Re: [galaxy-dev] Twill compares wrong file; was: Twill comparisons ignore GALAXY_TEST_NO_CLEANUP
Am Mittwoch, den 12.02.2014, 10:46 + schrieb Peter Cock: > On Tue, Feb 11, 2014 at 5:09 PM, Peter Cock wrote: > > On Tue, Feb 11, 2014 at 4:42 PM, Peter Cock > > wrote: > >> On Tue, Feb 11, 2014 at 3:41 PM, Dave Bouvier wrote: > >>> Peter, > >>> > >>> Thanks for pointing this out, I've applied your changes in > >>> 12478:15fc8675064e on the default branch. > >>> > >>>--Dave B. > >> > >> Thanks Dave, > >> > >> RE: http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-February/018154.html > >> https://bitbucket.org/galaxy/galaxy-central/commits/15fc8675064ea46b7e081d9643393be354f07d65 > >> > >> I'm still digging into the underlying problem, by focussing on just > >> one unit test ... > >> > >> As a workaround, I could probably provide expected data for all > >> four output files... > > Confirmed, providing a reference file for each output works: > > > > > > > ftype="fasta" /> > /> > ftype="mira" /> > ftype="txt" lines_diff="2000" /> > > > However, at only 5kb the FASTA file is small and fine to bundle - > but the BAM (49kb), log (123kb) and MAF (764kb) quickly add > up so I would prefer not to have to include these (under source > code control, and for the Tool Shed upload). Also, as you might > guess from the large number of allowed differences, the log > file is quite variable (lots of time stamps plus Galaxy's temp > filenames appear). Do you have any advise which filesize is feasible and at which point we should skip the tests? I'm working currently on MACS2 wrappers and to have reasonable tests I need up to 50mb ob test files. Providing gz input files would be one option to get it down to 10mb, but that does not work and it's still 10mb ... > > I've been talking to John (off list), he will reply here later, but in > > the meantime pointed me at a relevant commit, > > https://bitbucket.org/galaxy/galaxy-central/commits/d05be33ad6b772c2a688d875c4cf895d6afac4e3 > > > > Basically the current Twill tests are extremely fragile and expect the > > test output files in the same order used in the definitions > > and also there must be sample data for ALL the output files. > > > > (I may have hit this bug before, I forget now). > > I think it ought be possible to refactor the Twill test code to use > the same dictionary approach used in the API based testing - > and so support listing the test output in any order and only > testing some of the files. > > However, I'll wait and see what you guys have to say. > > Peter. > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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] Difficulty dispatching toolshed tool jobs via job_conf.xml
Hi Nate & Simon, was that solved? I think it's still not working? Or is that a regression. In particular shed_host/repos/owner/repo/tool_id is not working, and that is what is 90% needed, or? Thanks, Bjoern > > From: Nate Coraor [mailto:n...@bx.psu.edu] > > > This should work, it looks like there may be a bug with handling tool shed > > IDs when determining job destinations. You are actually supposed to be > > able to use any of: > > > > shed_host/repos/owner/repo/tool_id/version > > shed_host/repos/owner/repo/tool_id > > tool_id > > > > I'll take a look at this as soon as possible. One thing you might try in > > the short term is using the percent encoded tool id in the tag in > > job_conf.xml: > > Hi Nate, > > Using the percent encoded form was the first thing I tried (before emailing > the list). It didn't make any difference. I think there's another reason > it's not picking it up. Thanks for looking into this. > > cheers, > Simon > > > === > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > === > > ___ > 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] popup window possible?
Hi, Is it possible to get a popup dialog box to appear for a tool? If so any examples on this please? i.e. the popup may just give a warning or an info message etc... that the user can confirm before proceeding. Or maybe another way to achieve the same thing? Thanks Neil Neil Burdett Software Engineer | The Australian e-Health Research Centre Computational Informatics CSIRO E: neil.burd...@csiro.au T: 07 3253 3626 Address: Level 5, UQ Health Science Building 901/16 Royal Brisbane and Women's Hospital, Herston, Brisbane, QLD, 4029 www.csiro.au | http://milxview.csiro.au ___ 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] setting up Galaxy for torque pbs
Hi, I am trying to set up Galaxy to interface with a Cray system which runs Torque/PBS. After reading this Galaxy wiki page: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS I was able to scramble torque egg with the following command: LIBTORQUE_DIR=/opt/torque/2.4.11/lib/libtorque.so.2 python scripts/scramble.py -e pbs_python I do not fully understand the "parameters and configuration" part in PBS section of the wiki page. Where exactly the "runner" XML snippet with and should be placed? Also wondering if the snippet will be required for all tools that I want to run on compute nodes or is it a global setting? Can I tell existing tools to use this setup? Another question is, can I configure Galaxy to submit jobs to compute cluster as a mortal user and not an admin of the system? Thanks, -- Ketan ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Adding a tool with additional html/js interface to make input selection
Hi, We are trying to add a new tool to our local galaxy instance with the following requirements. When a user clicks on the tool in side panel from tools list, a table display should appear where the first element in each row is a clickable link. Users can click on any of the element, and then see only there selected row and another table with more options. Once user has made all the selections, then a form should appear describing that you have made the following selection, do you want to execute the tool now? And then users can submit the job. If we implement such a thing in galaxy, we need to load a page with aforementioned functionality, then map the users selection to the tool's inputs, and then run the tool. The question is, is there a way in galaxy to load an html with javascript and use it to prepare the inputs for the tool we want to run, using the xml wrapper. Thanks, Saba ___ 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] History panel filters
Hi, Federico Starting with the next distribution (and in the current 'galaxy-central'), you'll be able to do just that. Here's the documentation for it: https://wiki.galaxyproject.org/Learn/Managing%20Datasets#Searching_Datasets In future releases, we hope to enable the use of multiple selection and operations on multiple datasets with the search: https://bitbucket.org/galaxy/galaxy-central/commits/7ca065784d58e7aa77e5092952eacd963853df65 Good to see this will be useful for some and thanks for the suggestion, Carl On Mon, Feb 3, 2014 at 9:55 AM, Federico Zambelli < federico.zambe...@gmail.com> wrote: > Dear Galaxy devs, > > I apologize if somebody has already proposed this idea. > I think that it would be great to have a filter for the history panel > based on name, data type and so on similar to the one on the tools panel. I > really feel the need of it when working on histories with many datasets. > > Federico Zambelli > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] migrate_tools error with latest release (hg update release_2014.02.10 )
Geert, I'm glad everything is now working for you, and a database dump might be useful to determine the cause of that error. --Dave B. On 02/12/2014 08:46 AM, Geert Vandeweyer wrote: Hi Dave, I was able to get galaxy back up by doing a fresh install, moving the old database folder in the new install, reconfiguring universe and job_conf, and leaving tool_conf and all shed related items to default. I also truncated the tables 'tool_dependency', tool_shed_repository and tool_version associates. Finally I removed in tool_version all entries that had a tool_shed_repository_id !== NULL. Now I'm installing all my toolsheds again, and it's still working it seems. If you want, I can try to make my database dump (post-error, but before truncating) available to you. Best, Geert On 02/11/2014 10:56 PM, Dave Bouvier wrote: Geert, I have not yet been able to reproduce that error in my local Galaxy installation running on the release_2014.02.10 tag, but I am continuing to investigate. Are you able to determine which repository last succeeded in the migration script output? --Dave B. On 02/11/2014 10:29 AM, Geert Vandeweyer wrote: This message is also returned when I try to start the server without the migrate tools script (but after the initial error). Can I safely revert to a previous rel Best, Geert On 02/11/2014 03:18 PM, Geert Vandeweyer wrote: Hi, I'm having problems upgrading Galaxy to the latest release. The migrate tools script gives the following error. No handlers could be found for logger "galaxy.tools" Traceback (most recent call last): File "./scripts/migrate_tools/migrate_tools.py", line 21, in app = MigrateToolsApplication( sys.argv[ 1 ] ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/migrate/common.py", line 45, in __init__ self.installed_repository_manager = installed_repository_manager.InstalledRepositoryManager( self ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py", line 66, in __init__ self.load_dependency_relationships() File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py", line 269, in load_dependency_relationships self.add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py", line 147, in add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies tool_dependency_util.get_runtime_dependent_tool_dependency_tuples( self.app, tool_dependency, status=None ) File "/galaxy/galaxy-dist/lib/tool_shed/util/tool_dependency_util.py", line 323, in get_runtime_dependent_tool_dependency_tuples env_shell_file_path = td.get_env_shell_file_path( app ) File "/galaxy/galaxy-dist/lib/galaxy/model/tool_shed_install/__init__.py", line 533, in get_env_shell_file_path installation_directory = self.installation_directory( app ) File "/galaxy/galaxy-dist/lib/galaxy/model/tool_shed_install/__init__.py", line 548, in installation_directory self.tool_shed_repository.owner, AttributeError: 'NoneType' object has no attribute 'owner' Any help on how to resolve this? The 0009_tools.xml content is : Best, Geert ___ 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 installing VarScan from Toolshed
Graham, I was able to reproduce the error by updating to changeset 11216:c458a0fe1ba8, and I've determined that the bug causing this error was fixed in 11310:9bde6f2b9c59. I would recommend updating to the current stable release as described on the following page: https://wiki.galaxyproject.org/Admin/GetGalaxy#Keep_your_code_up_to_date The news brief for the current release can be found at: https://wiki.galaxyproject.org/DevNewsBriefs/2014_02_10 --Dave B. On 02/12/2014 08:50 AM, graham etherington (TSL) wrote: Hi Dave, Thanks for the prompt reply. Here’s the information that you asked for, plus some other bits and bobs. $ hg summary parent: 11216:c458a0fe1ba8 Merge security fix for filtering tools from stable/next-stable. branch: default commit: 9 modified, 193 unknown update: (current) $ python Python 2.6.6 (r266:84292, Nov 22 2013, 12:16:22) [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2 Cheers, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 From: Dave Bouvier mailto:d...@bx.psu.edu>> Date: Wednesday, 12 February 2014 13:44 To: "graham etherington (TSL)" mailto:graham.ethering...@sainsbury-laboratory.ac.uk>>, Galaxy Dev mailto:galaxy-dev@lists.bx.psu.edu>> Subject: Re: [galaxy-dev] Error installing VarScan from Toolshed Graham, I've not been able to duplicate that error on my local instance, which is running the most recent revision on the stable branch. To help track down this issue, could you paste the output of 'hg summary' run from the Galaxy installation path? --Dave B. On 02/12/2014 06:13 AM, graham etherington (TSL) wrote: Hi, I’m trying to install VarScan from the Main Toolshed. I’ve tried both the versions available (‘varscan’ from fcaramia and ‘varscan_version_2’ from devteam), but I get the same error each time: File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 294, in install_and_build_package_via_fabric fabric_util.install_and_build_package( app, tool_dependency, actions_dict ) File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py", line 619, in install_and_build_package destination=full_path_to_dir ) File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__ self.gen.throw(type, value, traceback) File "/tsl/services/galaxy/dist/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py", line 142, in _setenv yield File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py", line 309, in install_and_build_package dir = td_common_util.url_download( work_dir, downloaded_filename, url, extract=True ) File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py", line 434, in url_download archive = CompressedFile( file_path ) File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py", line 27, in __init__ self.type = self.file_type 'CompressedFile' object has no attribute 'file_type' Can anyone suggest what might be going wrong here? Many thanks, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error installing VarScan from Toolshed
Hi Dave, Thanks for the prompt reply. Here’s the information that you asked for, plus some other bits and bobs. $ hg summary parent: 11216:c458a0fe1ba8 Merge security fix for filtering tools from stable/next-stable. branch: default commit: 9 modified, 193 unknown update: (current) $ python Python 2.6.6 (r266:84292, Nov 22 2013, 12:16:22) [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)] on linux2 Cheers, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 From: Dave Bouvier mailto:d...@bx.psu.edu>> Date: Wednesday, 12 February 2014 13:44 To: "graham etherington (TSL)" mailto:graham.ethering...@sainsbury-laboratory.ac.uk>>, Galaxy Dev mailto:galaxy-dev@lists.bx.psu.edu>> Subject: Re: [galaxy-dev] Error installing VarScan from Toolshed Graham, I've not been able to duplicate that error on my local instance, which is running the most recent revision on the stable branch. To help track down this issue, could you paste the output of 'hg summary' run from the Galaxy installation path? --Dave B. On 02/12/2014 06:13 AM, graham etherington (TSL) wrote: Hi, I’m trying to install VarScan from the Main Toolshed. I’ve tried both the versions available (‘varscan’ from fcaramia and ‘varscan_version_2’ from devteam), but I get the same error each time: File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 294, in install_and_build_package_via_fabric fabric_util.install_and_build_package( app, tool_dependency, actions_dict ) File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py", line 619, in install_and_build_package destination=full_path_to_dir ) File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__ self.gen.throw(type, value, traceback) File "/tsl/services/galaxy/dist/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py", line 142, in _setenv yield File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py", line 309, in install_and_build_package dir = td_common_util.url_download( work_dir, downloaded_filename, url, extract=True ) File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py", line 434, in url_download archive = CompressedFile( file_path ) File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py", line 27, in __init__ self.type = self.file_type 'CompressedFile' object has no attribute 'file_type' Can anyone suggest what might be going wrong here? Many thanks, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] migrate_tools error with latest release (hg update release_2014.02.10 )
Hi Dave, I was able to get galaxy back up by doing a fresh install, moving the old database folder in the new install, reconfiguring universe and job_conf, and leaving tool_conf and all shed related items to default. I also truncated the tables 'tool_dependency', tool_shed_repository and tool_version associates. Finally I removed in tool_version all entries that had a tool_shed_repository_id !== NULL. Now I'm installing all my toolsheds again, and it's still working it seems. If you want, I can try to make my database dump (post-error, but before truncating) available to you. Best, Geert On 02/11/2014 10:56 PM, Dave Bouvier wrote: Geert, I have not yet been able to reproduce that error in my local Galaxy installation running on the release_2014.02.10 tag, but I am continuing to investigate. Are you able to determine which repository last succeeded in the migration script output? --Dave B. On 02/11/2014 10:29 AM, Geert Vandeweyer wrote: This message is also returned when I try to start the server without the migrate tools script (but after the initial error). Can I safely revert to a previous rel Best, Geert On 02/11/2014 03:18 PM, Geert Vandeweyer wrote: Hi, I'm having problems upgrading Galaxy to the latest release. The migrate tools script gives the following error. No handlers could be found for logger "galaxy.tools" Traceback (most recent call last): File "./scripts/migrate_tools/migrate_tools.py", line 21, in app = MigrateToolsApplication( sys.argv[ 1 ] ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/migrate/common.py", line 45, in __init__ self.installed_repository_manager = installed_repository_manager.InstalledRepositoryManager( self ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py", line 66, in __init__ self.load_dependency_relationships() File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py", line 269, in load_dependency_relationships self.add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py", line 147, in add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies tool_dependency_util.get_runtime_dependent_tool_dependency_tuples( self.app, tool_dependency, status=None ) File "/galaxy/galaxy-dist/lib/tool_shed/util/tool_dependency_util.py", line 323, in get_runtime_dependent_tool_dependency_tuples env_shell_file_path = td.get_env_shell_file_path( app ) File "/galaxy/galaxy-dist/lib/galaxy/model/tool_shed_install/__init__.py", line 533, in get_env_shell_file_path installation_directory = self.installation_directory( app ) File "/galaxy/galaxy-dist/lib/galaxy/model/tool_shed_install/__init__.py", line 548, in installation_directory self.tool_shed_repository.owner, AttributeError: 'NoneType' object has no attribute 'owner' Any help on how to resolve this? The 0009_tools.xml content is : id="compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom" version="1.0.0" file="execute_dwt_cor_aVa_perClass.xml" /> id="compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom" version="1.0.0" file="execute_dwt_cor_aVb_all.xml" /> id="compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom" version="1.0.0" file="execute_dwt_IvC_all.xml" /> id="compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom" version="1.0.0" file="execute_dwt_var_perClass.xml" /> file="express_wrapper.xml" /> file="fastq_stats.xml" /> Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer ___ Please keep all replies on the list by usi
Re: [galaxy-dev] Error installing VarScan from Toolshed
Graham, I've not been able to duplicate that error on my local instance, which is running the most recent revision on the stable branch. To help track down this issue, could you paste the output of 'hg summary' run from the Galaxy installation path? --Dave B. On 02/12/2014 06:13 AM, graham etherington (TSL) wrote: Hi, I’m trying to install VarScan from the Main Toolshed. I’ve tried both the versions available (‘varscan’ from fcaramia and ‘varscan_version_2’ from devteam), but I get the same error each time: File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 294, in install_and_build_package_via_fabric fabric_util.install_and_build_package( app, tool_dependency, actions_dict ) File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py", line 619, in install_and_build_package destination=full_path_to_dir ) File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__ self.gen.throw(type, value, traceback) File "/tsl/services/galaxy/dist/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py", line 142, in _setenv yield File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py", line 309, in install_and_build_package dir = td_common_util.url_download( work_dir, downloaded_filename, url, extract=True ) File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py", line 434, in url_download archive = CompressedFile( file_path ) File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py", line 27, in __init__ self.type = self.file_type 'CompressedFile' object has no attribute 'file_type' Can anyone suggest what might be going wrong here? Many thanks, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 ___ 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] cap3 in galaxy
Hi, I was pointed to CAP3 by a colleague who likes to have it included in our local Galaxy instance. Searching for cap3 in the Galaxy repositories I only found the packages "package_cap3_3" provided by jjohnson: http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=63e16d726d394a5e&changeset_revision=8b91ecadabb5 http://testtoolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=d7fe775c833f5d44&changeset_revision=a472ccd208e2 So here's my question: Is there any Galaxy integration of cap3? Best regards, Jens ___ 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] migrate_tools error with latest release (hg update release_2014.02.10 )
Thanks! I didn't get output before the error, so I think no tools were migrated successfully. I tried to strip down the XML to only hold the first tool, but that gave the same error. I hope to try a fresh install today keeping the database and all settings not related to toolshed ( ie copy them from the old install.) could I then reinstall all shed tools, or will there be conflicts from info in the MySQL database? Best Geert Van: Dave Bouvier [d...@bx.psu.edu] Verzonden: dinsdag 11 februari 2014 22:56 Aan: Vandeweyer Geert; galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] migrate_tools error with latest release (hg update release_2014.02.10 ) Geert, I have not yet been able to reproduce that error in my local Galaxy installation running on the release_2014.02.10 tag, but I am continuing to investigate. Are you able to determine which repository last succeeded in the migration script output? --Dave B. On 02/11/2014 10:29 AM, Geert Vandeweyer wrote: > This message is also returned when I try to start the server without the > migrate tools script (but after the initial error). > > Can I safely revert to a previous release somehow? > > Best, > > Geert > > On 02/11/2014 03:18 PM, Geert Vandeweyer wrote: >> Hi, >> >> I'm having problems upgrading Galaxy to the latest release. The >> migrate tools script gives the following error. >> >> No handlers could be found for logger "galaxy.tools" >> Traceback (most recent call last): >> File "./scripts/migrate_tools/migrate_tools.py", line 21, in >> app = MigrateToolsApplication( sys.argv[ 1 ] ) >> File >> "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/migrate/common.py", >> line 45, in __init__ >> self.installed_repository_manager = >> installed_repository_manager.InstalledRepositoryManager( self ) >> File >> "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py", >> line 66, in __init__ >> self.load_dependency_relationships() >> File >> "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py", >> line 269, in load_dependency_relationships >> self.add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies( >> tool_dependency ) >> File >> "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py", >> line 147, in >> add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies >> tool_dependency_util.get_runtime_dependent_tool_dependency_tuples( >> self.app, tool_dependency, status=None ) >> File >> "/galaxy/galaxy-dist/lib/tool_shed/util/tool_dependency_util.py", line >> 323, in get_runtime_dependent_tool_dependency_tuples >> env_shell_file_path = td.get_env_shell_file_path( app ) >> File >> "/galaxy/galaxy-dist/lib/galaxy/model/tool_shed_install/__init__.py", >> line 533, in get_env_shell_file_path >> installation_directory = self.installation_directory( app ) >> File >> "/galaxy/galaxy-dist/lib/galaxy/model/tool_shed_install/__init__.py", >> line 548, in installation_directory >> self.tool_shed_repository.owner, >> AttributeError: 'NoneType' object has no attribute 'owner' >> >> Any help on how to resolve this? >> >> The 0009_tools.xml content is : >> >> >> >> >> > name="bowtie2" description="Bowtie2"> >> >> >> > name="ccat" description="Control-based ChIP-seq Analysis Tool"> >> > file="ccat_wrapper.xml" /> >> >> > name="clustalw" description="ClustalW multiple sequence alignment >> program for DNA or proteins"> >> >> >> > name="dwt_cor_ava_perclass" description="Compute P-values and >> Correlation Coefficients for Feature Occurrences"> >> > id="compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom" >> version="1.0.0" file="execute_dwt_cor_aVa_perClass.xml" /> >> >> > name="dwt_cor_avb_all" description="Compute P-values and Correlation >> Coefficients for Occurrences of Two Set of Features"> >> > id="compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom" >> version="1.0.0" file="execute_dwt_cor_aVb_all.xml" /> >> >> > name="dwt_ivc_all" description="Compute P-values and Second Moments >> for Feature Occurrences"> >> > id="compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom" >> version="1.0.0" file="execute_dwt_IvC_all.xml" /> >> >> > name="dwt_var_perclass" description="Compute P-values and Max >> Variances for Feature Occurrences"> >> > id="compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom" >> version="1.0.0" file="execute_dwt_var_perClass.xml" /> >> >> > name="dwt_var_perfeature" description="Wavelet variance using Discrete >> Wavelet Transfoms"> >> > file="execute_dwt_var_perFeature.xml" /> >> >
[galaxy-dev] Error installing VarScan from Toolshed
Hi, I’m trying to install VarScan from the Main Toolshed. I’ve tried both the versions available (‘varscan’ from fcaramia and ‘varscan_version_2’ from devteam), but I get the same error each time: File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 294, in install_and_build_package_via_fabric fabric_util.install_and_build_package( app, tool_dependency, actions_dict ) File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py", line 619, in install_and_build_package destination=full_path_to_dir ) File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__ self.gen.throw(type, value, traceback) File "/tsl/services/galaxy/dist/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py", line 142, in _setenv yield File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py", line 309, in install_and_build_package dir = td_common_util.url_download( work_dir, downloaded_filename, url, extract=True ) File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py", line 434, in url_download archive = CompressedFile( file_path ) File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py", line 27, in __init__ self.type = self.file_type 'CompressedFile' object has no attribute 'file_type' Can anyone suggest what might be going wrong here? Many thanks, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 ___ 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] Twill compares wrong file; was: Twill comparisons ignore GALAXY_TEST_NO_CLEANUP
On Tue, Feb 11, 2014 at 5:09 PM, Peter Cock wrote: > On Tue, Feb 11, 2014 at 4:42 PM, Peter Cock wrote: >> On Tue, Feb 11, 2014 at 3:41 PM, Dave Bouvier wrote: >>> Peter, >>> >>> Thanks for pointing this out, I've applied your changes in >>> 12478:15fc8675064e on the default branch. >>> >>>--Dave B. >> >> Thanks Dave, >> >> RE: http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-February/018154.html >> https://bitbucket.org/galaxy/galaxy-central/commits/15fc8675064ea46b7e081d9643393be354f07d65 >> >> I'm still digging into the underlying problem, by focussing on just >> one unit test ... >> >> As a workaround, I could probably provide expected data for all >> four output files... Confirmed, providing a reference file for each output works: However, at only 5kb the FASTA file is small and fine to bundle - but the BAM (49kb), log (123kb) and MAF (764kb) quickly add up so I would prefer not to have to include these (under source code control, and for the Tool Shed upload). Also, as you might guess from the large number of allowed differences, the log file is quite variable (lots of time stamps plus Galaxy's temp filenames appear). > I've been talking to John (off list), he will reply here later, but in > the meantime pointed me at a relevant commit, > https://bitbucket.org/galaxy/galaxy-central/commits/d05be33ad6b772c2a688d875c4cf895d6afac4e3 > > Basically the current Twill tests are extremely fragile and expect the > test output files in the same order used in the definitions > and also there must be sample data for ALL the output files. > > (I may have hit this bug before, I forget now). I think it ought be possible to refactor the Twill test code to use the same dictionary approach used in the API based testing - and so support listing the test output in any order and only testing some of the files. However, I'll wait and see what you guys have to say. Peter. ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
