May 2016 - galaxy-dev - lists.galaxyproject.org

STACKS error
by Raphenya, Amogelang 20 May '16

20 May '16

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Error when executing cleanup scripts
by Scott Szakonyi 20 May '16

20 May '16

Hi all, I'm getting an error when executing the cleanup scripts in Galaxy 16.01. It appears the script is unable to import sqlalchemy, but my understanding is that Galaxy can't function without it, so I'm at a loss to explain. Here's the error I'm getting: $ sh scripts/cleanup_datasets/delete_userless_histories.sh Traceback (most recent call last): File "./scripts/cleanup_datasets/cleanup_datasets.py", line 13, in <module> import sqlalchemy as sa ImportError: No module named sqlalchemy We have relatively limited space on our storage server, so it's imperative that I be able to execute these scripts and be able to clean up deleted material. I welcome any suggestions. Best regards, -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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tool error on TopHat test during metadata manipulations
by Nick 19 May '16

19 May '16

Hi, All our workflows with TopHat finished with status: "tool error" & "Unable to finish job". We tested them on Galaxy 15.11 and 16.01 (latest works with python 2.6). Our batch system is SGE. TopHat is v2.0.14 revision 4eb3c3beb9c7 TopHat calculations on the cluster are fine and finished without any errors but during the running set_metadata_XYZ.py script (which is also called from submited script) job fails and reports above mentioned error status. Logs are: galaxy.jobs.runners.drmaa DEBUG 2016-05-19 13:53:18,054 (481/1533559) state change: job finished normally galaxy.jobs.output_checker INFO 2016-05-19 13:53:19,389 Job 481: Log: tool progress galaxy.jobs.output_checker INFO 2016-05-19 13:53:19,389 Job 481: Log: tool progress galaxy.datatypes.metadata DEBUG 2016-05-19 13:53:21,759 setting metadata externally failed for HistoryDatasetAssociation 1965: [Errno2] No such file or directory galaxy.jobs.runners ERROR 2016-05-19 13:53:24,367 (481/1533559) Job wrapper finish method failed Traceback (most recent call last): File "/ptmp/galaxy1/galaxy/lib/galaxy/jobs/runners/__init__.py", line 590, in finish_job job_state.job_wrapper.finish( stdout, stderr, exit_code ) File "/ptmp/galaxy1/galaxy/lib/galaxy/jobs/__init__.py", line 1221, in finish dataset.datatype.set_meta( dataset, overwrite=False ) File "/ptmp/galaxy1/galaxy/lib/galaxy/datatypes/binary.py", line 314, in set_meta exit_code = subprocess.call( args=command, stderr=open( stderr_name, 'wb' ) ) File "/usr/lib64/python2.6/subprocess.py", line 470, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib64/python2.6/subprocess.py", line 623, in __init__ errread, errwrite) File "/usr/lib64/python2.6/subprocess.py", line 1141, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory As I understand Galaxy operates with pickle data ( which were saved before submiting job in file with id 1965: metadata_in_HistoryDatasetAssociation_1965_sPyPfZ ) during running function set_metadata() and does not find some files and exit with error message [false, "[Errno 2] No such file or directory"] writen to the file metadata_results_HistoryDatasetAssociation_1965_k5I9PM and kill job. What causes this error and how to fix this behavior? Thanx in advance, Nick

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Re: [galaxy-dev] Update on Qiime in Galaxy?
by Oksana Korol 19 May '16

19 May '16

Hey Bjoern, I've just started learning qiime, so probably not the best person to write tests / do clean up at the moment. Galaxy tool would have made my life much easier, by way of figuring out this beast :). Oksana Hi Oksana, > > afaik a few more tests would be nice: > > https://github.com/galaxyproject/tools-iuc/pull/431 > > But it looks more a less good. > If you want to do the final cleanup, this PR is probably ready to merge. > > > Thanks! > Bjoern > > P.S. CC Bérénice as she was working on it as well > >

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Update on Qiime in Galaxy?
by Oksana Korol 19 May '16

19 May '16

Hi galaxy tool development team and community, In the recent metagenomics hackathon it looks like there has been lots of good work done on qiime. What is the status on the tools in qiime branch of iuc repo: https://github.com/galaxyproject/tools-iuc/tree/qiime/tools/qiime? I can see that the package the tools depend on ( package_python_2_7_qiime_1_9_1) is already available on main toolshed. What is the plan for making the wrappers, that depend on this package, available on main toolshed as well? Thanks a bunch! -- :: Oksana Korol

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The Galaxy release 16.04 is out !!!
by Jennifer Hillman-Jackson 18 May '16

18 May '16

Dear Community, *The Galaxy Committers team <https://github.com/galaxyproject/galaxy/blob/dev/doc/source/project/organiz…> is pleased to announce the April 2016 (v 16.04 <https://docs.galaxyproject.org/en/master/releases/16.04_announce.html>) release of Galaxy.* Please note that Python 2.6 is no longer supported as of this release. See the 16.01 release announcement <https://wiki.galaxyproject.org/News/2016_01_GalaxyRelease> for details. *Highlights* [image: Inline image 1] - *New* % git clone -b master https://github.com/galaxyproject/galaxy.git - *Update to latest stable release* % git checkout master && pull --ff-only origin master - *Update to this exact version* % hg update latest_16.04 See the Admin <http://usegalaxy.org> wiki for additional details regarding the source code locations. *Thanks for using Galaxy!* The Galaxy team <https://wiki.galaxyproject.org/GalaxyTeam> -- Jennifer Hillman-Jackson Galaxy Application Support http://usegalaxy.org http://galaxyproject.org http://biostar.usegalaxy.org

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Removing stale references from a history
by Scott Szakonyi 18 May '16

18 May '16

Hello, Due to some problems on our servers, one of our users has file references that are no longer valid in one of his histories. He's requested that I remove them, but I don't see any particular way to do so through the interface. Is there any way to achieve this? I've poked around in the database but don't see any obvious link between the history and data files. Thanks in advance, -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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LDAP not working release 16_01
by Mohamed Kassam 18 May '16

18 May '16

Dear all, I updated my galaxy this mornig to the release 16_01. But now my LDAP connection is nort working I have this error galaxy.auth.providers.ldap_ad DEBUG 2016-05-17 15:23:38,681 LDAP authenticate: could not load ldap module Do you have any idea, I checked the auth_conf.xml and it is still the same as the previous one. Mohamed

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Ordering dropdown Database/Build
by Scott Szakonyi 17 May '16

17 May '16

Hello, As we're indexing files through the data manager (bwa), we're noticing that they're appearing at the bottom of the dropdown, and are not ordered nicely like the default members of the list. Is there any way to order all the members of this dropdown? I've tried pushing back into the code but haven't had any luck finding out how that list is generated so far. Screenshot follows: [image: Inline image 1] Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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galaxy.masthead.js change
by Mohamed Kassam 17 May '16

17 May '16

Dear all, I would like to know which file replaced the galaxy.masthead.js file. Because I was putting in the banner the name and the logo of our local galaxy. Best regards, Mohamed

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