Re: [galaxy-dev] TestToolShed failure, Exception: History in error state.
Peter, I believe part of the problem is that the install and test framework is unable to resolve the dependency on blast+ 2.2.29 because it is defined as a repository dependency, not a tool dependency. I would recommend replacing the repository dependency in the blast_rbh repository with a tool dependency definition that references package_blast_plus_2_2_29. --Dave B. On 07/30/2014 05:27 AM, Peter Cock wrote: Hi all, I'm not sure when this started (having hardly looked at my Tool Shed test results since GCC2014), but I think this is a fairly recent problem with my BLAST RBH tests failing (which has held me back from posting this to the main Tool Shed). This could be some silly mistake in my tar-ball, but usually missing test files and the like get an explicit error. The tests are passing on my GitHub/TravisCI setup (using Twill and the API backend): e.g. https://travis-ci.org/peterjc/galaxy_blast/builds/30592097 Here is the current error (the same for the last few Test Tool Shed runs), https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 108, in test_tool self.do_it( td ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 35, in do_it self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 69, in _verify_outputs galaxy_interactor.verify_output( history, output_data, output_testdef=output_testdef, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 53, in verify_output self.wait_for_history( history_id, maxseconds ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 107, in wait_for_history self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 2453, in wait_for result = func() File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 107, in self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 257, in __history_ready return self._state_ready( state, error_msg="History in error state." ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 316, in _state_ready raise Exception( error_msg ) Exception: History in error state. Is a more detailed log available which might help debug this? Thanks, Peter As an aside, this looks like the Test Tool Shed is still using the Twill backend for the functional tests? ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Providing BLAST db in a data library
Thanks for tracking down the problem - it sounds like it is a Galaxy bug then so I have created a Trello card (https://trello.com/c/bNEKfOWR). -John On Wed, Jul 30, 2014 at 7:06 AM, Peter Cock wrote: > On Wed, Jul 30, 2014 at 11:52 AM, Ulf Schaefer > wrote: >> Dear Nate, dear Peter >> >> Again, sorry for the delay in replying. >> >> Yes I can. It looks like this >> >> [galaxy@srv ~]$ cat /galaxy/database/files/081/dataset_81002.dat >> [galaxy@srv ~]$ ls /galaxy/database/files/081/dataset_81002_files/ >> blastdb.nhd blastdb.nhi blastdb.nhr blastdb.nin blastdb.nog >> blastdb.nsd blastdb.nsi blastdb.nsq > > Good. Thanks for confirming that. > >> I think the simplest solution would be to put something in the primary >> file. Just a short string that gets the file size above 0. > > That won't help with all the existing datasets out there - I think we > rather need to fix something in the Galaxy code for composite files... > >> I personally have followed you initial suggestion and made the dbs >> available globally via the .loc file. >> >> Thanks again >> Ulf > > Great. > > Peter > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Secure Passwords
I don't believe this is possible and I am aware of not active plans to work on this. But if you are willing to hack on Galaxy I think you could enforce arbitrary constraints pretty easily (if you know Python) by modifying the validate_password function in lib/galaxy/security/validate_user_input.py. I have created a Trello card for this feature request though - it can be found here https://trello.com/c/g0sODME1. Please vote! -John On Wed, Jul 30, 2014 at 7:00 AM, Shaun Webb wrote: > > Hi, > is there any current functionality or plans to enforce secure passwords when > registering a new account? By secure I mean tests on length, use of capitals > and alphanumeric characters etc. > > > Thanks > Shaun Webb > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How can I populate a data_collection output ?
Hey David, Nothing on the wiki yet - the documentation I have been pointing people at is my GCC 2014 presentation on this work http://bit.ly/gcc2014workflows. It has details on tool developer side of this as well as some end-user screenshots. There was some initial support for dataset collections in the last (June) release - but they will be more flushed out in the coming early August release and the presentation describes features that were not in the June release but will be in the August release. Hope this helps, feel free to ask me any questions as they come up. -John On Tue, Jul 29, 2014 at 4:43 PM, David Kelly wrote: > Hi John, > > Is there any documentation that explains how dataset collections work? I'd > like to learn more about it. > > Thanks, > David > > > On Tue, Jul 29, 2014 at 3:20 PM, John Chilton wrote: >> >> Hello Julie, >> >> Right now Galaxy can implicitly create collections by running a tool >> that takes in a single input or a paired dataset over say a list of >> inputs or a list of paired inputs but tools cannot explicitly create >> dataset collections. I think Galaxy's current capabilities add a lot >> of useful functionality - but say tools that take a big input and >> split it into an arbitrary number of pieces or tools that >> normalize/summarize N inputs simultaneously and produce N outputs >> cannot be represented. A few people made some progress on this at the >> recent GCC Hackathon (https://trello.com/c/ndVQmt3G) and a lot more >> people have made it clear that it is an important feature. >> >> Sorry. >> >> -John >> >> >> On Mon, Jul 28, 2014 at 11:47 AM, julie dubois wrote: >> > Hi all, >> > I'm working with data_collection as type of input in xml files. but I >> > use all the datasets of a collection to compute some results that I >> > want to push in a "data_collection" output. >> > I know how take each dataset of a data_collection input with my >> > script, like this : >> > >> > ... >> > for $f in $input >> > ... >> > >> > where $input is defined by > > collection_type=list... in the top of my xml file. >> > >> > But if my script produce some outputs (number of outputs not defined >> > in advance), how can I populate an output as a data_collection with my >> > shscript and how should I define this output in the xml ? >> > >> > Thanks >> > Julie >> > ___ >> > 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/ > > ___ 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] Uploads with embedded citations causing red error on Tool Shed
OK - I ran the "Reset all repository metadata" action on both Tool Sheds - no errors reported. Thanks, Peter On Wed, Jul 30, 2014 at 12:23 PM, Greg Von Kuster wrote: > Yes, it looks like metadata just needs to be regenerated on the > affected repositories. Let me know if doing so uncovers something else. > > Greg > > On Jul 30, 2014, at 7:20 AM, John Chilton wrote: > >> ... that might be a Greg question. The tool shed isn't going to use >> the citation information in anyway at this time >> (https://trello.com/c/R8vKH4PQ) - so you won't gain anything from a >> citation-y perspective by re-uploading. That bug might have interfered >> with the tool shed metadata generation process though(?) so it might >> be worth regenerating that when the tool shed is updated(?). That is >> just a guess though - maybe Greg will weigh in on whether that makes >> sense. >> >> -John >> >> On Wed, Jul 30, 2014 at 7:14 AM, Peter Cock >> wrote: >>> Thanks John - is there any point/benefit to re-uploading >>> my tool once the fix is live on the Tool Shed? >>> >>> i.e. Was it a harmless warning? >>> >>> Peter >>> >>> >>> On Wed, Jul 30, 2014 at 12:12 PM, John Chilton wrote: Hey Peter, Opps sorry about that and thanks for the bug report. The tool shed code should be fixed with https://bitbucket.org/galaxy/galaxy-central/commits/38ba45d6ba5be65b3b743fc08739e16cd6e0ac8f - it is in next-stable so I think the tool shed should pick up that fix at next tool shed update. -John On Wed, Jul 30, 2014 at 5:43 AM, Peter Cock wrote: > Hi John, > > Following the work at the BOSC 2014 CodeFest to support > embedded citations within Galaxy Tool XML files [1], and your > work adding this to the BLAST tools as an example [2], I tried > uploading a minor tool using this to the Tool Shed. > > The upload seems to have worked, but there was a scary > red error message about metadata... see below (both main > and test toolsheds affected). > > Regards, > > Peter > > > [1] https://bitbucket.org/galaxy/galaxy-central/pull-request/440/ > > [2] > https://github.com/peterjc/galaxy_blast/commit/9d2e3906915895765ecc3f48421b91fabf2ccd8b > > -- > > Uploading on the Test Tool Shed, red error: > > Metadata may have been defined for some items in revision > '796dc2ff8e8e'. Correct the following problems if necessary and reset > metadata. > blastxml_to_top_descr.xml - 'UniverseApplication' object has no > attribute 'citations_manager' > > https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr > > -- > > Uploading on the Tool Shed, red error: > > Metadata may have been defined for some items in revision > 'fe1ed74793c9'. Correct the following problems if necessary and reset > metadata. > blastxml_to_top_descr.xml - 'UniverseApplication' object has no > attribute 'citations_manager' > > https://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr >> ___ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Packaging tools with language specific dependencies
Hi Björn, Thanks, this is exactly what I was looking for. Cheers, Renato Quoting Björn Grüning on 30-07-2014 12:04: > Hi Renato, > > Am 30.07.2014 um 12:21 schrieb Renato Alves: >> Hi everyone, >> >> Is there any standard or commonly used way to package tools that have >> language specific dependencies. >> >> I know that with Python libraries one can use setup_virtualenv and with >> Java jars the JAVA_JAR_LIB strategy is used. >> Is there anything equivalent for R, Perl and Ruby libraries? > > please have a look at: > https://github.com/bgruening/galaxytools/tree/master/test_repositories > > If you have any questions I'm happy to help you! > Bjoern > >> Thanks >> Renato >> >> >> >> >> >> ___ >> 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/ >> signature.asc Description: OpenPGP digital signature ___ 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] Uploads with embedded citations causing red error on Tool Shed
Both Galaxy Tool Sheds have been updated with this fix. Greg On Jul 30, 2014, at 7:14 AM, Peter Cock wrote: > Thanks John - is there any point/benefit to re-uploading > my tool once the fix is live on the Tool Shed? > > i.e. Was it a harmless warning? > > Peter > > > On Wed, Jul 30, 2014 at 12:12 PM, John Chilton wrote: >> Hey Peter, >> >> Opps sorry about that and thanks for the bug report. The tool shed >> code should be fixed with >> https://bitbucket.org/galaxy/galaxy-central/commits/38ba45d6ba5be65b3b743fc08739e16cd6e0ac8f >> - it is in next-stable so I think the tool shed should pick up that >> fix at next tool shed update. >> >> -John >> >> On Wed, Jul 30, 2014 at 5:43 AM, Peter Cock >> wrote: >>> Hi John, >>> >>> Following the work at the BOSC 2014 CodeFest to support >>> embedded citations within Galaxy Tool XML files [1], and your >>> work adding this to the BLAST tools as an example [2], I tried >>> uploading a minor tool using this to the Tool Shed. >>> >>> The upload seems to have worked, but there was a scary >>> red error message about metadata... see below (both main >>> and test toolsheds affected). >>> >>> Regards, >>> >>> Peter >>> >>> >>> [1] https://bitbucket.org/galaxy/galaxy-central/pull-request/440/ >>> >>> [2] >>> https://github.com/peterjc/galaxy_blast/commit/9d2e3906915895765ecc3f48421b91fabf2ccd8b >>> >>> -- >>> >>> Uploading on the Test Tool Shed, red error: >>> >>> Metadata may have been defined for some items in revision >>> '796dc2ff8e8e'. Correct the following problems if necessary and reset >>> metadata. >>> blastxml_to_top_descr.xml - 'UniverseApplication' object has no >>> attribute 'citations_manager' >>> >>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr >>> >>> -- >>> >>> Uploading on the Tool Shed, red error: >>> >>> Metadata may have been defined for some items in revision >>> 'fe1ed74793c9'. Correct the following problems if necessary and reset >>> metadata. >>> blastxml_to_top_descr.xml - 'UniverseApplication' object has no >>> attribute 'citations_manager' >>> >>> https://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Uploads with embedded citations causing red error on Tool Shed
Yes, it looks like metadata just needs to be regenerated on the affected repositories. Let me know if doing so uncovers something else. Greg On Jul 30, 2014, at 7:20 AM, John Chilton wrote: > ... that might be a Greg question. The tool shed isn't going to use > the citation information in anyway at this time > (https://trello.com/c/R8vKH4PQ) - so you won't gain anything from a > citation-y perspective by re-uploading. That bug might have interfered > with the tool shed metadata generation process though(?) so it might > be worth regenerating that when the tool shed is updated(?). That is > just a guess though - maybe Greg will weigh in on whether that makes > sense. > > -John > > On Wed, Jul 30, 2014 at 7:14 AM, Peter Cock wrote: >> Thanks John - is there any point/benefit to re-uploading >> my tool once the fix is live on the Tool Shed? >> >> i.e. Was it a harmless warning? >> >> Peter >> >> >> On Wed, Jul 30, 2014 at 12:12 PM, John Chilton wrote: >>> Hey Peter, >>> >>> Opps sorry about that and thanks for the bug report. The tool shed >>> code should be fixed with >>> https://bitbucket.org/galaxy/galaxy-central/commits/38ba45d6ba5be65b3b743fc08739e16cd6e0ac8f >>> - it is in next-stable so I think the tool shed should pick up that >>> fix at next tool shed update. >>> >>> -John >>> >>> On Wed, Jul 30, 2014 at 5:43 AM, Peter Cock >>> wrote: Hi John, Following the work at the BOSC 2014 CodeFest to support embedded citations within Galaxy Tool XML files [1], and your work adding this to the BLAST tools as an example [2], I tried uploading a minor tool using this to the Tool Shed. The upload seems to have worked, but there was a scary red error message about metadata... see below (both main and test toolsheds affected). Regards, Peter [1] https://bitbucket.org/galaxy/galaxy-central/pull-request/440/ [2] https://github.com/peterjc/galaxy_blast/commit/9d2e3906915895765ecc3f48421b91fabf2ccd8b -- Uploading on the Test Tool Shed, red error: Metadata may have been defined for some items in revision '796dc2ff8e8e'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager' https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr -- Uploading on the Tool Shed, red error: Metadata may have been defined for some items in revision 'fe1ed74793c9'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager' https://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr > ___ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Uploads with embedded citations causing red error on Tool Shed
... that might be a Greg question. The tool shed isn't going to use the citation information in anyway at this time (https://trello.com/c/R8vKH4PQ) - so you won't gain anything from a citation-y perspective by re-uploading. That bug might have interfered with the tool shed metadata generation process though(?) so it might be worth regenerating that when the tool shed is updated(?). That is just a guess though - maybe Greg will weigh in on whether that makes sense. -John On Wed, Jul 30, 2014 at 7:14 AM, Peter Cock wrote: > Thanks John - is there any point/benefit to re-uploading > my tool once the fix is live on the Tool Shed? > > i.e. Was it a harmless warning? > > Peter > > > On Wed, Jul 30, 2014 at 12:12 PM, John Chilton wrote: >> Hey Peter, >> >> Opps sorry about that and thanks for the bug report. The tool shed >> code should be fixed with >> https://bitbucket.org/galaxy/galaxy-central/commits/38ba45d6ba5be65b3b743fc08739e16cd6e0ac8f >> - it is in next-stable so I think the tool shed should pick up that >> fix at next tool shed update. >> >> -John >> >> On Wed, Jul 30, 2014 at 5:43 AM, Peter Cock >> wrote: >>> Hi John, >>> >>> Following the work at the BOSC 2014 CodeFest to support >>> embedded citations within Galaxy Tool XML files [1], and your >>> work adding this to the BLAST tools as an example [2], I tried >>> uploading a minor tool using this to the Tool Shed. >>> >>> The upload seems to have worked, but there was a scary >>> red error message about metadata... see below (both main >>> and test toolsheds affected). >>> >>> Regards, >>> >>> Peter >>> >>> >>> [1] https://bitbucket.org/galaxy/galaxy-central/pull-request/440/ >>> >>> [2] >>> https://github.com/peterjc/galaxy_blast/commit/9d2e3906915895765ecc3f48421b91fabf2ccd8b >>> >>> -- >>> >>> Uploading on the Test Tool Shed, red error: >>> >>> Metadata may have been defined for some items in revision >>> '796dc2ff8e8e'. Correct the following problems if necessary and reset >>> metadata. >>> blastxml_to_top_descr.xml - 'UniverseApplication' object has no >>> attribute 'citations_manager' >>> >>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr >>> >>> -- >>> >>> Uploading on the Tool Shed, red error: >>> >>> Metadata may have been defined for some items in revision >>> 'fe1ed74793c9'. Correct the following problems if necessary and reset >>> metadata. >>> blastxml_to_top_descr.xml - 'UniverseApplication' object has no >>> attribute 'citations_manager' >>> >>> https://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr ___ 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] Uploads with embedded citations causing red error on Tool Shed
Thanks John - is there any point/benefit to re-uploading my tool once the fix is live on the Tool Shed? i.e. Was it a harmless warning? Peter On Wed, Jul 30, 2014 at 12:12 PM, John Chilton wrote: > Hey Peter, > > Opps sorry about that and thanks for the bug report. The tool shed > code should be fixed with > https://bitbucket.org/galaxy/galaxy-central/commits/38ba45d6ba5be65b3b743fc08739e16cd6e0ac8f > - it is in next-stable so I think the tool shed should pick up that > fix at next tool shed update. > > -John > > On Wed, Jul 30, 2014 at 5:43 AM, Peter Cock wrote: >> Hi John, >> >> Following the work at the BOSC 2014 CodeFest to support >> embedded citations within Galaxy Tool XML files [1], and your >> work adding this to the BLAST tools as an example [2], I tried >> uploading a minor tool using this to the Tool Shed. >> >> The upload seems to have worked, but there was a scary >> red error message about metadata... see below (both main >> and test toolsheds affected). >> >> Regards, >> >> Peter >> >> >> [1] https://bitbucket.org/galaxy/galaxy-central/pull-request/440/ >> >> [2] >> https://github.com/peterjc/galaxy_blast/commit/9d2e3906915895765ecc3f48421b91fabf2ccd8b >> >> -- >> >> Uploading on the Test Tool Shed, red error: >> >> Metadata may have been defined for some items in revision >> '796dc2ff8e8e'. Correct the following problems if necessary and reset >> metadata. >> blastxml_to_top_descr.xml - 'UniverseApplication' object has no >> attribute 'citations_manager' >> >> https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr >> >> -- >> >> Uploading on the Tool Shed, red error: >> >> Metadata may have been defined for some items in revision >> 'fe1ed74793c9'. Correct the following problems if necessary and reset >> metadata. >> blastxml_to_top_descr.xml - 'UniverseApplication' object has no >> attribute 'citations_manager' >> >> https://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr ___ 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] Uploads with embedded citations causing red error on Tool Shed
Hey Peter, Opps sorry about that and thanks for the bug report. The tool shed code should be fixed with https://bitbucket.org/galaxy/galaxy-central/commits/38ba45d6ba5be65b3b743fc08739e16cd6e0ac8f - it is in next-stable so I think the tool shed should pick up that fix at next tool shed update. -John On Wed, Jul 30, 2014 at 5:43 AM, Peter Cock wrote: > Hi John, > > Following the work at the BOSC 2014 CodeFest to support > embedded citations within Galaxy Tool XML files [1], and your > work adding this to the BLAST tools as an example [2], I tried > uploading a minor tool using this to the Tool Shed. > > The upload seems to have worked, but there was a scary > red error message about metadata... see below (both main > and test toolsheds affected). > > Regards, > > Peter > > > [1] https://bitbucket.org/galaxy/galaxy-central/pull-request/440/ > > [2] > https://github.com/peterjc/galaxy_blast/commit/9d2e3906915895765ecc3f48421b91fabf2ccd8b > > -- > > Uploading on the Test Tool Shed, red error: > > Metadata may have been defined for some items in revision > '796dc2ff8e8e'. Correct the following problems if necessary and reset > metadata. > blastxml_to_top_descr.xml - 'UniverseApplication' object has no > attribute 'citations_manager' > > https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr > > -- > > Uploading on the Tool Shed, red error: > > Metadata may have been defined for some items in revision > 'fe1ed74793c9'. Correct the following problems if necessary and reset > metadata. > blastxml_to_top_descr.xml - 'UniverseApplication' object has no > attribute 'citations_manager' > > https://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr ___ 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] Providing BLAST db in a data library
On Wed, Jul 30, 2014 at 11:52 AM, Ulf Schaefer wrote: > Dear Nate, dear Peter > > Again, sorry for the delay in replying. > > Yes I can. It looks like this > > [galaxy@srv ~]$ cat /galaxy/database/files/081/dataset_81002.dat > [galaxy@srv ~]$ ls /galaxy/database/files/081/dataset_81002_files/ > blastdb.nhd blastdb.nhi blastdb.nhr blastdb.nin blastdb.nog > blastdb.nsd blastdb.nsi blastdb.nsq Good. Thanks for confirming that. > I think the simplest solution would be to put something in the primary > file. Just a short string that gets the file size above 0. That won't help with all the existing datasets out there - I think we rather need to fix something in the Galaxy code for composite files... > I personally have followed you initial suggestion and made the dbs > available globally via the .loc file. > > Thanks again > Ulf Great. Peter ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Packaging tools with language specific dependencies
Hi Renato, Am 30.07.2014 um 12:21 schrieb Renato Alves: Hi everyone, Is there any standard or commonly used way to package tools that have language specific dependencies. I know that with Python libraries one can use setup_virtualenv and with Java jars the JAVA_JAR_LIB strategy is used. Is there anything equivalent for R, Perl and Ruby libraries? please have a look at: https://github.com/bgruening/galaxytools/tree/master/test_repositories If you have any questions I'm happy to help you! Bjoern Thanks Renato ___ 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] Secure Passwords
Hi, is there any current functionality or plans to enforce secure passwords when registering a new account? By secure I mean tests on length, use of capitals and alphanumeric characters etc. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ 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] Providing BLAST db in a data library
Dear Nate, dear Peter Again, sorry for the delay in replying. Yes I can. It looks like this [galaxy@srv ~]$ cat /galaxy/database/files/081/dataset_81002.dat [galaxy@srv ~]$ ls /galaxy/database/files/081/dataset_81002_files/ blastdb.nhd blastdb.nhi blastdb.nhr blastdb.nin blastdb.nog blastdb.nsd blastdb.nsi blastdb.nsq I think the simplest solution would be to put something in the primary file. Just a short string that gets the file size above 0. I personally have followed you initial suggestion and made the dbs available globally via the .loc file. Thanks again Ulf On 28/07/14 09:43, Peter Cock wrote: > On Mon, Jul 28, 2014 at 8:28 AM, Ulf Schaefer wrote: >> Dear Nate, dear Peter >> >> Sorry for the delay in replying. >> >> I can import both HTML and blastdb from a history to a data library. If >> I try to get the data out of the library into anothre history, I am >> successful for the html but not for the blastdb. The problem seems to be >> that the primary data file (the /path/dataset_12345.dat) is empty for >> the blastdb, while the html primary file has something in it. > > OK. Can you tell where Galaxy thinks the library files are on disk, > and check to see if the folder of BLAST database files is actually > there? > >> When I try to import the blastdb (from library to history) there is a >> message along the lines of "can't import empty file". I hypothesise >> (admittedly without having looked at a line of code) that there is a >> test for file size 0 somewhere that is either altogether unnecessary or, >> more likely, does not take into account that for composite datatypes it >> might be completely legitimate for the primary file to be empty. > > This guess makes sense - but I've not yet tried to trace through > the code either. > >> Or is my primary blastdb file not supposed to be empty in the first >> place? I can blast against it just fine. > > The BLAST databases do not define/populate a primary file, so > Galaxy seems to create a dummy empty file on its own. I have > wondered about altering the BLAST database datatype definition > to have a human readable text file as the "primary file" (i.e. the > information currently saved as a text log file when creating a > database). > >> Thanks a lot for your help >> Ulf > > You too - you've found an "interesting" bug... > > Peter > ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE ** ___ 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] Packaging tools with language specific dependencies
Hi everyone, Is there any standard or commonly used way to package tools that have language specific dependencies. I know that with Python libraries one can use setup_virtualenv and with Java jars the JAVA_JAR_LIB strategy is used. Is there anything equivalent for R, Perl and Ruby libraries? Thanks Renato signature.asc Description: OpenPGP digital signature ___ 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] Uploads with embedded citations causing red error on Tool Shed
Hi John, Following the work at the BOSC 2014 CodeFest to support embedded citations within Galaxy Tool XML files [1], and your work adding this to the BLAST tools as an example [2], I tried uploading a minor tool using this to the Tool Shed. The upload seems to have worked, but there was a scary red error message about metadata... see below (both main and test toolsheds affected). Regards, Peter [1] https://bitbucket.org/galaxy/galaxy-central/pull-request/440/ [2] https://github.com/peterjc/galaxy_blast/commit/9d2e3906915895765ecc3f48421b91fabf2ccd8b -- Uploading on the Test Tool Shed, red error: Metadata may have been defined for some items in revision '796dc2ff8e8e'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager' https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr -- Uploading on the Tool Shed, red error: Metadata may have been defined for some items in revision 'fe1ed74793c9'. Correct the following problems if necessary and reset metadata. blastxml_to_top_descr.xml - 'UniverseApplication' object has no attribute 'citations_manager' https://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr ___ 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] TestToolShed failure, Exception: History in error state.
Hi all, I'm not sure when this started (having hardly looked at my Tool Shed test results since GCC2014), but I think this is a fairly recent problem with my BLAST RBH tests failing (which has held me back from posting this to the main Tool Shed). This could be some silly mistake in my tar-ball, but usually missing test files and the like get an explicit error. The tests are passing on my GitHub/TravisCI setup (using Twill and the API backend): e.g. https://travis-ci.org/peterjc/galaxy_blast/builds/30592097 Here is the current error (the same for the last few Test Tool Shed runs), https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 108, in test_tool self.do_it( td ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 35, in do_it self._verify_outputs( testdef, test_history, shed_tool_id, data_list, galaxy_interactor ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 69, in _verify_outputs galaxy_interactor.verify_output( history, output_data, output_testdef=output_testdef, shed_tool_id=shed_tool_id, maxseconds=maxseconds ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 53, in verify_output self.wait_for_history( history_id, maxseconds ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 107, in wait_for_history self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 2453, in wait_for result = func() File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 107, in self.twill_test_case.wait_for( lambda: not self.__history_ready( history_id ), maxseconds=maxseconds) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 257, in __history_ready return self._state_ready( state, error_msg="History in error state." ) File "/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 316, in _state_ready raise Exception( error_msg ) Exception: History in error state. Is a more detailed log available which might help debug this? Thanks, Peter As an aside, this looks like the Test Tool Shed is still using the Twill backend for the functional tests? ___ 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] change in file of Galaxy version
Hello, In our old version of Galaxy (July,2012), we have this file GalaxyDIR/templates/webapps/galaxy/base_panels.mako that has changed a lot of to actual version (latest_2014.06.02). Do you have some documentation about this? Because when we used an iframe, all upper menu disappear, Any clue? Thank in advance for your answer -- With Regards Yassine ___ 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] How can I populate a data_collection output ?
Hello John, Thank you for your answer. We shall thus wait. Julie 2014-07-29 22:43 GMT+02:00 David Kelly : > Hi John, > > Is there any documentation that explains how dataset collections work? I'd > like to learn more about it. > > Thanks, > David > > > On Tue, Jul 29, 2014 at 3:20 PM, John Chilton wrote: >> >> Hello Julie, >> >> Right now Galaxy can implicitly create collections by running a tool >> that takes in a single input or a paired dataset over say a list of >> inputs or a list of paired inputs but tools cannot explicitly create >> dataset collections. I think Galaxy's current capabilities add a lot >> of useful functionality - but say tools that take a big input and >> split it into an arbitrary number of pieces or tools that >> normalize/summarize N inputs simultaneously and produce N outputs >> cannot be represented. A few people made some progress on this at the >> recent GCC Hackathon (https://trello.com/c/ndVQmt3G) and a lot more >> people have made it clear that it is an important feature. >> >> Sorry. >> >> -John >> >> >> On Mon, Jul 28, 2014 at 11:47 AM, julie dubois wrote: >> > Hi all, >> > I'm working with data_collection as type of input in xml files. but I >> > use all the datasets of a collection to compute some results that I >> > want to push in a "data_collection" output. >> > I know how take each dataset of a data_collection input with my >> > script, like this : >> > >> > ... >> > for $f in $input >> > ... >> > >> > where $input is defined by > > collection_type=list... in the top of my xml file. >> > >> > But if my script produce some outputs (number of outputs not defined >> > in advance), how can I populate an output as a data_collection with my >> > shscript and how should I define this output in the xml ? >> > >> > Thanks >> > Julie >> > ___ >> > 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/ > > ___ 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/
