Re: [galaxy-dev] Galaxy admin access
Hi Aneisha, When you say you cannot alter config/galaxy.ini, what do you mean? You should be able to create (if not there) and edit this file in your regular terminal on that machine. Does a different user own the file, perhaps a 'galaxy' one? If so, you could change to that user and then edit. On Fri, Jun 12, 2015 at 5:13 PM Davenport, Aneisha wrote: > Hi, I work at the It service desk at the GRU Health and Science campus Ed > Commons GB building and I have a customer trying to get admin access for > the local installation of galaxy. We tried to follow the online > instructions "In order to control your new Galaxy through the UI > (installing tools, managing users, creating groups etc.) you have to become > an administrator. First register as a new user and then give the user admin > privileges like this: You add the Galaxy login ( email ) to the Galaxy > configuration file (config/galaxy.ini). If the file does not exist you can > copy it from the provided sample (config/galaxy.ini.sample). Note that you > have to restart Galaxy after modifying the configuration for changes to > take effect. > > > # this should be a comma-separated list of valid Galaxy users > admin_users = us...@example.com,us...@example.com" but we cannot alter > the config/galaxy.ini file. Can you please give us assistance? Do you run > in console or Terminal (this is a Macbook Air Laptop)? > > > Aneisha Davenport > ___ > 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/
[galaxy-dev] Galaxy admin access
Hi, I work at the It service desk at the GRU Health and Science campus Ed Commons GB building and I have a customer trying to get admin access for the local installation of galaxy. We tried to follow the online instructions "In order to control your new Galaxy through the UI (installing tools, managing users, creating groups etc.) you have to become an administrator. First register as a new user and then give the user admin privileges like this: You add the Galaxy login ( email ) to the Galaxy configuration file (config/galaxy.ini). If the file does not exist you can copy it from the provided sample (config/galaxy.ini.sample). Note that you have to restart Galaxy after modifying the configuration for changes to take effect. # this should be a comma-separated list of valid Galaxy users admin_users = us...@example.com,us...@example.com" but we cannot alter the config/galaxy.ini file. Can you please give us assistance? Do you run in console or Terminal (this is a Macbook Air Laptop)? Aneisha Davenport ___ 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/
Re: [galaxy-dev] keep job output and scripts on failed tests
Hmm. That may need a tweak - using GALAXY_TEST_NO_CLEANUP is not the default, so this could easily be a regression. Peter On Fri, Jun 12, 2015 at 6:09 PM, Ryan G wrote: > I tried that and the directories don't get removed however the job files > still get deleted. > > On Fri, Jun 12, 2015 at 12:03 PM, Peter Cock > wrote: >> >> Hi Ryan, >> >> Something very handy for tool developers running functional tests >> is if the environment variable GALAXY_TEST_NO_CLEANUP >> is set, run_tests.sh shouldn't remove the test output. >> >> This is great when debugging why a test is failing. >> >> Peter >> >> >> On Fri, Jun 12, 2015 at 4:29 PM, Ryan G >> wrote: >> > I'd like to recommend a change. If jobs fail to run during functional >> > tests, I'd like to keep the failed job files around to be examined. I >> > added >> > the following to do so: >> > >> > +++ scripts/functional_tests.py >> > @@ -372,6 +372,7 @@ def main(): >> > user_library_import_dir=user_library_import_dir, >> > master_api_key=master_api_key, >> > use_tasked_jobs=True, >> > + cleanup_job='onsuccess' >> > ) >> > if install_database_connection is not None: >> > kwargs[ 'install_database_connection' ] = >> > install_database_connection >> > >> > >> > >> > >> > >> > ___ >> > 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/
Re: [galaxy-dev] picard_MarkDuplicatesWithMateCigar functional test failure
done
On Fri, Jun 12, 2015 at 11:33 AM, Nicola Soranzo
wrote:
> Hi Ryan,
> please open a pull request at
> https://github.com/galaxyproject/tools-devteam
>
> The file is in tools/picard/ directory.
>
> Thanks,
> Nicola
>
> Il 12.06.2015 17:23 Ryan G ha scritto:
>
> The functional test for this tool fails. Looking at the XML wrapper, it
> looks like $comments is invalidit doesn't exist anywhere else in the
> xml file. I know that comments can be specified multiple times however
> there is no way to get the comments fields to appear multiple times in the
> UI as far as I can tell. So, I changed it from
>
> #for $element in $comments:
> COMMENT="${element.comment}"
> #end for
>
> to
>
> COMMENT="${comment}"
>
> and the functional test passes.
>
>
>
>
>
>
>
>
> Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate,
> le video chiamate e persino le chiamate di gruppo.
> E chiami gratis anche i numeri fissi e mobili nel mondo!
> Scarica subito l’app Vai su https://www.indoona.com/
>
>
___
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Re: [galaxy-dev] keep job output and scripts on failed tests
I tried that and the directories don't get removed however the job files still get deleted. On Fri, Jun 12, 2015 at 12:03 PM, Peter Cock wrote: > Hi Ryan, > > Something very handy for tool developers running functional tests > is if the environment variable GALAXY_TEST_NO_CLEANUP > is set, run_tests.sh shouldn't remove the test output. > > This is great when debugging why a test is failing. > > Peter > > > On Fri, Jun 12, 2015 at 4:29 PM, Ryan G > wrote: > > I'd like to recommend a change. If jobs fail to run during functional > > tests, I'd like to keep the failed job files around to be examined. I > added > > the following to do so: > > > > +++ scripts/functional_tests.py > > @@ -372,6 +372,7 @@ def main(): > > user_library_import_dir=user_library_import_dir, > > master_api_key=master_api_key, > > use_tasked_jobs=True, > > + cleanup_job='onsuccess' > > ) > > if install_database_connection is not None: > > kwargs[ 'install_database_connection' ] = > > install_database_connection > > > > > > > > > > > > ___ > > 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/
Re: [galaxy-dev] Functional test for BAM output
Thanks John, that's quite the detailed response. I agree with your reasoning, and I can see the progress in planemo -- the shed_test command is great and I'm using it to see why some of my tool tests fail. In this particular case there is nothing wrong with the framework though, as the planemo test will also fail if samtools is not in the path. I guess it's just because samtools is not installed on the machine that runs the testing framework. In the light of the proposed changes I understand if you don't want to touch this aspect anymore, and I'm happy to have samtools installed when doing the (planemo) testing! Marius On 12 June 2015 at 17:37, John Chilton wrote: > tl;dr - The devteam is planning to remove the display of those test > results from the tool shed UI and replace them with something better > hopefully by the end of 2015. > > Full Details: > > As Peter has documented very well over the last year, there are large > number of problems with the install and test framework right now - it > has been very consistently broken. I think the samtools problem > specifically has been reported before for instance. At a recent > devteam meeting - I think the devteam reached a reluctant consensus > that it is very important (testing installs and tools) but until such > a time that we feel we can devote the the engineering time to keep it > up and running consistently or that the framework improves to the > point where this engineering effort is minimal - it would be better to > just remove the display of these tests in the tool shed interface - > since they are making perfectly functional tools look broken. > > Planemo now implements a shed_test command > (http://planemo.readthedocs.org/en/latest/commands.html#shed-test-command) > that supports similar functionality to the install and test framework. > On the plus side it is much easier to run the tests through planemo > and the output is better and more flexible. It is not a complete > replacement right now however - since it doesn't hook into the tool > shed display at this point and isn't a service the Galaxy project is > providing. I think the team will do both of these - hopefully by > sometime this Fall - and then we will have a framework for installing > and testing tools that makes it trivial to run the tools from the > command-line or use within a tool shed display. I have created a > Planemo milestone to track some of these developments - > https://github.com/galaxyproject/planemo/milestones/Planemo-as-a-Service. > > This may make people unhappy - it certainly doesn't make me happy - > but a year worth of brokenness does need to be addressed. So I would > encourage everyone to please respond with comments if you feel > strongly one way or the other - maybe we can make a new thread for > that and a more formal announcement of this change. > > -John > > On Thu, Jun 11, 2015 at 9:43 AM, Marius van den Beek > wrote: > > Hi list, > > > > I’ve been trying to write functional tests for a tool that produces BAM > > files as output. The tests run fine when using planemo locally, > > but not on the testtoolshed or on machines that do not have samtools > > installed. > > Apparently galaxy automatically tries to convert BAM to SAM to compare > > the output line by line, and so this fails. Surprisingly this is also > true > > when > > comparing by size. > > This is the error: > > > > Tool id: bowtieForSmallRNA > > Tool version: bowtieForSmallRNA > > Test: test_tool_00 > > ( > functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.0 > ) > > Stderr: > > > > Traceback: > > Traceback (most recent call last): > > File > > > "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", > > line 270, in test_tool > > self.do_it( td ) > > File > > > "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", > > line 67, in do_it > > raise e > > JobOutputsError: History item different than expected, difference (using > > diff): > > ( > > /tmp/shed_tools/ > testtoolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/316124e85b8d/msp_sr_bowtie/test-data/output.bam > > v. > > > /tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpjxtteB/tmpQMbAfNoutput.bam > > ) > > Converting local (test-data) bam to sam failed: (cmd=[samtools view -h -o > > > "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpjxtteB/local_bam_converted_to_sam_8Ym0af.sam" > > "/tmp/shed_tools/ > testtoolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/316124e85b8d/msp_sr_bowtie/test-data/output.bam > "], > > stdout=[], stderr=[/bin/sh: 1: samtools: not found > > ]) > > > > Should samtools perhaps be added to the list of tools required for > running > > galaxy? > > > > Best, > > Mari
Re: [galaxy-dev] keep job output and scripts on failed tests
Hi Ryan, Something very handy for tool developers running functional tests is if the environment variable GALAXY_TEST_NO_CLEANUP is set, run_tests.sh shouldn't remove the test output. This is great when debugging why a test is failing. Peter On Fri, Jun 12, 2015 at 4:29 PM, Ryan G wrote: > I'd like to recommend a change. If jobs fail to run during functional > tests, I'd like to keep the failed job files around to be examined. I added > the following to do so: > > +++ scripts/functional_tests.py > @@ -372,6 +372,7 @@ def main(): > user_library_import_dir=user_library_import_dir, > master_api_key=master_api_key, > use_tasked_jobs=True, > + cleanup_job='onsuccess' > ) > if install_database_connection is not None: > kwargs[ 'install_database_connection' ] = > install_database_connection > > > > > > ___ > 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/
Re: [galaxy-dev] Functional test for BAM output
On Fri, Jun 12, 2015 at 4:37 PM, John Chilton wrote: > tl;dr - The devteam is planning to remove the display of those test > results from the tool shed UI and replace them with something better > hopefully by the end of 2015. > > > > This may make people unhappy - it certainly doesn't make me happy - > but a year worth of brokenness does need to be addressed. So I would > encourage everyone to please respond with comments if you feel > strongly one way or the other - maybe we can make a new thread for > that and a more formal announcement of this change. > > -John I'd agree with John that this is not ideal, but would still be an improvement on the current situation where the Tool Shed test results are not useful to anyone. A new thread formally announcing this proposed change would be a good idea. 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Functional test for BAM output
tl;dr - The devteam is planning to remove the display of those test results from the tool shed UI and replace them with something better hopefully by the end of 2015. Full Details: As Peter has documented very well over the last year, there are large number of problems with the install and test framework right now - it has been very consistently broken. I think the samtools problem specifically has been reported before for instance. At a recent devteam meeting - I think the devteam reached a reluctant consensus that it is very important (testing installs and tools) but until such a time that we feel we can devote the the engineering time to keep it up and running consistently or that the framework improves to the point where this engineering effort is minimal - it would be better to just remove the display of these tests in the tool shed interface - since they are making perfectly functional tools look broken. Planemo now implements a shed_test command (http://planemo.readthedocs.org/en/latest/commands.html#shed-test-command) that supports similar functionality to the install and test framework. On the plus side it is much easier to run the tests through planemo and the output is better and more flexible. It is not a complete replacement right now however - since it doesn't hook into the tool shed display at this point and isn't a service the Galaxy project is providing. I think the team will do both of these - hopefully by sometime this Fall - and then we will have a framework for installing and testing tools that makes it trivial to run the tools from the command-line or use within a tool shed display. I have created a Planemo milestone to track some of these developments - https://github.com/galaxyproject/planemo/milestones/Planemo-as-a-Service. This may make people unhappy - it certainly doesn't make me happy - but a year worth of brokenness does need to be addressed. So I would encourage everyone to please respond with comments if you feel strongly one way or the other - maybe we can make a new thread for that and a more formal announcement of this change. -John On Thu, Jun 11, 2015 at 9:43 AM, Marius van den Beek wrote: > Hi list, > > I’ve been trying to write functional tests for a tool that produces BAM > files as output. The tests run fine when using planemo locally, > but not on the testtoolshed or on machines that do not have samtools > installed. > Apparently galaxy automatically tries to convert BAM to SAM to compare > the output line by line, and so this fails. Surprisingly this is also true > when > comparing by size. > This is the error: > > Tool id: bowtieForSmallRNA > Tool version: bowtieForSmallRNA > Test: test_tool_00 > (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.0) > Stderr: > > Traceback: > Traceback (most recent call last): > File > "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", > line 270, in test_tool > self.do_it( td ) > File > "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", > line 67, in do_it > raise e > JobOutputsError: History item different than expected, difference (using > diff): > ( > /tmp/shed_tools/testtoolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/316124e85b8d/msp_sr_bowtie/test-data/output.bam > v. > /tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpjxtteB/tmpQMbAfNoutput.bam > ) > Converting local (test-data) bam to sam failed: (cmd=[samtools view -h -o > "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/repositories_with_tools/tmp/tmpjxtteB/local_bam_converted_to_sam_8Ym0af.sam" > "/tmp/shed_tools/testtoolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/316124e85b8d/msp_sr_bowtie/test-data/output.bam"], > stdout=[], stderr=[/bin/sh: 1: samtools: not found > ]) > > Should samtools perhaps be added to the list of tools required for running > galaxy? > > Best, > Marius > > > ___ > 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/
Re: [galaxy-dev] picard_MarkDuplicatesWithMateCigar functional test failure
Hi Ryan,
please open a pull request at
https://github.com/galaxyproject/tools-devteam
The file is in
tools/picard/ directory.
Thanks,
Nicola
Il 12.06.2015 17:23 Ryan G ha
scritto:
> The functional test for this tool fails. Looking at the XML
wrapper, it looks like $comments is invalidit doesn't exist anywhere
else in the xml file. I know that comments can be specified multiple
times however there is no way to get the comments fields to appear
multiple times in the UI as far as I can tell. So, I changed it from
>
> #for $element in $comments:
> COMMENT="${element.comment}"
> #end
for
>
> to
>
> COMMENT="${comment}"
>
> and the functional test
passes.
Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le
video chiamate e persino le chiamate di gruppo.
E chiami gratis anche i numeri fissi e mobili nel mondo!
Scarica subito l’app Vai su https://www.indoona.com/
___
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:
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[galaxy-dev] keep job output and scripts on failed tests
I'd like to recommend a change. If jobs fail to run during functional tests, I'd like to keep the failed job files around to be examined. I added the following to do so: +++ scripts/functional_tests.py @@ -372,6 +372,7 @@ def main(): user_library_import_dir=user_library_import_dir, master_api_key=master_api_key, use_tasked_jobs=True, + cleanup_job='onsuccess' ) if install_database_connection is not None: kwargs[ 'install_database_connection' ] = install_database_connection ___ 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/
[galaxy-dev] picard_MarkDuplicatesWithMateCigar functional test failure
The functional test for this tool fails. Looking at the XML wrapper, it
looks like $comments is invalidit doesn't exist anywhere else in the
xml file. I know that comments can be specified multiple times however
there is no way to get the comments fields to appear multiple times in the
UI as far as I can tell. So, I changed it from
#for $element in $comments:
COMMENT="${element.comment}"
#end for
to
COMMENT="${comment}"
and the functional test passes.
___
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:
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Re: [galaxy-dev] functional tests / database lock
Is there a known cause for this? On Fri, Jun 12, 2015 at 10:52 AM, Nicola Soranzo wrote: > Hi Ryan, > there is no know fix for this, apart from moving to PostgreSQL. > > Cheers, > Nicola > > Il 12.06.2015 16:43 Ryan G ha scritto: > > Hi all - I'm running functional tests on a set of tools using > 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and run > the tool tests individually, they succeed. So I looked into why they fail > when running them in batch, and it turns out to be a database lock. I'm > using the default sqllite database that run_tests.sh creates. Does this > need to be tuned somehow? > > > galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched > Error - : (OperationalError) database is locked u'SELECT api_keys.id AS > api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id > AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys \nWHERE > api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) > URL: > http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746714beb6212bc8 > File > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py', > line 149 in __call__ > app_iter = self.application(environ, sr_checker) > File > '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', > line 84 in __call__ > return self.application(environ, start_response) > File > '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', > line 633 in __call__ > return self.application(environ, start_response) > File > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', > line 132 in __call__ > return self.handle_request( environ, start_response ) > File > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', > line 159 in handle_request > trans = self.transaction_factory( environ ) > File > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', > line 71 in > self.set_transaction_factory( lambda e: self.transaction_chooser( e, > galaxy_app, session_cookie ) ) > File > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', > line 102 in transaction_chooser > return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) > File > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', > line 194 in __init__ > self.error_message = self._authenticate_api( session_cookie ) > File > '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', > line 283 in _authenticate_api > provided_key = self.sa_session.query( self.app.model.APIKeys ).filter( > self.app.model.APIKeys.table.c.key == api_key ).one() > File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2184 in > one > File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2227 in > __iter__ > File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2242 in > _execute_and_instances > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1449 > in execute > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1584 > in _execute_clauseelement > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1698 > in _execute_context > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1691 > in _execute_context > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py', line 331 > in do_execute > OperationalError: (OperationalError) database is locked u'SELECT > api_keys.id AS api_keys_id, api_keys.create_time AS api_keys_create_time, > api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM > api_keys \nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) > > > > > > Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, > le video chiamate e persino le chiamate di gruppo. > E chiami gratis anche i numeri fissi e mobili nel mondo! > Scarica subito l’app Vai su https://www.indoona.com/ > > ___ 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/
Re: [galaxy-dev] BioBlend Dependency Issues
The virtual environment still gave me the same Fetch failed error. Any other options to try? Thanks, Medini On Jun 11, 2015 2:02 PM, "Nicola Soranzo" wrote: > Hi, > I'd suggest you to try to run Galaxy in a virtualenv: > > $ cd galaxy/ > $ virtualenv .venv > $ ./run.sh > > Cheers, > Nicola > > Il 11.06.2015 19:51 Medini Annavajhala ha scritto: > > Hi All, > Trying to install Galaxy via instructions online and having issues with > fetching the eggs. Very similar issue to this thread: > http://dev.list.galaxyproject.org/Bioblend-dependency-error-tt4664688.html#a4664698 > , except that the dependency issue was "poster" instead of "mock". I tried > the fixes in that thread (even trying to do run.sh in a clean virtual > environment) but nothing worked. Any other ideas? > Attached is the logfile showing the error messages. > Thanks, > -- > Medini Annavajhala > M.S./Ph.D. Candidate > Dept. of Earth & Environmental Engineering > Columbia University > 500 W 120th St | MUDD 1045 > NY, NY 10027 > > > > > Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, > le video chiamate e persino le chiamate di gruppo. > E chiami gratis anche i numeri fissi e mobili nel mondo! > Scarica subito l’app Vai su https://www.indoona.com/ > > ___ 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/
Re: [galaxy-dev] functional tests / database lock
Hi Ryan, there is no know fix for this, apart from moving to PostgreSQL. Cheers, Nicola Il 12.06.2015 16:43 Ryan G ha scritto: > Hi all - I'm running functional tests on a set of tools using 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and run the tool tests individually, they succeed. So I looked into why they fail when running them in batch, and it turns out to be a database lock. I'm using the default sqllite database that run_tests.sh creates. Does this need to be tuned somehow? > > galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched > Error - : (OperationalError) database is locked u'SELECT api_keys.id [1] AS api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key nFROM api_keys nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) > URL: http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746714beb6212bc8 [2] > File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ > app_iter = self.application(environ, sr_checker) > File '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ > return self.application(environ, start_response) > File '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ > return self.application(environ, start_response) > File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', line 132 in __call__ > return self.handle_request( environ, start_response ) > File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', line 159 in handle_request > trans = self.transaction_factory( environ ) > File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 71 in > self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) > File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 102 in transaction_chooser > return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) > File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 194 in __init__ > self.error_message = self._authenticate_api( session_cookie ) > File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 283 in _authenticate_api > provided_key = self.sa_session.query( self.app.model.APIKeys ).filter( self.app.model.APIKeys.table.c.key == api_key ).one() > File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2184 in one > File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2227 in __iter__ > File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2242 in _execute_and_instances > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1449 in execute > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1584 in _execute_clauseelement > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1698 in _execute_context > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1691 in _execute_context > File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py', line 331 in do_execute > OperationalError: (OperationalError) database is locked u'SELECT api_keys.id [3] AS api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key nFROM api_keys nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/ ___ 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/
[galaxy-dev] functional tests / database lock
Hi all - I'm running functional tests on a set of tools using 'run_tests.sh -sid ...'. A few of the tests fail. When I go back and run the tool tests individually, they succeed. So I looked into why they fail when running them in batch, and it turns out to be a database lock. I'm using the default sqllite database that run_tests.sh creates. Does this need to be tuned somehow? galaxy.jobs.handler INFO 2015-06-12 10:28:35,854 (14) Job dispatched Error - : (OperationalError) database is locked u'SELECT api_keys.id AS api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys \nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) URL: http://localhost:8363/api/histories/cb227cec8ca83994?key=e4fe9bf787edb9ef746714beb6212bc8 File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/apps/sys/galaxy/galaxy-v15.05-staging/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/base.py', line 159 in handle_request trans = self.transaction_factory( environ ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 71 in self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 102 in transaction_chooser return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 194 in __init__ self.error_message = self._authenticate_api( session_cookie ) File '/apps/sys/galaxy/galaxy-v15.05-staging/lib/galaxy/web/framework/webapp.py', line 283 in _authenticate_api provided_key = self.sa_session.query( self.app.model.APIKeys ).filter( self.app.model.APIKeys.table.c.key == api_key ).one() File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2184 in one File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2227 in __iter__ File 'build/bdist.linux-x86_64/egg/sqlalchemy/orm/query.py', line 2242 in _execute_and_instances File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1449 in execute File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1584 in _execute_clauseelement File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1698 in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/base.py', line 1691 in _execute_context File 'build/bdist.linux-x86_64/egg/sqlalchemy/engine/default.py', line 331 in do_execute OperationalError: (OperationalError) database is locked u'SELECT api_keys.id AS api_keys_id, api_keys.create_time AS api_keys_create_time, api_keys.user_id AS api_keys_user_id, api_keys."key" AS api_keys_key \nFROM api_keys \nWHERE api_keys."key" = ?' (u'e4fe9bf787edb9ef746714beb6212bc8',) ___ 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/
Re: [galaxy-dev] Functional test for BAM output
Hello Peter, I didn't read it in the docs -- I was just assuming that the instance that runs the functional tests would have all the dependencies installed, which appears not to be the case. Best, Marius On 12 June 2015 at 10:41, Peter Cock wrote: > On Thu, Jun 11, 2015 at 2:43 PM, Marius van den Beek > wrote: > > Hi list, > > > > I’ve been trying to write functional tests for a tool that produces BAM > > files as output. The tests run fine when using planemo locally, > > but not on the testtoolshed or on machines that do not have samtools > > installed. > > Apparently galaxy automatically tries to convert BAM to SAM to compare > > the output line by line, and so this fails. ... > > > > Should samtools perhaps be added to the list of tools required for > running > > galaxy? > > Hi Marius, > > I thought samtools was on the list of base dependencies for Galaxy - is > it missing from somewhere you were reading (URL please)? > > Thanks, > > 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Functional test for BAM output
On Thu, Jun 11, 2015 at 2:43 PM, Marius van den Beek wrote: > Hi list, > > I’ve been trying to write functional tests for a tool that produces BAM > files as output. The tests run fine when using planemo locally, > but not on the testtoolshed or on machines that do not have samtools > installed. > Apparently galaxy automatically tries to convert BAM to SAM to compare > the output line by line, and so this fails. ... > > Should samtools perhaps be added to the list of tools required for running > galaxy? Hi Marius, I thought samtools was on the list of base dependencies for Galaxy - is it missing from somewhere you were reading (URL please)? Thanks, 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
