.run(args) File /galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py, line 218, in run result = self.command() File /galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py, line 276, in command relative_to=base, global_conf=vars) File /galaxy/galaxy_test/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py, line 313, in loadapp **kw) File /galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 204, in loadapp return loadobj(APP, uri, name=name, **kw) File /galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 224, in loadobj global_conf=global_conf) File /galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 248, in loadcontext global_conf=global_conf) File /galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 278, in _loadconfig return loader.get_context(object_type, name, global_conf) File /galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 413, in get_context section) File /galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 458, in _context_from_explicit value = import_string(found_expr) File /galaxy/galaxy_test/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py, line 18, in import_string return pkg_resources.EntryPoint.parse(x=+s).load(False) File /galaxy/galaxy_test/lib/pkg_resources.py, line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File /galaxy/galaxy_test/lib/galaxy/web/buildapp.py, line 19, inmodule from galaxy import config, jobs, util, tools File /galaxy/galaxy_test/lib/galaxy/tools/__init__.py, line 33, in module from galaxy.util.shed_util import * File /galaxy/galaxy_test/lib/galaxy/util/shed_util.py, line 14, in module from mercurial import ui, commands File /galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/commands.py, line 12, inmodule import hg, scmutil, util, revlog, extensions, copies, error, bookmarks File /galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/hg.py, line 12, inmodule import localrepo, bundlerepo, httprepo, sshrepo, statichttprepo, bookmarks File /galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httprepo.py, line 11, inmodule import changegroup, statichttprepo, error, httpconnection, url, util, wireproto File /galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/statichttprepo.py, line 11, inmodule import changelog, byterange, url, error File /galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/url.py, line 13, inmodule import httpconnection as httpconnectionmod File /galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpconnection.py, line 16, inmodule from mercurial import httpclient File /galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/__init__.py, line 48, inmodule import socketutil File /galaxy/galaxy_test/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs2.egg/mercurial/httpclient/socketutil.py, line 82, inmodule class FakeSocket(httplib.FakeSocket): AttributeError: 'module' object has no attribute 'FakeSocket' Any help appreciated. Thanks. Sarah I had this happen to me last month, https://twitter.com/#!/pjacock/statuses/194797125375234053 Quote: Just recompiled #Python 2.6 ... missing ssl libraries last time finally bit me with import error doing 'from httplib import FakeSocket' Basically (outside Galaxy), using the same Python that Galaxy uses, try 'from httplib import FakeSocket' - if you get an ImportError that explains why Galaxy breaks. In my case this was a locally compiled Python (since we are using CentOS where the system Python is too old), and we'd compiled it without the SSL libraries. Until relatively recently this didn't mater for using Galaxy - now it does. Peter ___ Please keep all replies on the list by using reply all in your mail client. To
Re: [galaxy-dev] Error when exporting history to file
Hi Jeremy, I was able to reproduce the error on the public Galaxy server. I shared the history with you (jeremy.goe...@emory.edu). It's named export history to file bug. Thanks. Sarah - Original Message - From: Sarah Diehl di...@immunbio.mpg.de To: Jeremy Goecks jeremy.goe...@emory.edu Cc: galaxy-dev@lists.bx.psu.edu List galaxy-dev@lists.bx.psu.edu Sent: Wednesday, May 9, 2012 11:40:50 AM Subject: Re: [galaxy-dev] Error when exporting history to file Hi Jeremy, I'm using galaxy-dist, but it's quite possible that I'm a version or two behind. I'm not yet able to reproduce the problem on the public server, but I'm still missing some steps from the input to the problematic dataset. I'll get back to you if I'm able to reproduce it or if it still persist when I have updated our Galaxy server. Thanks for your help! Best regards, Sarah On 05/09/2012 02:09 AM, Jeremy Goecks wrote: Sarah, I'm not able to reproduce your issue using galaxy-central. This could mean that this bug has been fixed in galaxy-central but hasn't made it to galaxy-dist yet—it appears you are using galaxy-dist—or there's other information needed to reproduce this issue. A couple more questions: Are you using galaxy-dist? Can you reproduce the issue on our public server using the problematic dataset and/or workflow? Thanks, J. On May 7, 2012, at 12:33 PM, Sarah Diehl wrote: Sort (version 1.0.1) on column: c5 with flavor: Numerical sort everything in: Descending order On 05/07/2012 06:28 PM, Jeremy Goecks wrote: Sarah, What tool was used to create the problematic dataset? Thanks, J. On May 7, 2012, at 12:17 PM, Sarah Diehl wrote: Hi all, I get the following error when I try to export a specific history to file: 10.1.5.190 - - [07/May/2012:18:01:08 +0200] GET /history/export_archive HTTP/1.1 500 - http://galaxy.immunbio.mpg.de/; Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24) Gecko/2008 Fedora/3.6.24-1.fc14 Firefox/3.6.24 Error -type 'exceptions.TypeError':galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0 is not JSON serializable URL: http://galaxy.immunbio.mpg.de/history/export_archive File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line 106 in execute include_deleted=incoming[ 'include_deleted' ] ) File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in setup_job jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py', line 268 in dumps File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 214 in encode File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 282 in iterencode File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in default return simplejson.JSONEncoder.default( self, obj ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 190 in default TypeError:galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0 is not JSON serializable I tracked the problem down to a single bed file. I copied it into a new empty history and I can still not export this history to a file. This file doesn't have any special characters in either its name, info or annotation. I can't find anything special about this file... Any help is greatly appreciated! Best regards, Sarah ___ 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
Re: [galaxy-dev] Error when exporting history to file
Hi Jeremy, I'm using galaxy-dist, but it's quite possible that I'm a version or two behind. I'm not yet able to reproduce the problem on the public server, but I'm still missing some steps from the input to the problematic dataset. I'll get back to you if I'm able to reproduce it or if it still persist when I have updated our Galaxy server. Thanks for your help! Best regards, Sarah On 05/09/2012 02:09 AM, Jeremy Goecks wrote: Sarah, I'm not able to reproduce your issue using galaxy-central. This could mean that this bug has been fixed in galaxy-central but hasn't made it to galaxy-dist yet—it appears you are using galaxy-dist—or there's other information needed to reproduce this issue. A couple more questions: Are you using galaxy-dist? Can you reproduce the issue on our public server using the problematic dataset and/or workflow? Thanks, J. On May 7, 2012, at 12:33 PM, Sarah Diehl wrote: Sort (version 1.0.1) on column: c5 with flavor: Numerical sort everything in: Descending order On 05/07/2012 06:28 PM, Jeremy Goecks wrote: Sarah, What tool was used to create the problematic dataset? Thanks, J. On May 7, 2012, at 12:17 PM, Sarah Diehl wrote: Hi all, I get the following error when I try to export a specific history to file: 10.1.5.190 - - [07/May/2012:18:01:08 +0200] GET /history/export_archive HTTP/1.1 500 - http://galaxy.immunbio.mpg.de/; Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24) Gecko/2008 Fedora/3.6.24-1.fc14 Firefox/3.6.24 Error -type 'exceptions.TypeError':galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0 is not JSON serializable URL: http://galaxy.immunbio.mpg.de/history/export_archive File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line 106 in execute include_deleted=incoming[ 'include_deleted' ] ) File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in setup_job jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py', line 268 in dumps File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 214 in encode File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 282 in iterencode File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in default return simplejson.JSONEncoder.default( self, obj ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 190 in default TypeError:galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0 is not JSON serializable I tracked the problem down to a single bed file. I copied it into a new empty history and I can still not export this history to a file. This file doesn't have any special characters in either its name, info or annotation. I can't find anything special about this file... Any help is greatly appreciated! Best regards, Sarah ___ 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/
[galaxy-dev] Error when exporting history to file
Hi all, I get the following error when I try to export a specific history to file: 10.1.5.190 - - [07/May/2012:18:01:08 +0200] GET /history/export_archive HTTP/1.1 500 - http://galaxy.immunbio.mpg.de/; Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24) Gecko/2008 Fedora/3.6.24-1.fc14 Firefox/3.6.24 Error - type 'exceptions.TypeError': galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0 is not JSON serializable URL: http://galaxy.immunbio.mpg.de/history/export_archive File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line 106 in execute include_deleted=incoming[ 'include_deleted' ] ) File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in setup_job jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py', line 268 in dumps File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 214 in encode File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 282 in iterencode File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in default return simplejson.JSONEncoder.default( self, obj ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 190 in default TypeError: galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0 is not JSON serializable I tracked the problem down to a single bed file. I copied it into a new empty history and I can still not export this history to a file. This file doesn't have any special characters in either its name, info or annotation. I can't find anything special about this file... Any help is greatly appreciated! Best regards, Sarah ___ 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] Questions about configuring upload via FTP
Hi everybody, how up-to-date is http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP? I just set up a ProFTPd according to those directions, but had to change some things, especially regarding permissions of directories and files. I had to set Umask 000 CreateHome on 755 dirmode 755 All files and directories are created by the user nobody the server runs as. However, the galaxy user needs to access those and also wants to delete files. So I had the make the directories readable to all and the files even writeable for all. Is there a better way to do this? I tried running proftpd as the galaxy user, but the files still belonged to nobody. All my attempts to get the server to create files as the galaxy user or chown to galaxy failed. Best regards, Sarah ___ 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] Allow dataset with custom build to be displayed in local IGV
Hi all,
is there some way I can allow datasets (specifically bam files) that are
annotated with a custom build to be displayed in a local IGV (assuming a
genome with the same name was generated for IGV)?
I tried some things with display_applications/igv/bam.xml, but I
couldn't get it to work properly. One challenge is to disable the filter
for the local igv and the second challenge is to not do the build name
mapping for custom builds. Here is what I tried, but didn't work (filter
is still applied to local IGV):
filter
#if $site_id.startswith( 'local_' )
${dataset.dbkey in $site_dbkeys}
#end if
/filter
param type=template name=site_organism strip=True
#if $bam_file.dbkey in $site_dbkeys
$site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ]
#else
$bam_file.dbkey
#end if
/param
Any help is greatly appreciated!
Best regards,
Sarah
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[galaxy-dev] KeyError: 'datatypes_config'
Hi all, I just updated our Galaxy from the latest dist to the latest central release. When I had previously updatet to the dist release, the emboss datatypes were installed as a shed tool. However when restarting the server after the update the datatypes_conf.xml in the emboss shed directory got deleted. After some back and forth I ended up with the following error, which I can't seem to resolve. galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-24 16:32:28,780 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-24 16:32:28,780 Loaded reference to tool shed: Galaxy test tool shed Traceback (most recent call last): File /galaxy/galaxy_server/lib/galaxy/web/buildapp.py, line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /galaxy/galaxy_server/lib/galaxy/app.py, line 58, in __init__ self.installed_repository_manager.load_proprietary_datatypes() File /galaxy/galaxy_server/lib/galaxy/tool_shed/__init__.py, line 21, in load_proprietary_datatypes datatypes_config = metadata[ 'datatypes_config' ] KeyError: 'datatypes_config' Any help would be greatly appreciated! Thanks! Sarah ___ 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] KeyError: 'datatypes_config'
Hi Greg, thanks for the help! However, the error still persists. I tried to play around with lots of things, but nothing seems to change the error. Sarah On 02/24/2012 05:06 PM, Greg Von Kuster wrote: Hello Sarah, This is due to a known bug (not yet fixed in the distribution). The bug causes the file named datatypes_conf.xml included in installed repositories to be deleted. You'll need to go to the directory on disk where your emboss_datatypes repository is installed ( make sure you are in the directory where the file named datatypes_conf.xml exists in the installed repository directory) and type the following command (this will undelete the file). %hg revert datatypes_conf.xml If you'd like to apply a fix to the code in your local instance, do the following. You'll need to apply the fix to the file ~/lib/galaxy/util/shed_util.py. The end of the method named alter_config_and_load_proprietary_datatypes() looks like the following (these lines should be about 601 - 607 in your version of the file, I believe). # Load proprietary datatypes app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=proprietary_datatypes_config, deactivate=deactivate, override=override ) try: os.unlink( proprietary_datatypes_config ) except: pass return converter_path, display_path You'll need to make this change (note the if statement that now contains the try block): # Load proprietary datatypes app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=proprietary_datatypes_config, deactivate=deactivate, override=override ) if datatype_files: try: os.unlink( proprietary_datatypes_config ) except: pass return converter_path, display_path Sorry for the inconvenience - I'll get this fix out as soon as I possibly can. Let me know if you bump into any problems with this. Greg Von Kuster On Feb 24, 2012, at 10:42 AM, Sarah Diehl wrote: Hi all, I just updated our Galaxy from the latest dist to the latest central release. When I had previously updatet to the dist release, the emboss datatypes were installed as a shed tool. However when restarting the server after the update the datatypes_conf.xml in the emboss shed directory got deleted. After some back and forth I ended up with the following error, which I can't seem to resolve. galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-24 16:32:28,780 Loaded reference to tool shed: Galaxy main tool shed galaxy.tool_shed.tool_shed_registry DEBUG 2012-02-24 16:32:28,780 Loaded reference to tool shed: Galaxy test tool shed Traceback (most recent call last): File /galaxy/galaxy_server/lib/galaxy/web/buildapp.py, line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /galaxy/galaxy_server/lib/galaxy/app.py, line 58, in __init__ self.installed_repository_manager.load_proprietary_datatypes() File /galaxy/galaxy_server/lib/galaxy/tool_shed/__init__.py, line 21, in load_proprietary_datatypes datatypes_config = metadata[ 'datatypes_config' ] KeyError: 'datatypes_config' Any help would be greatly appreciated! Thanks! Sarah ___ 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] How to learn about new tools in the official Tool Shed
Hello, one quick question: is there a way to get news about new tools in the Tool Shed? I saw that I can subscribe to get news about already existing tools, but how about newly created ones? I would also be fine with some subscription to any changes in the Tool Shed in general. Best regards, Sarah ___ 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] xml tool wrapper conditional
I'm only guessing here, but maybe the issue is that the parameter names are all the same (namely model). Did you try with only unique names? Especially this one: param name=models type=select label=model source help=History or installed models? value=local should get it's own name. Sarah On 02/06/2012 03:38 PM, Holger Klein wrote: Dear all, I'm working on a tool wrapper which for a sequence scoring tool. It's supposed to score sequences either using a library installed to galaxy (tool-data/models.loc) or datasets from the user history. I tried to implement this behavior using theconditional /when value mechanism, simplified code follows below. Using locally installed models (from models.loc) fails with NotFound: cannot find 'models', although in the details view of the failed tool run model database points to the right file. Using the model file from the history works. Defining _only_ locally installed models from models.loc also works (removing theconditional stuff and leaving only the part insidewhen value='local' /when). The commandline might look a bit strange but is correct. Can anybody spot what is going wrong here? Regards, Holger -- command calcModels --scoreFasta -- --fa $fasta_in --bgFa $fasta_background --models $models $output_table /command inputs param format=fasta name=fasta_in type=data label=Input Fasta File / param format=fasta name=fasta_background type=data label=Background Fasta File / conditional name=ModelSource param name=models type=select label=model source help=History or installed models? value=local option value=localLocally installed models/option option value=historyModels from your history/option /param when value=local param name=models type=select label=model database options from_file=models.loc column name=name index=1/ column name=value index=2/ /options /param /when when value=history param name=models type=data format=tabular label=model database / /when /conditional /inputs ___ 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] help with complicated conditional output format
Hello, I'm trying to write a wrapper for the intersectBed tool from the BEDTools suite. The difficulty lies in the possible combinations of input and output data formats. Input can be either bed or bam. When the input is bed, the output is also bed. However, when the input is bam the output can be either bam (default) or bed (by an additional command-line switch). I cannot figure out how to dynamically set the output format correctly. The wrapper always fails in at least one of the three cases. I collect the input as follows: inputs conditional name=intype param name=inselect type=select label=Select input file type option value=bed selected=trueBED, GFF/option option value=bamBAM/option /param when value=bed param name=inputBed type=data format=bed,gff label=Input A help=Each feature in A is compared to B in search of overlaps./ /when when value=bam param name=inputBam type=data format=bam label=Input A help=Each BAM alignment in A is compared to B in search of overlaps./ param name=bed type=boolean truevalue=-bed falsevalue= checked=False label=Write output as BED help=The default is to write output in BAM when using BAM as input./ /when /conditional param name=input type=data format=bed label=Input B/ /inputs I really want to keep the conditional and the select, because the program behaves slightly different depending on the input format. I tried to define the output like that: outputs data name=output format=input/ change_format when input=intype.bed value= format=bam/ /change_format /outputs However, this fails when the input is bam and I want a bed output. I tried many different things I found in the wiki and on the mailing list, but nothing worked properly. I'm grateful for any ideas how to solve this problem. Thanks for your help in advance! Sarah ___ 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] help with complicated conditional output format
Ok, I found the problem myself. I was totally searching in the wrong place for the error. It was simply a syntax problem. The output definition should be like follows: outputs data name=output format=bed change_format when input=intype.bed value= format=bam/ /change_format /data /outputs I was closing the data tag too early. On 10/06/2011 11:40 AM, Sarah Diehl wrote: Hello, I'm trying to write a wrapper for the intersectBed tool from the BEDTools suite. The difficulty lies in the possible combinations of input and output data formats. Input can be either bed or bam. When the input is bed, the output is also bed. However, when the input is bam the output can be either bam (default) or bed (by an additional command-line switch). I cannot figure out how to dynamically set the output format correctly. The wrapper always fails in at least one of the three cases. I collect the input as follows: inputs conditional name=intype param name=inselect type=select label=Select input file type option value=bed selected=trueBED, GFF/option option value=bamBAM/option /param when value=bed param name=inputBed type=data format=bed,gff label=Input A help=Each feature in A is compared to B in search of overlaps./ /when when value=bam param name=inputBam type=data format=bam label=Input A help=Each BAM alignment in A is compared to B in search of overlaps./ param name=bed type=boolean truevalue=-bed falsevalue= checked=False label=Write output as BED help=The default is to write output in BAM when using BAM as input./ /when /conditional param name=input type=data format=bed label=Input B/ /inputs I really want to keep the conditional and the select, because the program behaves slightly different depending on the input format. I tried to define the output like that: outputs data name=output format=input/ change_format when input=intype.bed value= format=bam/ /change_format /outputs However, this fails when the input is bam and I want a bed output. I tried many different things I found in the wiki and on the mailing list, but nothing worked properly. I'm grateful for any ideas how to solve this problem. Thanks for your help in advance! Sarah ___ 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] Multiple fastq files per forward/reverse mates (tophat and related tools)
Hi Gus, for parameters of the type select you can enable the option to select multiple options. However, this isn't really suitable for files, I think. I recommend to use the repeat tag (see http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax) around the existing parameter to make it possible to select multiple files. Sarah On 07/11/2011 02:18 AM, W. Augustine Dunn III wrote: I want to customize the tophat and related interfaces to allow more than one fastq file per fwd/rev set as is allowed and very helpful in the CLI version: $ tophat -o output -p 8 -r 125 -G annotation.gtf myBowtieIndex run1_fwd.fastq,run2_fwd.fastq run1_rev.fastq,run2_rev.fastq Is there a way to select multiple items from a dropdown menu or can/should i convert that part of the interface to a text input field so I can simply feed the command a list of files like on the command line? This last method seems like it might be a little unsafe though. But even if its not, it divorces the file management from the history which seems like its not a good idea. Has anyone done this? Thanks, Gus -- In science, fact can only mean confirmed to such a degree that it would be perverse to withhold provisional assent. I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms. /-Stephen Jay Gould/ ___ 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 when changing default permissions for new histories
Hello, when I go to the user preferences and try to change the default permissions for new histories, I always get the following error (full message in attachment): Error - type 'exceptions.TypeError': set_default_permissions() takes exactly 3 non-keyword arguments (2 given) URL: http://solweb2.immunbio.mpg.de/user/set_default_permissions File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) TypeError: set_default_permissions() takes exactly 3 non-keyword arguments (2 given) I would greatly appreciate any help to solve this problem. Thanks in advance! Best regards, Sarah 10.1.5.190 - - [08/Jul/2011:09:36:14 +0200] POST /user/set_default_permissions HTTP/1.1 500 - http://solweb2.immunbio.mpg.de/user/set_default_permissions?cntrller=user; Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.17) Gecko/20110428 Fedora/3.6.17-1.fc14 Firefox/3.6.17 Error - type 'exceptions.TypeError': set_default_permissions() takes exactly 3 non-keyword arguments (2 given) URL: http://solweb2.immunbio.mpg.de/user/set_default_permissions File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) TypeError: set_default_permissions() takes exactly 3 non-keyword arguments (2 given) CGI Variables - CONTENT_LENGTH: '-1' CONTENT_TYPE: 'application/x-www-form-urlencoded' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_CHARSET: 'ISO-8859-1,utf-8;q=0.7,*;q=0.7' HTTP_ACCEPT_ENCODING: 'gzip,deflate' HTTP_ACCEPT_LANGUAGE: 'en-us,en;q=0.5' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: 'galaxysession=f611411aa8a0c665b61db8293a8ea068714c7d705211c2d710c72adcfca0d053c2f647fee2d5d9cd' HTTP_HOST: 'solweb2.immunbio.mpg.de' HTTP_REFERER: 'http://solweb2.immunbio.mpg.de/user/set_default_permissions?cntrller=user' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.17) Gecko/20110428 Fedora/3.6.17-1.fc14 Firefox/3.6.17' HTTP_X_FORWARDED_FOR: '10.1.5.190' HTTP_X_FORWARDED_HOST: 'solweb2.immunbio.mpg.de' HTTP_X_FORWARDED_SERVER: 'solweb2' ORGINAL_HTTP_HOST: 'localhost:8081' ORGINAL_REMOTE_ADDR: '127.0.0.1' PATH_INFO: '/user/set_default_permissions' REMOTE_ADDR: '10.1.5.190' REQUEST_METHOD: 'POST' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8081' SERVER_PROTOCOL: 'HTTP/1.1' Configuration - __file__: '/galaxy/galaxy_server/universe_wsgi.webapp.ini' admin_users: 'di...@immunbio.mpg.de' allow_library_path_paste: 'False' allow_user_creation: 'True' allow_user_dataset_purge: 'True' allow_user_deletion: 'True' apache_xsendfile: 'True' bugs_email: 'di...@immunbio.mpg.de' cookie_path: '/' database_connection: 'postgres://user:password@localhost/galaxy' database_engine_option_server_side_cursors: 'True' database_engine_option_strategy: 'threadlocal' datatypes_config_file: 'datatypes_conf.xml' debug: 'False' enable_api: 'True' enable_job_running: 'False' enable_pages: 'True' enable_tracks: 'True' error_email_to: 'di...@immunbio.mpg.de' external_service_type_config_file: 'external_service_types_conf.xml' external_service_type_path: 'external_service_types' file_path: 'database/files' fulltext_max_size: '200' fulltext_noindex_filetypes: 'bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger' gbrowse_display_sites: 'wormbase,tair,modencode_worm,modencode_fly,local_mouse,local_human,local_fly' genetrack_display_sites: 'main,test' here: '/galaxy/galaxy_server' id_secret: 'MPI-IE' job_working_directory: 'database/job_working_directory' len_file_path: 'tool-data/shared/ucsc/chrom' library_import_dir: '/galaxy/galaxy_server/data' local_job_queue_workers: '15' log_actions: 'True' log_events: 'True' log_level: 'DEBUG' new_file_path: 'database/tmp' new_user_dataset_access_role_default_private: 'False' nglims_config_file: 'tool-data/nglims.yaml' require_login: 'False' set_metadata_externally:
Re: [galaxy-dev] bug or feature :)
I just also found out about this bug (or feature). It is exactly the same for me and I'm running an older Galaxy version (galaxy-dist from April 8, 2011). On 07/06/2011 09:32 PM, Bossers, Alex wrote: In our local instance (central version) up to changeset (June 28th) I noticed in the admin panel to manage jobs some odd behaviour; When I set the update Jobs cutoff on 10 seconds and press refresh the item below (administrative Job Lock) is also activated and new jobs are locked. Is that a planned feature, a bug or is something wrong in our local instance. Another refresh toggles it back to normal. Alex ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ 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 using build_profile_indexes.py on hg19
Hi everybody, when I run the build_profile_indexes.py script in the scripts/tools/annotation_profiler/ directory on hg19 (downloaded yesterday from UCSC), I get the following error: Created table dir (profiled_annotations/hg19/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal). ['fileName'] Table wgEncodeOpenChromFaireGlioblaBaseOverlapSignal (/galaxy/galaxy_data/ucsc_data/hg19/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal.sql) does not appear to have a chromosome, a start, or a stop. Removing empty table (wgEncodeOpenChromFaireGlioblaBaseOverlapSignal) directory (profiled_annotations/hg19/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal). Created table dir (profiled_annotations/hg19/wgEncodeCshlShortRnaSeqK562ChromatinShortTransfrags). ['bin', 'chrom', 'chromStart', 'chromEnd', 'name', 'score', 'strand', 'length', 'numUnique', 'numReads', 'minSeqCount', 'maxSeqCount', 'aveSeqCount', 'firstSeqCount', 'medSeqCount', 'thirdSeqCount', 'minReadCount', 'maxReadCount', 'aveReadCount', 'firstReadCount', 'medReadCount', 'thirdReadCount', 'numRegions', 'regStart', 'regLength', 'seqCount', 'regCount', 'sumCount', 'KEY', 'KEY'] Traceback (most recent call last): File /galaxy/galaxy_backup/galaxy-dist/scripts/tools/annotation_profiler/build_profile_indexes.py, line 338, in module if __name__ == __main__: __main__() File /galaxy/galaxy_backup/galaxy-dist/scripts/tools/annotation_profiler/build_profile_indexes.py, line 310, in __main__ bitset_dict[ chrom ].set_range( start, end - start ) File bitset.pyx, line 128, in bx.bitset.BitSet.set_range (lib/bx/bitset.c:1130) File bitset.pyx, line 93, in bx.bitset.b_check_range_count (lib/bx/bitset.c:656) IndexError: End 16573 is larger than the size of this BitSet (16571). Everything worked fine with mm9 and dm3. Since the script wasn't changed in the last year, I suspect it has to do with the UCSC data. We don't really use hg19, so I'm fine with just leaving it out for now, but I wanted to report the error anyway. Best regards, Sarah ___ 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] UnicodeDecodeError
Hello everybody, currently I have some trouble with the following kind of error: UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 155: ordinal not in range(128) We have encountered it twice now. The first time it was related to a shared library, which could not be opened anymore because of this error. So we deleted the library and set it up again. The second time it was related to a workflow. Clicking on Run caused this error to appear, while editing still worked. This time I saved the error message and you can find it attached to this mail. The cause of the error was a sign in a renaming step inside the workflow (the was part of the new name). After removing the everything worked again. However, when using the in a history item, it works without a problem. Unfortunately I cannot reproduce the error currently on my machine. The computer that caused it was a Mac. Should we just try to avoid any special characters or is this actually a bug which could be fixed? Best regards, Sarah 10.1.4.162 - - [09/Jun/2011:10:56:28 +0200] GET /workflow/run?id=91cc5a0bc3008f7d HTTP/1.1 500 - http://solweb2/workflow/list_for_run; Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.16) Gecko/20110319 Firefox/3.6.16 Error - type 'exceptions.UnicodeDecodeError': 'ascii' codec can't decode byte 0xe2 in position 155: ordinal not in range(128) URL: http://solweb2/workflow/run?id=91cc5a0bc3008f7d File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py', line 1397 in run incoming=kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 650 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 661 in fill_template_mako return template.render( **data ) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/template.py', line 133 in render return runtime._render(self, self.callable_, args, data) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 364 in _render _render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data)) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/galaxy/galaxy_server/database/compiled_templates/base.mako.py', line 40 in render_body __M_writer(unicode(next.body())) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 255 in lambda return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/galaxy/galaxy_server/database/compiled_templates/workflow/run.mako.py', line 226 in render_body __M_writer(unicode(do_inputs( module.get_runtime_inputs(type_filter), step.state.inputs, errors.get( step.id, dict() ), , step ))) File '/galaxy/galaxy_server/database/compiled_templates/workflow/run.mako.py', line 39 in do_inputs return render_do_inputs(context.locals_(__M_locals),inputs,values,errors,prefix,step,other_values) File '/galaxy/galaxy_server/database/compiled_templates/workflow/run.mako.py', line 391 in render_do_inputs __M_writer(unicode(row_for_param( input, values[ input.name ], other_values, errors, prefix, step ))) File '/galaxy/galaxy_server/database/compiled_templates/workflow/run.mako.py', line 297 in row_for_param return render_row_for_param(context,param,value,other_values,error_dict,prefix,step) File '/galaxy/galaxy_server/database/compiled_templates/workflow/run.mako.py', line 466 in render_row_for_param __M_writer(unicode(param.get_html_field( t, value, other_values ).get_html( str(step.id) + | + prefix ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 155: ordinal not in range(128) CGI Variables - CONTENT_LENGTH: '0' HTTP_ACCEPT: 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_CHARSET: 'ISO-8859-1,utf-8;q=0.7,*;q=0.7' HTTP_ACCEPT_ENCODING: 'gzip,deflate' HTTP_ACCEPT_LANGUAGE: 'en-us,en;q=0.5' HTTP_CONNECTION: 'Keep-Alive' HTTP_COOKIE: 'galaxysession=f611411aa8a0c6655dce25cc8ce7931696473135a41884694eefb704cf34d98429880ec7e01926f8' HTTP_HOST: 'solweb2' HTTP_REFERER:
[galaxy-dev] Update of cufflinks
Hello everybody, I just found out that there was a major update to cufflinks on 5/5/2011. At least for us it now makes no sense anymore to use the old version, besides the fact that the cufflinks team highly recommends upgrading. Does anybody already have new wrappers for all the cuff... tools ready? Do you know if/when the Galaxy codebase will be updated to the new cufflinks version? Best regards, Sarah ___ 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 user registration
Hello, it seems since I updated to the newest galaxy-dist, I always get an error when trying to register a new user. When I try it from the admin panel, the error is the following: Error - type 'exceptions.NameError': Undefined URL: http://solweb2.immunbio.mpg.de/user/create?cntrller=adminwebapp=galaxy File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/user.py', line 523 in create status=status ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 650 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 661 in fill_template_mako return template.render( **data ) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/template.py', line 133 in render return runtime._render(self, self.callable_, args, data) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 364 in _render _render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data)) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/galaxy/galaxy_server/database/compiled_templates/base.mako.py', line 40 in render_body __M_writer(unicode(next.body())) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 255 in lambda return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 69 in render_body __M_writer(unicode(render_registration_form())) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 40 in render_registration_form return render_render_registration_form(context.locals_(__M_locals),form_action) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 121 in render_render_registration_form form_action = h.url_for( controller='user', action='create', admin_view=admin_view ) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/util.py', line 248 in url_for url = config.mapper.generate(*route_args, **newargs) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/mapper.py', line 823 in generate path = route.generate(**kargs) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/route.py', line 736 in generate fragments.append((key, _str_encode(val, self.encoding))) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/util.py', line 129 in _str_encode s = unicode(string).encode(encoding) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 128 in __str__ raise NameError(Undefined) NameError: Undefined If I log out and try it from the User menu, I get the following error: Error - type 'exceptions.TypeError': create() takes at least 3 arguments (2 given) URL: http://solweb2.immunbio.mpg.de/user/create File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) TypeError: create() takes at least 3 arguments (2 given) I have no idea what is going on, any help is greatly appreciated, thank you! Best regards, Sarah Diehl ___ 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 in user registration
Hello Greg, first thank you for your help. I tried reloading everything, cleared the cache of my browser and tried it on a different computer whose browser never before was on the Galaxy website. All of this did not work. What worked in the end was deleting the compiled_templates directory. Best regards, Sarah On 04/15/2011 03:14 PM, Greg Von Kuster wrote: Hello Sarah, The method signature for the user controller's index method changed in the latest distribution update, and your browser cache is causing the problem because it is using the old method signature. Refreshing the masthead in your browser should solve the problem. By masthead, I mean the following - right click on it and select Reload page, or whatever your browser provides for an option: On Apr 15, 2011, at 8:31 AM, Sarah Diehl wrote: Hello, it seems since I updated to the newest galaxy-dist, I always get an error when trying to register a new user. When I try it from the admin panel, the error is the following: Error -type 'exceptions.NameError': Undefined URL: http://solweb2.immunbio.mpg.de/user/create?cntrller=adminwebapp=galaxy File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/user.py', line 523 in create status=status ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 650 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py', line 661 in fill_template_mako return template.render( **data ) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/template.py', line 133 in render return runtime._render(self, self.callable_, args, data) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 364 in _render _render_context(template, callable_, context, *args, **_kwargs_for_callable(callable_, data)) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 381 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 414 in _exec_template callable_(context, *args, **kwargs) File '/galaxy/galaxy_server/database/compiled_templates/base.mako.py', line 40 in render_body __M_writer(unicode(next.body())) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 255 inlambda return lambda *args, **kwargs:callable_(self.context, *args, **kwargs) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 69 in render_body __M_writer(unicode(render_registration_form())) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 40 in render_registration_form return render_render_registration_form(context.locals_(__M_locals),form_action) File '/galaxy/galaxy_server/database/compiled_templates/user/register.mako.py', line 121 in render_render_registration_form form_action = h.url_for( controller='user', action='create', admin_view=admin_view ) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/util.py', line 248 in url_for url = config.mapper.generate(*route_args, **newargs) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/mapper.py', line 823 in generate path = route.generate(**kargs) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/route.py', line 736 in generate fragments.append((key, _str_encode(val, self.encoding))) File '/galaxy/galaxy_server/eggs/Routes-1.12.3-py2.6.egg/routes/util.py', line 129 in _str_encode s = unicode(string).encode(encoding) File '/galaxy/galaxy_server/eggs/Mako-0.2.5-py2.6.egg/mako/runtime.py', line 128 in __str__ raise NameError(Undefined) NameError: Undefined If I log out and try it from the User menu, I get the following error: Error -type 'exceptions.TypeError': create() takes at least 3 arguments (2 given) URL: http://solweb2.immunbio.mpg.de/user/create File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ
Re: [galaxy-dev] Error when trying to download workflow
I could narrow it down even further. As soon as I set anything to To be
set at runtime the download fails.
On 04/14/2011 03:46 PM, Sarah Diehl wrote:
Hi Jeremy,
I could narrow the problem down to the histogram tool. I attached a
screenshot of a really simple workflow whose download fails. I recreated
the workflow at the public instance at http://main.g2.bx.psu.edu and
shared it with you. There the download also fails for me.
Best regards,
Sarah
On 04/14/2011 02:55 PM, Jeremy Goecks wrote:
Sarah,
Can you make your server available to me and I'll take a look? If not,
you'll have to do some debugging yourself. Here are some things you
might try:
*on your local instance, try exporting simpler workflows and seeing if
there's a tool or configuration that does or does work.
*on our public instance, try creating a workflow identical to the one
that's failing for you and seeing if you can export it.
If we can figure out how to reproduce the problem on a Galaxy instance
that I have access to, I can probably fix it.
Thanks,
J.
On Apr 14, 2011, at 3:11 AM, Sarah Diehl wrote:
Hi Jeremy,
I just updated to the newest galaxy-dist and the export of the
workflow still does not work. The error is the same.
Best regards,
Sarah
On 04/07/2011 03:37 PM, Jeremy Goecks wrote:
Hi Sarah,
I created your workflow on my Galaxy instance and was able to export
it successfully, so updating your Galaxy instance may solve your
problem. If not, let us know and we'll take a closer look.
Finally, please direct your questions to one of our mailing lists
rather than individual galaxy developers for community and archival
purposes; I've cc'd this one to galaxy-dev.
Thanks,
J.
On Apr 7, 2011, at 8:00 AM, Sarah Diehl wrote:
Hi Jeremy,
I encounter a similar error like the one already posted on the
galaxy-dev list
(http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-November/003699.html)
when trying to download a workflow.
Were you able to find a solution or are you still working on it? I
attached a screenshot of the workflow (like you also requested on
the list). Let me know if I can provide you with any additional
details to help with the debugging.
Best regards,
Sarah
10.1.5.190 - - [07/Apr/2011:13:33:42 +0200] GET
/workflow/export_to_file?id=0ac5da8467dc9e07 HTTP/1.1 500 -
http://solweb2.immunbio.mpg.de/workflow/export?id=0ac5da8467dc9e07;
Mozilla/5.0
(X11; U; Linux x86_64; en-US; rv:1.9.2.16) Gecko/20110322
fil
e:///home/diehl/Pictures/Screenshot.png
Fedora/3.6.16-1.fc14 Firefox/3.6.16
Error -type 'exceptions.TypeError': 'WorkflowStep' object is
unsubscriptable
URL:
http://solweb2.immunbio.mpg.de/workflow/export_to_file?id=0ac5da8467dc9e07
File
'/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py',
line 143 in __call__
app_iter = self.application(environ, start_response)
File
'/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line
80 in __call__
return self.application(environ, start_response)
File
'/galaxy/galaxy_server/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py',
line 632 in __call__
return self.application(environ, start_response)
File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line
145 in __call__
body = method( trans, **kwargs )
File '/galaxy/galaxy_server/lib/galaxy/web/framework/__init__.py',
line 74 in decorator
return simplejson.dumps( func( self, trans, *args, **kwargs ),
indent=4, sort_keys=True )
File
'/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py',
line 1078 in export_to_file
stored_dict = self._workflow_to_dict( trans, stored )
File
'/galaxy/galaxy_server/lib/galaxy/web/controllers/workflow.py',
line 1571 in _workflow_to_dict
step['inputs'].append( { name : name, description : runtime
parameter for tool %s % module.get_name() } )
TypeError: 'WorkflowStep' object is unsubscriptable
Screenshot.png
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Re: [galaxy-dev] Server error from history view
Hi Isabelle, thank you for your help. However filter-with=gzip is disabled in our configuration. I set everything according to the guide on https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer. The gzip option you see in my log is from the Apache server. Sarah On 03/10/2011 07:08 PM, Isabelle Phan wrote: Hello Sarah, (my galaxy-dev account is broken, read your post on nabble) You need to disable filter-with=gzip in order to set debug=False But in any case, I have not seen a difference in the log, so my take is that galaxy only ever runs in debug mode. Isabelle ___ 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] rpy and R
Hi Nate, thank you very much for your help! I managed to figure out the problem. There seemed to be an old version of R and somehow (I still don't know how) the rpy installation did only find the old one. I hard-coded the directory of the new R in the setup.py (everything else failed) and then it compiled against the new R version. Best regards, Sarah On 03/03/2011 05:11 PM, Nate Coraor wrote: Sarah Diehl wrote: Hi all, I'm currently working on setting up a fresh Galaxy server at our institute. I'm going through the tool dependencies list and install everything on it. I installed the latest R version (2.12.2) and now I'm trying to install rpy. With some workarounds I managed to compile rpy, but when I try to import it in python, I get the following error: import rpy Traceback (most recent call last): File stdin, line 1, inmodule File rpy.py, line 134, inmodule % RVERSION) RuntimeError: No module named _rpy2122 RPy module can not be imported. Please check if your rpy installation supports R 2.12.2. If you have multiple R versions installed, you may need to set RHOME before importing rpy. For example: from rpy_options import set_options set_options(RHOME='c:/progra~1/r/rw2011/') from rpy import * It looks like my version of R isn't supported by rpy. Does anybody know which version of R still works with rpy? I couldn't find anything about it. What about rpy2? Is it not supported by Galaxy? Hi Sarah, Although I haven't tested with 2.12.2, I know it works with at least 2.11.0. The error above is indicating that rpy is installed somewhere on python's path but the C-extension module for the version of R found on your $PATH (2.12.2) is not present. Most likely this is because rpy was already installed, and is being found earlier on python's path than the version of rpy that you installed. The older rpy was built against a different version of R. If you find the original installation of rpy you should be able to determine from _rpyversion.so what version of R it was built against, and put that version of R ahead of 2.12.2 in your $PATH. Alternatively, you can find and uninstall the old version of rpy, which should allow your newer version to be found and used. python's path can be determined with: python -c 'import sys; print \n.join( sys.path )' There is some effort underway in the community to rewrite rpy tools to use rpy2, but this work is not yet complete. Hope this helps, --nate Thanks very much in advance for your help! Best regards, Sarah Diehl ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
