- galaxy-dev - lists.galaxyproject.org

Set Galaxy as server
by Djurdjevic, Marija 09 Nov '15

09 Nov '15

Dir Sir/Madam, I am working in the Center for Medical Research and my new task is to establish Galaxy as server. Could you be so kind to give me some basic instruction regarding the Linux distribution which is the most suitable and stable for Galaxy? I already tried with Centos 7 and Virtual Box, but it wasn't successful. Is there any good tutorial to follow during setting up? Thank you in advance. Kind regards, Mag. Marija Đurđević Core Facility Computational Bioanalytics Medical University of Graz Center for Medical Research Stiftingtalstraße 24, A-8010 Graz Austria Phone: +43 316/385-73024 Fax:+43 316/385-73009 Email: marija.djurdjevic(a)klinikum-graz.at Web: https://zmf.medunigraz.at/

2 1

email activation setting failed
by Jun Fan 09 Nov '15

09 Nov '15

Hi all, I am using smtp.gmail.com as the smtp server with gmail account. It worked perfectly fine in the past. Just this morning, I received an email reporting the issue of failing to receive the activation email. The error message from Galaxy is "This account has not been activated yet but we are unable to send the activation link. " Similarly in the error report function, there is also an expected error: "An error occurred sending the report by email: [Errno-3] temporary failure in name resolution". Any ideas of how to solve the issue? Best regards! Jun

2 1

login problem (redirection to the login page)
by Floreline TOUCHARD 09 Nov '15

09 Nov '15

Hi, this is not the first time I encounter this problem : I change the authentication mode (external to internal). And since then I cannot login with any account. Each time I'm redirected to the login page. Yet I haven't any log error. I have the galaxy-master 15.07 version. I cleared the firefox cache and cookies, from the browser and command line. But the problem's still there. The last time I uninstalled my postgresql database. I saw this post : http://dev.list.galaxyproject.org/Login-problem-tt4139426.html Is there a way to find the modifications (without unistall my galaxy instance) ? Thanks ! F.T

4 8

OpenMS caused Error downloading from URL
by Mic 09 Nov '15

09 Nov '15

Hello I tried to install OpenMS ( toolshed.g2.bx.psu.edu/repos/galaxyp/openms/42b843627623/openms) but I have got the following error: File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 128, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( install_environment, tool_dependency, actions_dict ) File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 86, in install_and_build_package initial_download=True ) File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step initial_download=initial_download ) File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 694, in execute_step dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums ) File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 187, in url_download raise Exception( err_msg ) Error downloading from URL http://downloads.sourceforge.net/project/open-ms/OpenMS/OpenMS-1.10.0/OpenM… : HTTP Error 404: Not Found Thank you in advance. Mic

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JBrowse failed to install
by Mic 09 Nov '15

09 Nov '15

Hello, I tried JBrowse from toolshed and testtoolshed to install, but in both cases it fails, because of xz ( *testtoolshed.g2.bx.psu.edu/repos/iuc/package_xz_5_0_5/50c34f0ab0e4/package_xz_5_0_5 <http://testtoolshed.g2.bx.psu.edu/repos/iuc/package_xz_5_0_5/50c34f0ab0e4/p…>* ): *Error downloading from URL* *http://tukaani.org/xz/xz-5.0.5.tar.bz2 <http://tukaani.org/xz/xz-5.0.5.tar.bz2>:* *HTTP Error 403: Forbidden* How is it possible to fix it? Thank you in advance. Mic

2 2

Error in sh manage_db.sh -c ./config/galaxy.ini upgrade
by rbrown1422＠comcast.net 06 Nov '15

06 Nov '15

Dear Galaxy Dev Team, We upgraded our Galaxy instance to the git repository from mercurial old Galaxy-dist to Galaxy. When running the sh manage_db.sh -c ./config/galaxy.ini upgrade we get the following error. Can you explain this error and more importantly how to correct the problem> Thanks, Bob -bash-4.2$ sh manage_db.sh -c ./config/galaxy.ini upgradeTraceback (most recent call last): File "./scripts/manage_db.py", line 33, in <module> invoke_migrate_main() File "./scripts/manage_db.py", line 30, in invoke_migrate_main main( repository=repo, url=db_url ) File "/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/shell.py", line 209, in main ret = command_func(**kwargs) File "/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/api.py", line 186, in upgrade return _migrate(url, repository, version, upgrade=True, err=err, **opts) File "<string>", line 2, in _migrate File "/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/util/__init__.py", line 160, in with_engine return f(*a, **kw) File "/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/api.py", line 342, in _migrate schema = ControlledSchema(engine, repository) File "/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/schema.py", line 33, in __init__ self.load() File "/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/schema.py", line 54, in load exceptions.DatabaseNotControlledError(str(exc)), tb) File "/shelter/rppa/galaxy/eggs/sqlalchemy_migrate-0.9.6-py2.7.egg/migrate/versioning/schema.py", line 50, in load data = list(result)[0]migrate.exceptions.DatabaseNotControlledError: list index out of range-bash-4.2$

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Re: [galaxy-dev] R: Re: FASTQ Groomer tool
by Fernandez Edgar 06 Nov '15

06 Nov '15

Thank you so much guys! I appreciate your help immensely! On Nov 5, 2015 7:12 PM, Nicola Soranzo <nsoranzo(a)tiscali.it> wrote: Hi Edgar, to add to Martin's explanation, it is my understanding that only the web process from which the tool installation is initiated knows about the new tool. The other web and handler processes will know about it only after a restart. Cheers, Nicola ---- Martin Čech ha scritto ---- Hi Edgar, Galaxy loads tools on start so if you install a tool it will show it in the panel (because that config is independent and already updated) however the toolbox will not have it yet until the restart. I updated the wiki (https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial) to make it more clear. Thank you for using Galaxy. M. On Thu, Nov 5, 2015 at 3:01 PM Fernandez Edgar <edgar.fernandez(a)umontreal.ca<mailto:edgar.fernandez@umontreal.ca>> wrote: Hello Nicola and Martin, The service galaxy restart worked. Can you guys give me a small explanation please? Just for my understanding… Cordialement / Regards, Edgar Fernandez De : Nicola Soranzo [mailto:nicola.soranzo@gmail.com<mailto:nicola.soranzo@gmail.com>] De la part de Nicola Soranzo Envoyé : November-05-15 2:33 PM À : Fernandez Edgar; galaxy-dev(a)bx.psu.edu<mailto:galaxy-dev@bx.psu.edu> Objet : Re: [galaxy-dev] FASTQ Groomer tool Hi Edgar, you can try to restart Galaxy (both web and handler processes) and re-run the tool. Cheers, Nicola On 05/11/15 19:18, Fernandez Edgar wrote: Hello again, I installed today the tool : fastq_all_to_sanger I get the same SQL error with that one too. Any ideas guys? Thank you!!! Cordialement / Regards, Edgar Fernandez De : Fernandez Edgar Envoyé : November-04-15 8:58 AM À : 'galaxy-dev(a)bx.psu.edu<mailto:galaxy-dev@bx.psu.edu>' Objet : [galaxy-dev] FASTQ Groomer tool Hello gents, I just installed "FASTQ Groomer tool" for the teachers to try it out and I’ve been getting the following error than I do not understand: galaxy.jobs<http://galaxy.jobs> DEBUG 2015-11-04 08:16:19,957 (756) Working directory for job is: /home/galaxy/galaxy-prod/database/job_working_directory/000/756 galaxy.jobs.handler WARNING 2015-11-04 08:16:19,958 (756) Tool 'toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4<http://toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0…>' removed from tool config, unable to run job galaxy.jobs.handler ERROR 2015-11-04 08:16:20,159 failure running job 756 Traceback (most recent call last): File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 273, in __monitor_step job_state = self.__check_job_state( job ) File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 342, in __check_job_state state, job_destination = self.__verify_job_ready( job, job_wrapper ) File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 362, in __verify_job_ready job_wrapper.fail( e ) File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/__init__.py", line 984, in fail self.sa_session.flush() File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/scoping.py", line 150, in do return getattr(self.registry(), name)(*args, **kwargs) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2004, in flush self._flush(objects) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2122, in _flush transaction.rollback(_capture_exception=True) File "build/bdist.linux-x86_64/egg/sqlalchemy/util/langhelpers.py", line 60, in __exit__ compat.reraise(exc_type, exc_value, exc_tb) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2086, in _flush flush_context.execute() File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 373, in execute rec.execute(self) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 532, in execute uow File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 170, in save_obj mapper, table, update) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 673, in _emit_update_statements execute(statement, multiparams) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 914, in execute return meth(self, multiparams, params) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1010, in _execute_clauseelement compiled_sql, distilled_params File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1146, in _execute_context context) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1332, in _handle_dbapi_exception exc_info File "build/bdist.linux-x86_64/egg/sqlalchemy/util/compat.py", line 199, in raise_from_cause reraise(type(exception), exception, tb=exc_tb) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1139, in _execute_context context) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 442, in do_execute cursor.execute(statement, parameters) File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py", line 173, in execute self.errorhandler(self, exc, value) File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py", line 36, in defaulterrorhandler raise errorclass, errorvalue ProgrammingError: (_mysql_exceptions.ProgrammingError) (1064, "You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '), blurb='tool error' WHERE history_dataset_association.id<http://history_dataset_association.id> = 1498' at line 1") [SQL: u'UPDATE history_dataset_association SET update_time=%s, info=%s, blurb=%s WHERE history_dataset_association.id<http://history_dataset_association.id> = %s'] [parameters: (datetime.datetime(2015, 11, 4, 13, 16, 20, 153739), ('This tool was disabled before the job completed. Please contact your Galaxy administrator.',), 'tool error', 1498L)] According to the tool shed repo, fastq_groomer is installed properly. Mysql is at its latest for oracle linux 6: [0]# mysql --version mysql Ver 14.14 Distrib 5.1.73, for redhat-linux-gnu (x86_64) using readline 5.1 [0]# rpm -qa | grep -i mysql mysql-5.1.73-5.el6_6.x86_64 The only thing I have not done is update galaxy for the last 6 months because they’re students using it and I do not want to change anything while it’s in production. I’m a little bit lost: Would you please indicate what I should check next? Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication ( Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218 ___________________________________________________________ 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: https://lists.galaxyproject.org/ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

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Re: [galaxy-dev] FASTQ Groomer tool
by Fernandez Edgar 06 Nov '15

06 Nov '15

Hello again, I installed today the tool : fastq_all_to_sanger I get the same SQL error with that one too. Any ideas guys? Thank you!!! Cordialement / Regards, Edgar Fernandez De : Fernandez Edgar Envoyé : November-04-15 8:58 AM À : 'galaxy-dev(a)bx.psu.edu' Objet : [galaxy-dev] FASTQ Groomer tool Hello gents, I just installed "FASTQ Groomer tool" for the teachers to try it out and I've been getting the following error than I do not understand: galaxy.jobs DEBUG 2015-11-04 08:16:19,957 (756) Working directory for job is: /home/galaxy/galaxy-prod/database/job_working_directory/000/756 galaxy.jobs.handler WARNING 2015-11-04 08:16:19,958 (756) Tool 'toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.0.4' removed from tool config, unable to run job galaxy.jobs.handler ERROR 2015-11-04 08:16:20,159 failure running job 756 Traceback (most recent call last): File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 273, in __monitor_step job_state = self.__check_job_state( job ) File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 342, in __check_job_state state, job_destination = self.__verify_job_ready( job, job_wrapper ) File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", line 362, in __verify_job_ready job_wrapper.fail( e ) File "/home/galaxy/galaxy-prod/lib/galaxy/jobs/__init__.py", line 984, in fail self.sa_session.flush() File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/scoping.py", line 150, in do return getattr(self.registry(), name)(*args, **kwargs) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2004, in flush self._flush(objects) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2122, in _flush transaction.rollback(_capture_exception=True) File "build/bdist.linux-x86_64/egg/sqlalchemy/util/langhelpers.py", line 60, in __exit__ compat.reraise(exc_type, exc_value, exc_tb) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/session.py", line 2086, in _flush flush_context.execute() File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 373, in execute rec.execute(self) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/unitofwork.py", line 532, in execute uow File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 170, in save_obj mapper, table, update) File "build/bdist.linux-x86_64/egg/sqlalchemy/orm/persistence.py", line 673, in _emit_update_statements execute(statement, multiparams) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 914, in execute return meth(self, multiparams, params) File "build/bdist.linux-x86_64/egg/sqlalchemy/sql/elements.py", line 323, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1010, in _execute_clauseelement compiled_sql, distilled_params File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1146, in _execute_context context) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1332, in _handle_dbapi_exception exc_info File "build/bdist.linux-x86_64/egg/sqlalchemy/util/compat.py", line 199, in raise_from_cause reraise(type(exception), exception, tb=exc_tb) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py", line 1139, in _execute_context context) File "build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py", line 442, in do_execute cursor.execute(statement, parameters) File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/cursors.py", line 173, in execute self.errorhandler(self, exc, value) File "build/bdist.linux-x86_64-ucs4/egg/MySQLdb/connections.py", line 36, in defaulterrorhandler raise errorclass, errorvalue ProgrammingError: (_mysql_exceptions.ProgrammingError) (1064, "You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '), blurb='tool error' WHERE history_dataset_association.id = 1498' at line 1") [SQL: u'UPDATE history_dataset_association SET update_time=%s, info=%s, blurb=%s WHERE history_dataset_association.id = %s'] [parameters: (datetime.datetime(2015, 11, 4, 13, 16, 20, 153739), ('This tool was disabled before the job completed. Please contact your Galaxy administrator.',), 'tool error', 1498L)] According to the tool shed repo, fastq_groomer is installed properly. Mysql is at its latest for oracle linux 6: [0]# mysql --version mysql Ver 14.14 Distrib 5.1.73, for redhat-linux-gnu (x86_64) using readline 5.1 [0]# rpm -qa | grep -i mysql mysql-5.1.73-5.el6_6.x86_64 The only thing I have not done is update galaxy for the last 6 months because they're students using it and I do not want to change anything while it's in production. I'm a little bit lost: Would you please indicate what I should check next? Cordialement / Regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication * Bur. : 1-514-343-6111 poste 16568 Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-218

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Galaxy Url for Fasta and Bed index files
by Asma Riyaz 05 Nov '15

05 Nov '15

Hello, What is an appropriate galaxy URL to use to obtain bed and fasta index files? I have tried below: myGalaxy.org:port/dataset/get_metadata_file?hda_id=[fasta_dataset_id]&metadata_name=fasta.fai {for fasta index} and myGalaxy.org:port/dataset/get_metadata_file?hda_id=[bed_dataset_id]&metadata_name=bed.idx {for bed index} While looking through metadata for both bed and fasta file at: myGalaxy.org:port/api/histories/[history_id]/contents/[api_id] I realized that it lacks a meta_files list. Is there a way to populate this list for bed and fasta files as well? Example: For bam files this list populates as bam_index and hence I use metadata_name=bam_index and an appropriate bai file downloads. Thank you Asma

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package_xz_5_0_5 - Error downloading from URL:
by Mic 05 Nov '15

05 Nov '15

Hello, package_xz_5_0_5 ( toolshed.g2.bx.psu.edu/repos/iuc/package_xz_5_0_5/9c92f8d0575b/package_xz_5… ) is causing the following error: File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 128, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( install_environment, tool_dependency, actions_dict ) File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/install_manager.py", line 86, in install_and_build_package initial_download=True ) File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step initial_download=initial_download ) File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 694, in execute_step dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums ) File "/home/lorencm/galaxy/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 187, in url_download raise Exception( err_msg ) *Error downloading from URL* *http://tukaani.org/xz/xz-5.0.5.tar.bz2 <http://tukaani.org/xz/xz-5.0.5.tar.bz2>:* *HTTP Error 403: Forbidden* How is it possible to fix it? Thank you in advance. Mic

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