- galaxy-dev - lists.galaxyproject.org

Error with Sam tools in Galaxy 4
by UMD Bioinformatics 20 Dec '13

20 Dec '13

Hello Devteam, I’ve just updated my local instance to the latest version. With the migration of tools to the tool shed I used the migrate command to keep my tools as they were in the previous versions. $ sh ./scripts/migrate_tools/0008_tools.sh install_dependencies and I’ve updated the database to 117 $ sh manage_db.sh upgrade However, when I’m using samtools I’m getting an error related to the data. I’m not sure what the issue is and I’ve check all the .loc and .sh files and everything is pointing to the proper locations. Any ideas what the issue might be? An error occurred with this dataset:Could not determine Samtools version /bin/sh: line 1: 1616 Segmentation fault: 11 samtools 2>&1 Error extracting alignments from (/galaxy-dist/database/files/001/dataset_1585.dat), Cheers Ian

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New Galaxy won't start, SQLite (OperationalError) database is locked
by Peter Cock 20 Dec '13

20 Dec '13

Hello all, While attempting a fresh Galaxy install from both galaxy-central and galaxy-dist, I ran into a problem initialising the default SQLite database (database/universe.sqlite), $ hg clone https://bitbucket.org/galaxy/galaxy-dist ... $ cd galaxy-dist $ ./run.sh ... galaxy.model.migrate.check DEBUG 2013-10-31 10:28:26,143 pysqlite>=2 egg successfully loaded for sqlite dialect Traceback (most recent call last): ... OperationalError: (OperationalError) database is locked u'PRAGMA table_info("dataset")' () After some puzzlement, I realised this was down to the file system - I was trying this under my home directory mounted via a distributed file system (gluster I think). Repeating the experiment under /tmp on a local hard disk worked :) (I'm posting this message for future reference; hopefully Google and/or mailing list searches will help anyone else facing this error) Regards, Peter

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Sysadmin Question
by Shrum, Donald C 19 Dec '13

19 Dec '13

Hi, I'm at the Florida State University HPC and setting up an a Galaxy server that will be used to submit jobs to our HPC cluster. I'm using apache as a proxy for the Galaxy server and I'm in the process of setting up ldap authentication. I had planned to mount our HPC file system (with user home directories) on the Galaxy server so that users would have access to their data but I'm wondering if I have the wrong idea about how Galaxy works and if there is a way to map users to their home directories in Galaxy easily. Thanks for any pointers. Donny Shrum

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Consultez mon profil LinkedIn
by Rémy Dernat 19 Dec '13

19 Dec '13

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Error with tool migration
by Kerry Deutsch 19 Dec '13

19 Dec '13

Hello - I pulled down the latest changes today (it was long overdue), and am running into the following error when I run the tool migration: sh ./scripts/migrate_tools/0008_tools.sh install_dependencies No handlers could be found for logger "galaxy.tools.data" Repositories will be installed into configured tool_path location ../shed_tools [localhost] local: rm -rf ./database/tmp/tmp-toolshed-mtdWuQjBx Skipping installation of tool dependency samtools version 0.1.18 since it is installed in /users/galaxy/galaxy_deps/bin/samtools/0.1.18/devteam/package_samtools_0_1_18/171cd8bc208d Traceback (most recent call last): File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module> app = MigrateToolsApplication( sys.argv[ 1 ] ) File "/users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/migrate/common.py", line 83, in __init__ install_dependencies=install_dependencies ) File "/users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 121, in __init__ is_repository_dependency=is_repository_dependency ) File "/users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 509, in install_repository is_repository_dependency=is_repository_dependency ) File "/users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 351, in handle_repository_contents guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config ) File "/users/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 259, in get_guid full_path = str( os.path.abspath( os.path.join( root, name ) ) ) UnboundLocalError: local variable 'name' referenced before assignment Ideas? Thanks much! Kerry

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GCC2014 Training Day: Topic Nomination is now open
by Dave Clements 18 Dec '13

18 Dec '13

Hello all, Training Day topics are nominated by you <http://bit.ly/gcc2014tdnom>, the Galaxy Community. Please take a minute to nominate a topic. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic. If you are looking for ideas, see - what was offered at GCC2013<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> , - what topics were nominated in 2013 <http://bit.ly/1i2j1gN>, and - the Events <http://wiki.galaxyproject.org/Events> and the Events Archive<http://wiki.galaxyproject.org/Events/Archive> pages. Nominated topics will be published on the Training Day<http://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> page as they come in. *Nominations close December 20*. Topics will be compiled into a uniform list by the GCC2014 Organizing Committee, and topics will be posted and voted on by the Galaxy Community, January 6-17. Nominate a topic now! <http://bit.ly/gcc2014tdnom> Topics will then be selected and scheduled based on topic interest, and the organizers' ability to confirm instructors for each session. Some very popular sessions may be scheduled more than once. The final schedule will be posted before registration opens. See you in Baltimore! GCC2014 Organizing Committee<http://wiki.galaxyproject.org/Events/GCC2014/Organizers> --- *About GCC2014:* The 2014 Galaxy Community Conference (GCC2014)<http://galaxyproject.org/gcc2014>will be held at the Homewood Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewo…> of Johns Hopkins University <http://jhu.edu/>, inBaltimore, Maryland<http://visitors.baltimorecity.gov/>, United States, from June 30 through July 2, 2014. Galaxy Community Conferences are an opportunity to participate in presentations, discussions, poster sessions, keynotes, lightning talks and bird-of-a-feather gatherings, all about high-throughput biology and the tools that support it. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Error running CCAT test
by Jennifer Jackson 18 Dec '13

18 Dec '13

Hi Nicola, This doesn't appear to be a known functional test failure (if I am reading the logs right), but I am also not the best resource to troubleshoot this particular type of problem. I am going to move this to the dev list for more feedback. If you want to add more details about your system (local? tracking galaxy-dist or central?) that might help. Best, Jen Galaxy team On 12/18/13 2:42 AM, Nicolas Lapalu wrote: > Hi, > > I tried to run CCAT functionnal test, but I get an exception (same > problem via web form) > Data are well associated with the hg18 build, which is available in > test-data/chrom/hg18.len > > > Error running CCAT. > Traceback (most recent call last): > File "/home/galaxy-dev/tools/peak_calling/ccat_wrapper.py", line 41, > in <module> > if __name__ == "__main__": main() > File "/home/galaxy-dev/tools/peak_calling/ccat_wrapper.py", line 38, > in main > return stop_err( tmp_dir, e ) > File "/home/galaxy-dev/tools/peak_calling/ccat_wrapper.py", line 13, > in stop_err > raise exception > AssertionError: The required chromosome length file does not exist. > > Any Idea ? > > Thanks, Nicolas > > -- Jennifer Hillman-Jackson http://galaxyproject.org

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Re: [galaxy-dev] problems with exporting or importing data from file
by Lukasse, Pieter 18 Dec '13

18 Dec '13

Hi Jeremy, Anna, I'm having a similar problem here as well. I would like to get a history from one Galaxy server to another and I followed the export and import steps. I even did a wget at the destination Galaxy server to check whether it could download the tar.gz file and this worked. When using the web UI I also get this message on my log showing it is actually doing something when I trigger the import: 10.85.13.89 - - [18/Dec/2013:15:10:48 +0200] "POST /history/import_archive HTTP/1.1" 200 - "http://dev1.ab.wurnet.nl:8088/history/import_archive" "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" galaxy.jobs DEBUG 2013-12-18 15:10:48,391 (3201) Working directory for job is: /home/lukas007/galaxy-dist/database/job_working_directory/003/3201 galaxy.jobs.handler DEBUG 2013-12-18 15:10:48,404 (3201) Dispatching to local runner galaxy.jobs DEBUG 2013-12-18 15:10:48,478 (3201) Persisting job destination (destination id: local:///) galaxy.jobs.handler INFO 2013-12-18 15:10:48,514 (3201) Job dispatched galaxy.jobs.runners.local DEBUG 2013-12-18 15:10:48,742 (3201) executing: export GALAXY_SLOTS="1"; python /home/lukas007/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py http://galaxy.wur.nl/galaxy_production/history/export_archive?id=b1f249e032… /home/lukas007/galaxy-dist/database/tmp/tmpPGL6le --url galaxy.jobs DEBUG 2013-12-18 15:10:48,786 (3201) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2013-12-18 15:10:48,875 execution finished: export GALAXY_SLOTS="1"; python /home/lukas007/galaxy-dist/lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py http://galaxy.wur.nl/galaxy_production/history/export_archive?id=b1f249e032… /home/lukas007/galaxy-dist/database/tmp/tmpPGL6le --url galaxy.jobs DEBUG 2013-12-18 15:10:49,040 job 3201 ended galaxy.datatypes.metadata DEBUG 2013-12-18 15:10:49,040 Cleaning up external metadata files However, nothing is visible in my histories list. What could be wrong? I also don't see any error messages in the log above. Thanks and regards, Pieter. From: galaxy-dev-bounces(a)lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Jeremy Goecks Sent: dinsdag 11 juni 2013 19:06 To: Edlund, Anna Cc: galaxy-dev(a)bx.psu.edu; Nicola Segata Subject: Re: [galaxy-dev] problems with exporting or importing data Anna, Try following these steps: (1) Make your history accessible (Share or Publish --> Make History Accessible by Link). (2) Export your history again; make sure to wait until you can use the URL to download a .gz file of your history. (3) Try importing it via URL to the Huttenhower Lab Galaxy. Let us know if you have any problems. Best, J. On Jun 10, 2013, at 11:45 AM, Edlund, Anna wrote: Hi. I have uploaded fasta files on the main galaxy server through my FileZilla program. In want to transfer them to the Galaxy at the Huttenhower Lab (see http://huttenhower.org/galaxy/root) page and to do that go to history list when I am logged in at both locations and I select 'Import a History from an archive'. I paste the url address from the main galaxy server (where my archive is located) and select submit. Then I waited for 2 days and nothing was transferred? I am clearly doing something wrong and would really like you input asap. Thank you very much!! Best regards, Anna Edlund My user name is aedlund(a)jcvi.org<mailto:aedlund@jcvi.org> ___________________________________________________________ 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/

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sort list of ftp uploaded files
by Ulf Schaefer 18 Dec '13

18 Dec '13

Dear all Is there a way to sort the list of files that a user has uploaded via FTP? Currently they appear on the form of the tool 'Upload File' in random order it seems. There is not much documentation on the <param type="ftpfile" /> tag unfortunately. If the user just selects all files they end up in his/her history in the same random order, which causes a slight inconvenience when using these files as paired multiple input for a workflow. The obvious work-around is to put the files into the history one pair at a time, but this becomes a bit onerous for larger number of files. Thanks a lot for your help. Cheers Ulf ************************************************************************** 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 **************************************************************************

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Re: [galaxy-dev] How to use Galaxy API?
by Martin Čech 18 Dec '13

18 Dec '13

Hello, by API controller I meant the Python module that takes control over the endpoints of API thus providing logic. You don't need to 'use them' - you can create API requests by many different means by specifying URL (sometimes +params+payload). Look at the extension link I have sent you, that will help you call the API from the browser. M. On Wed, Dec 18, 2013 at 3:15 AM, xlwang <xlwang_0903(a)163.com> wrote: > Hi, > thank you very much for such a quick relpy. > Now, I can connect to galaxy via API. > In addition, please tell me what is API controller?How to use those > modules and where are they in galaxy? > > > > > > At 2013-12-18 12:13:58,"Martin Čech" <marten(a)bx.psu.edu> wrote: > > Hi, > > the best start for using the API, that you found already, is the > documentation that, with a nice introduction, is nicely available here: > https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.… > > Regarding libraries your main controllers of interest are: *libraries*, > *library_contents*, *folders, **folder_contents* - *please beware that > folders API is considered work-in-progress and will probably be deprecated > in future releases.* > > If you want to test how the API behaves you can use something like Postman > extension ( > https://chrome.google.com/webstore/detail/postman-rest-client/fdmmgilgnpjig…) > for chrome or other browser that allows you to nicely simulate API calls. > > As of your error make sure that your local Galaxy, that you are trying to > connect to via API, runs on the 4096 port that you specified for the script > (by default local Galaxy runs at port 8080 - see universe_wsgi.ini for > config changes). > > Thank you for using Galaxy and let us know how it goes! > > Martin, Galaxy Team > > > > On Tue, Dec 17, 2013 at 9:26 PM, xlwang <xlwang_0903(a)163.com> wrote: > >> Hello, >> I want to know how to use Galaxy API(the path is >> /galaxy-dist/scripts/api). I follow the README but get errors. For >> instance, I have generated my_key and use this script: >> ./display.py my_key http://localhost:4096/api/libraries >> I get an error: >> <urlopen error [Errno 111] Connection refused> >> I do not know how it happened. Please tell me how to fix it. Thank you! >> >> In addition, my main purpose is to manage the data library in another >> system. Should I use the api such as library_create_library.py, >> library_upload_from_import_dir.py and so on? >> >> >> >> ___________________________________________________________ >> 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/ >> > > > >

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