[galaxy-dev] I can't impersonate an user
Dear all, We are currently using the stable build of Galaxy and we are encountering the following problem: When we try to impersonate an user, the user drop down menu hangs in looking up the user. In consequence, we can not impersonate the user. This behaviour started when we upgraded to the Feb 10, 2014 version. Do we have to modify a configuration file to make this to work again? Thank you all, --Ricardo Perez ___ 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 searching for tools in local instance.
Hi Sam, No it did not fix the issue. When I checked we were in fact in the stable branch. I am sorry for my delayed response, --Ricardo Perez - Original Message - From: sam guerler aysam.guer...@gmail.com To: Ricardo Perez ricky_...@neo.tamu.edu Cc: Galaxy-dev Galaxy-dev galaxy-dev@lists.bx.psu.edu Sent: Friday, January 24, 2014 5:21:56 PM Subject: Re: [galaxy-dev] Error when searching for tools in local instance. Hey Ricardo, Did that fix your issue? Does the problem occur in one of the branches? If yes, please let me know which one. Thanks, Sam On Wed, Jan 22, 2014 at 10:51 AM, Perez, Ricardo ricky_...@neo.tamu.edu wrote: Hello Sam, I believe we are using the default branch. I will try to change branches now. Thank you, --Ricardo Perez - Original Message - From: sam guerler aysam.guer...@gmail.com To: Ricardo Perez ricky_...@neo.tamu.edu Cc: Galaxy-dev Galaxy-dev galaxy-dev@lists.bx.psu.edu Sent: Tuesday, January 21, 2014 3:19:07 PM Subject: Re: [galaxy-dev] Error when searching for tools in local instance. Hi Ricardo, Are you using the newest version from the stable branch or from default? Thanks, Sam On Tue, Jan 21, 2014 at 3:53 PM, Perez, Ricardo ricky_...@neo.tamu.edu wrote: Dear All, When I go to my Galaxy Distibution I go the following place: Admin - Manage installed tool shed repositories When I search for a tool in here with the provided search bar, I get the following (I believe this is a bug): URL: https://galaxy.tamu.edu/admin_toolshed/browse_repositories?async=falsesort=namepage=1show_item_checkboxes=falsef-deleted=Falsef-free-text-search=search File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 229 in decorator return func( self, trans, *args, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 153 in browse_repositories return self.installed_repository_grid( trans, **kwd ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 138 in __call__ query = column.filter( trans, trans.user, query, column_filter ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 616 in filter clause_list.append( column.get_filter( trans, user, column_filter ) ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 400 in get_filter return self.get_single_filter( user, column_filter ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 413 in get_single_filter if self.key.find( '.' ) -1: AttributeError: 'NoneType' object has no attribute 'find' How would I go to fix this. Thank you, --Ricardo Perez ___ 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] Error when searching for tools in local instance.
Dear All, When I go to my Galaxy Distibution I go the following place: Admin - Manage installed tool shed repositories When I search for a tool in here with the provided search bar, I get the following (I believe this is a bug): URL: https://galaxy.tamu.edu/admin_toolshed/browse_repositories?async=falsesort=namepage=1show_item_checkboxes=falsef-deleted=Falsef-free-text-search=search File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 229 in decorator return func( self, trans, *args, **kwargs ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py', line 153 in browse_repositories return self.installed_repository_grid( trans, **kwd ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 138 in __call__ query = column.filter( trans, trans.user, query, column_filter ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 616 in filter clause_list.append( column.get_filter( trans, user, column_filter ) ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 400 in get_filter return self.get_single_filter( user, column_filter ) File '/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/grids.py', line 413 in get_single_filter if self.key.find( '.' ) -1: AttributeError: 'NoneType' object has no attribute 'find' How would I go to fix this. Thank you, --Ricardo Perez ___ 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] Velvet optimizer problems : Urgent help.
Dear all, When trying to run velvet optimizer in galaxy, all the files we get return the following: No peek When looking at the output of galaxy, we get the following: galaxy.jobs.runners.local DEBUG 2013-07-31 09:31:46,829 execution finished: perl /usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/simon-gladman/velvet_optimiser/43c89d82a7d3/velvet_optimiser/velvet_optimiser_wrapper_vlsci.pl '19' '23' '2' '0' 'short' 'False' 'galaxy.datatypes.sequence.FastqSanger object at 0x6e664d0' '/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2067.dat''not_shortMP''other:''no_amos''not_verbose' '/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2665.dat''/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2666.dat' '/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2667.dat''/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2663.dat' '/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2668.dat' /usr/local/galaxy/galaxy-dist/database/files/002/dataset_2664.dat galaxy.jobs.runners DEBUG 2013-07-31 09:31:47,027 executing external set_meta script for job 1983: /usr/local/galaxy/galaxy-dist/set_metadata.sh ./database/files /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983 . /usr/local/galaxy/galaxy-dist/universe_wsgi.ini /usr/local/galaxy/galaxy-dist/database/tmp/tmp3460Jz /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/galaxy.json /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3117_enOT5T,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3117_vy3tDq,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3117_IFmVK8,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3117_0j3kza,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_over! ride_HistoryDatasetAssociation_3117_zwMKHf /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3116_YppZ1L,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3116_Sniis0,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3116_l9RPFx,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3116_It8rUk,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3116_AwvXlS /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3115_TOhpBs,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3115_wUomyo,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_Histo! ryDatasetAssociation_3115_nsUrJl,/usr/local/galaxy/galaxy-dist! /databas e/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3115_DAmGEt,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3115_hFGdc0 /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3114_59uEii,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3114_UcezIt,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3114_YmOlHD,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3114_owVBfP,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3114_O3UH82 /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3113_vMrQrs,/usr/local/galaxy/galaxy-dist/database/! job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3113_YhwIGZ,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3113_pAG6wP,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3113_9ImAZ6,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3113_uI5cbM
[galaxy-dev] Bowtie2 error: Creates a 62 kb file.
Dear all, Today we ran some problems when running bowtie2. When we run bowtie2, the run manages to complete. However, bowtie2 creates a 62kb file. The error log that we get is the following: galaxy.jobs DEBUG 2013-07-23 17:09:42,378 (1483) Persisting job destination (destination id: local:///) galaxy.jobs.handler INFO 2013-07-23 17:09:42,392 (1483) Job dispatched galaxy.tools DEBUG 2013-07-23 17:09:42,556 Building dependency shell command for dependency 'bowtie2' galaxy.tools WARNING 2013-07-23 17:09:42,556 Failed to resolve dependency on 'bowtie2', ignoring galaxy.tools DEBUG 2013-07-23 17:09:42,556 Building dependency shell command for dependency 'samtools' galaxy.tools WARNING 2013-07-23 17:09:42,556 Failed to resolve dependency on 'samtools', ignoring galaxy.jobs.runners.local DEBUG 2013-07-23 17:09:42,626 (1483) executing: bowtie2 --version /usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1483; python /usr/local/galaxy/galaxy-dist/tools/sr_mapping/bowtie2_wrapper.py --num-threads=4 --output=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1673.dat --indexes-path=/data/db/fungidb/Ncrassa_OR74A/bowtie2/Ncrassa_wt_Chr01.Chr07.+ChrM.+rDNA_v12 --single-paired=paired --input1=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1668.dat --input2=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1669.dat -I 0 -X 250 --settings=preSet galaxy.jobs DEBUG 2013-07-23 17:09:42,696 (1483) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2013-07-23 17:09:42,766 execution finished: bowtie2 --version /usr/local/galaxy/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1483; python /usr/local/galaxy/galaxy-dist/tools/sr_mapping/bowtie2_wrapper.py --num-threads=4 --output=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1673.dat --indexes-path=/data/db/fungidb/Ncrassa_OR74A/bowtie2/Ncrassa_wt_Chr01.Chr07.+ChrM.+rDNA_v12 --single-paired=paired --input1=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1668.dat --input2=/usr/local/galaxy/galaxy-dist/database/files/001/dataset_1669.dat -I 0 -X 250 --settings=preSet galaxy.jobs.runners DEBUG 2013-07-23 17:09:42,850 executing external set_meta script for job 1483: /usr/local/galaxy/galaxy-dist/set_metadata.sh ./database/files /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483 . /usr/local/galaxy/galaxy-dist/universe_wsgi.ini /usr/local/galaxy/galaxy-dist/database/tmp/tmpUiqpPD /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/galaxy.json /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_in_HistoryDatasetAssociation_1767_wqhEmr,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_kwds_HistoryDatasetAssociation_1767_qVZjpG,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_out_HistoryDatasetAssociation_1767_vIfpRO,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_results_HistoryDatasetAssociation_1767_UNl6OR,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1483/metadata_over! ride_HistoryDatasetAssociation_1767_MZilrL 165.91.11.135 - - [23/Jul/2013:17:09:43 -0500] GET /api/histories/ca8efa3c47500414 HTTP/1.1 200 - http://galaxy.tamu.edu/history; Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.22 (KHTML, like Gecko) Ubuntu Chromium/25.0.1364.160 Chrome/25.0.1364.160 Safari/537.22 165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] GET /history HTTP/1.1 200 - http://galaxy.tamu.edu/tool_runner/index; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 Safari/537.36 165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] GET /api/histories/1ab12f1e464820dd HTTP/1.1 200 - http://galaxy.tamu.edu/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 Safari/537.36 165.91.11.231 - - [23/Jul/2013:17:09:43 -0500] GET /history/get_display_application_links HTTP/1.1 200 - http://galaxy.tamu.edu/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_6_8) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/28.0.1500.71 Safari/537.36 galaxy.jobs.runners DEBUG 2013-07-23 17:09:44,457 execution of external set_meta for job 1483 finished galaxy.datatypes.metadata DEBUG 2013-07-23 17:09:44,545 loading metadata from file for: HistoryDatasetAssociation 1767 We currently have the most recent version of bowtie2 and samtools. Anyone know how to fix this? Thank you for your time, --Ricardo Perez ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to
Re: [galaxy-dev] Trackster and bedtools error
Thank you for your quick response. However, I have checked and bedtools are indeed in the galaxy path. When reviewind the log, I get the following: galaxy.jobs.runners.local DEBUG 2013-07-09 16:59:15,937 execution finished: grep -v '^#' /usr/local/galaxy/galaxy-dist/database/files/000/dataset_515.dat | sort -k1,1 | bedtools genomecov -bg -split -i stdin -g /usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len temp.bg ; bedGraphToBigWig temp.bg /usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len /usr/local/galaxy/galaxy-dist/database/files/000/dataset_519.dat After reading the log, I ran the following command in my terminal: bedtools genomecov -bg -split -i stdin -g /usr/local/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/hg19.len However this crashes. After looking in my computer, I find that bedtools do not contain the file genomecov. Is this an erroneous assumption of mine or have I installed something wrong? Than you for your time, --Ricardo Perez ___ 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] Trackster and bedtools error
Dear all, As I was trying to do visualize my data set in trackster, I get the following error: /bin/sh: 1: bedtools: not found sort: fflush failed: standard output: Broken pipe sort: write error needLargeMem: trying to allocate 0 bytes (limit: 1000) When doing a sudo find / -name bedtools in my system, I get the following output: /usr/share/bedtools /usr/share/doc/bedtools Do I have bedtools installed in the wrong place? Thank you for your help, --Ricardo Perez ___ 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] Question about bowtie2_indeces.loc
Dear all, When adding a genome I understand that the format are added in the following way: unique_build_id dbkey display_name file_base_path My question is, what is the difference between the unique_build_id and the dbkey? Thank you for your time, --Ricardo Perez ___ 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] How were liftover and nib files generated?
Dear all, When I rsync files from let say the following command: rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/dm3 . The system will sync files that are related to genome aligments, liftover, and nibs. How did the Galaxy team generated this files? The reason I ask is because I would lather will like to generate similar files to custom genomes to be used in galaxy. Thank you for your time, --Ricardo Perez ___ 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] Configuring the time of permanently deleting data sets.
Dear all, I am currently trying to find a way to decrease the time the users need to wait to permanently delete their data sets. In galaxy I read the following Histories that have been deleted for more than a time period specified by the Galaxy administrator(s) may be permanently deleted.; I am wondering where can I configure this option in my local instance of galaxy. I have looked for such an option in the universe_wsgi.ini file but I have not found it. I would greatly appreciate if someone can point me to the right direction to modify this. Thank you all, --Ricardo Perez ___ 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] Initial display with Simulate (version 1.0.0)
Dear all, When running Simulate (version 1.0.0)I am missing a graph in the initial display. Is this a bug or is it my instance problem. On a side note, when running Simulate I found out that if you don't place parameters in Frequency/ies for minor allele: and Detection thresholds: the job will fail. It would be nice to indicate that those parameters are a must for running the tool. Thank you, --Ricardo Perez ___ 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] Errors when starting galaxy
Dear all, I get the following errors when starting galaxy, is there any way to fix this. Error loading display application (./display_applications/genetrack.xml): [Errno 2] No such file or directory: './display_applications/genetrack.xml' Traceback (most recent call last): File /usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py, line 498, in load_display_applications display_app = DisplayApplication.from_file( config_path, self ) File /usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/display_applications/application.py, line 163, in from_file return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry ) File /usr/local/galaxy/galaxy-dist/lib/galaxy/util/__init__.py, line 143, in parse_xml tree = ElementTree.parse(fname) File /usr/local/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py, line 859, in parse tree.parse(source, parser) File /usr/local/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py, line 576, in parse source = open(source, rb) Error loading display application (./display_applications/genetrack.xml): [Errno 2] No such file or directory: './display_applications/genetrack.xml' Traceback (most recent call last): File /usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py, line 498, in load_display_applications display_app = DisplayApplication.from_file( config_path, self ) File /usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/display_applications/application.py, line 163, in from_file return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry ) File /usr/local/galaxy/galaxy-dist/lib/galaxy/util/__init__.py, line 143, in parse_xml tree = ElementTree.parse(fname) File /usr/local/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py, line 859, in parse tree.parse(source, parser) File /usr/local/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py, line 576, in parse source = open(source, rb) Best, --Ricardo Perez ___ 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] How to distribute our local installation via git(logistics)
Hello, We want to able to distribute Galaxy configured with the UCSC browser, specially for people who are not too UNIX savvy. We had a question on how to do this, since we are planning to do it via git. How can we set up the git server, in such a way that it doesn't compromise important files that are specific to our installation. For example, in our universe_wsgi.ini file we have passwords for our database that we do not want to distribute. However, we do want to distribute universe_wsgi.ini in releases so people can be updated in important changes. We were thinking that maybe we should have a test machine to make sure all the changes does not break Galaxy, and then push the changes to our server machine an to our git server. However, we are not sure if this is the most efficient way to do it. Does anyone know how we can accomplish this without complicating too many things? Thank you for your time and patience, --Ricardo Perez ___ 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] Error when trying to display data on gene track
Hello, We are running a local instance of galaxy and we get the following error when trying to display genes from our history in the ucsc browser. I got the error as I was following the galaxy 101 video in the galaxy website (last step). Thanks, --Ricardo Perez URL: http://galaxy.tamu.edu/dataset/display_application?user_id=Noneapp_name=genetrack_intervallink_name=genetrackdataset_id=b938ed79e37fc797 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:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:185 in handle_request body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.dataset:748 in display_application display_link = display_app.get_link( link_name, data, dataset_hash, user_hash, trans ) Module galaxy.datatypes.display_applications.application:189 in get_link return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans ) Module galaxy.datatypes.display_applications.application:129 in __init__ self.ready, self.parameters = self.link.build_parameter_dict( self.data, self.dataset_hash, self.user_hash, trans ) Module galaxy.datatypes.display_applications.application:66 in build_parameter_dict if param.ready( other_values ): Module galaxy.datatypes.display_applications.parameters:119 in ready raise Exception( 'A data display parameter is in the error state: %s' % ( self.name ) ) Exception: A data display parameter is in the error state: genetrack_file extra data full traceback URL: http://galaxy.tamu.edu/dataset/display_application?user_id=Noneapp_name=genetrack_intervallink_name=genetrackdataset_id=b938ed79e37fc797 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:132 in __call__ return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:185 in handle_request body = method( trans, **kwargs ) Module galaxy.webapps.galaxy.controllers.dataset:748 in display_application display_link = display_app.get_link( link_name, data, dataset_hash, user_hash, trans ) Module galaxy.datatypes.display_applications.application:189 in get_link return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans ) Module galaxy.datatypes.display_applications.application:129 in __init__ self.ready, self.parameters = self.link.build_parameter_dict( self.data, self.dataset_hash, self.user_hash, trans ) Module galaxy.datatypes.display_applications.application:66 in build_parameter_dict if param.ready( other_values ): Module galaxy.datatypes.display_applications.parameters:119 in ready raise Exception( 'A data display parameter is in the error state: %s' % ( self.name ) ) Exception: A data display parameter is in the error state: genetrack_file ___ 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] Extract genomic DNA job error
Hello, I am getting this error when using Extract Genomic DNA (version 2.2.2) empty format: fasta, database: hg19 924 warnings, 1st is: Chromosome by name 'chr22' was not found for build 'hg19'. Skipped 924 invalid lines, 1st is #1, chr22 1625633116287937 NM_001136213 0 - 16258185 16287885 0 11 346,119,167,45,71,71,138,107,174,115,684, 0,1853,10597,11805,13541,188 We set up a local instance of Galaxy and a local mirror of the UCSC Table browser in our servers. Thank you for your help, --Ricardo Perez ___ 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] Database source
Hello Galaxy, We are implementing a fresh instance of Galaxy in the school server for teaching purposes. So obtaining genomic data from the UCSC servers can present a problem by overloading the connection. To make things faster, we want to obtain the data for the genomic data and have it in our servers, speeding up data retrieval. At first I was under the impression that we had to use MySQL for this, and downloaded MySQL files from the UCSC servers by using: $ rsync -avzP rsync:// hgdownload.cse.ucsc.edu/mysql . We have successfully added the data to MySQL in our server, but now do not know how to make galaxy see the data. However after searching more about the problem, I found out that I could have used the following instead: $ rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/ . Was downloading the mysql files unnecessary or can I still be able to use them? Also, would it be more efficient to use the second rsync option instead? Thank you for your help, --Ricardo Perez ___ 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] (no subject)
Hi, We are having problems fetching sequences from our mysql database to galaxy. Does anyone know how to do so? Thank you for your help. --Ricardo Perez. ___ 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] Local Instance permissions.
Hi, We are implementing a local instance of Galaxy and I had a quick question, is it wrong to give Galaxy access to the UCSC databases? Thank you for your time and patience, --Ricardo Perez ___ 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] Local data
Hi, I am sorry for the trivial question. Does anyone know how I can make a local instance of Galaxy use our local database files? We have downloaded the database from USCS and would like to use the downloaded files instead of retrieving it from the UCSC Table Browser when processing data. Thank you very much for your help, --Ricardo Perez ___ 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] Downloading UCSC complete database
Dear all, I am currently working on downloading the genome data from the UCSC database. I have figured out how to obtain the genome of one species at a time, however this would take a bit of time if I have to type every command by hand. Is there any command that would download the all the data from the UCSC databases? If not, how would I go to start in writing a script that would do so. Thank you for your time. -Ricardo ___ 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/
