- galaxy-dev - lists.galaxyproject.org

What are these called and where can I learn about them...
by Gordon Botha 01 Aug '13

01 Aug '13

Hi all Apologies if I am in the wrong channel to post this. I have been using Galaxy for a couple of months now and I'm still finding my way around the mass of info Some of the XML config file tags have a string interpolation type of variable such as ${tool.name} in: label="${tool.name} on ${on_string}: insertions" Where can I read up more on these and learn what others exist? I tried http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax and found a titbit at the end of the page but nothing more. Thanx gordon

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fail to run gatk
by Karen Chait 01 Aug '13

01 Aug '13

Hello, I am trying to run GATK on a local galaxy installation. I get the following error: ##### ERROR ---------------------------------------------------------------------------- -------------- ##### ERROR A USER ERROR has occurred (version 1.5-21-g979a84a): ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki ##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa ##### ERROR ##### ERROR MESSAGE: Walker requires a reference but none was provided. ##### ERROR ---------------------------------------------------------------------------- -------------- I choose a fasta file from the history. When I try to run it directly from the server it works fine but not through the galaxy interface. I guess something is incorrect in the wrapper. Any advice? Thanks, Karen

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Downsampling of SAM/BAM files
by Alexander Kurze 01 Aug '13

01 Aug '13

Hello, I am running a local galaxy server and tried to add the downsampling script for SAM/BAM files from Brad Longhorst which I found on Github. It uses a modified picard_wrapper.py. I get everything running except that the end file shows up empty. I realised when looking at the log file that the Input directory differs from the output directory also instead of adding a .data file it produces a .metrics.txt file. Does anyone know how to fix this, or does anyone have another script which can be used on Galaxy for downsampling SAM/BAM files? Thanks a lot, Alex

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job_conf.xml questions
by Ido Tamir 01 Aug '13

01 Aug '13

Hi, I work myself through the job_conf.xml and have a question: a) In your advanced example you have: <destination id="remote_cluster" runner="drmaa" tags="longjobs"/> <destination id="real_user_cluster" runner="drmaa">  <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> Does this mean that remote_cluster jobs can not be killed unless I add the 3 scripts to this destination? Or does this have to do with the "run jobs as real user" that I don't need currently. I am using the galaxy user for all jobs for the moment? To phrase this differently: Do I need these three scripts? b) Can I set a wall time limit for only for my local runners? like: <destination id="local" runner="local"/> <param id="Resource_List">walltime=72:00:00</param> </destination> When I set it in limits, will it work for local runners and then I have to override it in every destination? thank you very much, ido

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importing data from other public websites into galaxy
by Prasun Dutta 01 Aug '13

01 Aug '13

Hi, I wish to import data into my local instance of galaxy from another website. Kindly let me know how to achieve that and what all is required. I want to import data from a chemoinformatic database (mainly compound structures) into galaxy and run my own analysis tools on them. Regards, Prasun Dutta MSc (Bioinformatics) School of Biological Sciences University of Edinburgh, UK

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Velvet optimizer problems : Urgent help.
by Perez, Ricardo 01 Aug '13

01 Aug '13

Dear all, When trying to run velvet optimizer in galaxy, all the files we get return the following: "No peek" When looking at the output of galaxy, we get the following: galaxy.jobs.runners.local DEBUG 2013-07-31 09:31:46,829 execution finished: perl /usr/local/galaxy/bioinfosoft/shed_tools/toolshed.g2.bx.psu.edu/repos/simon-gladman/velvet_optimiser/43c89d82a7d3/velvet_optimiser/velvet_optimiser_wrapper_vlsci.pl '19' '23' '2' '0' 'short' 'False' '<galaxy.datatypes.sequence.FastqSanger object at 0x6e664d0>' '/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2067.dat''not_shortMP''other:''no_amos''not_verbose' '/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2665.dat''/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2666.dat' '/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2667.dat''/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2663.dat' '/usr/local/galaxy/galaxy-dist/database/files/002/dataset_2668.dat' > /usr/local/galaxy/galaxy-dist/database/files/002/dataset_2664.dat galaxy.jobs.runners DEBUG 2013-07-31 09:31:47,027 executing external set_meta script for job 1983: /usr/local/galaxy/galaxy-dist/set_metadata.sh ./database/files /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983 . /usr/local/galaxy/galaxy-dist/universe_wsgi.ini /usr/local/galaxy/galaxy-dist/database/tmp/tmp3460Jz /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/galaxy.json /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3117_enOT5T,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3117_vy3tDq,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3117_IFmVK8,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3117_0j3kza,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3117_zwMKHf /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3116_YppZ1L,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3116_Sniis0,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3116_l9RPFx,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3116_It8rUk,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3116_AwvXlS /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3115_TOhpBs,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3115_wUomyo,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3115_nsUrJl,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3115_DAmGEt,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3115_hFGdc0 /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3114_59uEii,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3114_UcezIt,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3114_YmOlHD,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3114_owVBfP,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3114_O3UH82 /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3113_vMrQrs,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3113_YhwIGZ,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3113_pAG6wP,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3113_9ImAZ6,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3113_uI5cbM /usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_in_HistoryDatasetAssociation_3112_NwB9j6,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_kwds_HistoryDatasetAssociation_3112_LK2cWo,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_out_HistoryDatasetAssociation_3112__FDnXW,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_results_HistoryDatasetAssociation_3112_mZQULN,,/usr/local/galaxy/galaxy-dist/database/job_working_directory/001/1983/metadata_override_HistoryDatasetAssociation_3112_k3SWCq However when running velvet optimizer from the command line (the first command from above) we get the correct output just fine. We have re-installed the tools and velvet. It seems like galaxy is passing the command just fine, but we are getting nothing back to galaxy. Anyone has ideas on how to fix this problem? Thank you very much for your time and support, --Ricardo Perez

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Problems with sharing datasets
by Ricardo Perez 31 Jul '13

31 Jul '13

Dear all, When trying to share a dataset in galaxy among users, usually this sharing fails. Usually when we go to "Dataset Securities" and try to change the permissions of the datasets the sharing fails. Instead, it keeps the original configuration and then it will open another galaxy page inside the galaxy browser that we already have. Is this due to misconfiguration that I may have? Thank you for your time, --Ricardo Perez

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Build the Galaxy under Cluster
by shenwiyn 31 Jul '13

31 Jul '13

Hi everyone, I want to install my local Galaxy under the Cluster with TORQUE.I have a question about how they work together successfully.In addition,after my local Galaxy and TORQUE install successfully,anything else should I do to the Cluster Galaxy?Thank you very much. shenwiyn

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Galaxy Proteomics mailing list
by Ira Cooke 31 Jul '13

31 Jul '13

Dear All, The galaxy community now has a mailing list dedicated to proteomics. If you're using galaxy to do proteomics, or if you are thinking of doing so then this list if for you. In case you missed it, there is also a proteomics wiki page at http://wiki.galaxyproject.org/Proteomics To subscribe to the galaxy-proteomics list please add your email address to the list here: http://lists.bx.psu.edu/listinfo/galaxy-proteomics See http://wiki.g2.bx.psu.edu/Mailing%20Lists for more information on this and other Galaxy mailing lists, including links to searchable archives of all Galaxy lists. Many thanks to Dave C. and the Galaxy team for setting this up. Thanks Ira

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Running RabbitMQ listener requires a path update
by Ganote, Carrie L 30 Jul '13

30 Jul '13

Hi list, I ran into the following problem: $ sh run_galaxy_listener.sh Traceback (most recent call last): File "scripts/galaxy_messaging/server/amqp_consumer.py", line 33, in <module> from galaxy.web.api.requests import RequestsAPIController ImportError: No module named api.requests Changed this line in scripts/galaxy_messaging/server/amqp_consumer.py: from galaxy.webapps.galaxy.api.requests import RequestsAPIController Just an artifact from the restructuring of Galaxy. Hope this helps! Sincerely, Carrie Ganote

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