Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?
Hi, We have two galaxy instances installed within our institute, and I am very interested in communicating with other galaxy users. Please count me in. Zhibin Lu Bioinformatics Support: Databases Applications Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 647-260-7944 Toll-free: 1-866-678-6427 www.oicr.on.ca Date: Fri, 27 Apr 2012 13:45:16 -0500 From: annbl...@eng.uiowa.edu To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally? Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ 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/ ___ 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/
[galaxy-dev] Problem to link bam files when uploading through system paths
Hello, When i try to upload bam files into galaxy data library though system paths with link to files without copying into galaxy option, galaxy always complains that The uploaded files need grooming, so change your*Copy data into Galaxy?*selection to be*Copy files into Galaxy*instead of*Link to files without copying into Galaxy*so grooming can be performed. no matter if the bam files are sorted or not. in galaxy-dist/tools/data_source/upload.py: 285: if dataset.type in ( 'server_dir', 'path_paste' ) and link_data_only == 'link_to_files': 286: # Never alter a file that will not be copied to Galaxy's local file store. 287:if datatype.dataset_content_needs_grooming( output_path ): 288: err_msg = 'The uploaded files need grooming, so change your bCopy data into Galaxy?/b selection to be ' + \ 289: 'bCopy files into Galaxy/b instead of bLink to files without copying into Galaxy/b so grooming can be performed.' The 'output_path' is alwasy *None* when using *'link_to_files'*, so the grooming check always returns False. I think we need to check the original bam file instead at line 287 like: *287: if datatype.dataset_content_needs_grooming( databset.path ):* And the following code also needs to change: 314: if datatype.dataset_content_needs_grooming( output_path ): 315: # Groom the dataset content if necessary 316: datatype.groom_dataset_content( output_path ) A quick dirty fix would be: *314: if not (dataset.type in ( 'server_dir', 'path_paste' ) and link_data_only == 'link_to_files') and datatype.dataset_content_needs_grooming( output_path ): * Please advise, -- *Zhibin Lu* Bioinformatics Support *Ontario Institute for Cancer Research* MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 647-260-7944 Toll-free: 1-866-678-6427 www.oicr.on.ca http://www.oicr.on.ca/ ___ 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/
Re: [galaxy-dev] cluster path question
Hi, I had same problem since we do not install software in the system directory. I had to add PATH into ./lib/galaxy/jobs/runners/drmaa.py manually. I do not know if anyone has better solution. Zhibin Lu Bioinformatics Support Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 www.oicr.on.ca Date: Fri, 18 Feb 2011 13:17:26 -0500 From: n...@bx.psu.edu To: golha...@umdnj.edu CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cluster path question Ryan Golhar wrote: Ryan Golhar wrote: I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing, because the tools are in the default system path. How do I tell galaxy to append a directory to the path used by jobs? Hi Ryan, Whatever user is running the jobs will need to modify the $PATH in its shell startup files. If you're using bash, this would probably be ~/.bash_profile It already is in .bashrc (which is called by .bash_profile) for the galaxy user. I can submit the script from the shell and it runs okay so something is up with either how the galaxy app is submitting the job or the environment being used by the galaxy job. When you say submit via the shell, do you mean with qsub, or by logging in to a node and running the wrapper script? I haven't tested Torque with the drmaa runner so perhaps it's submitting in a way which starts the shell in non-interactive, non-login mode. Let me know if you can determine for certain that no shell startup files are being read, and I'll try to replicate this in my environment. I'd like to modify the job script to print out some debugging information to determine what environment variables are set when the job gets executed. Actually, this would be a useful tool within Galaxy to test the cluster. That's probably the simplest method, to just create a tool that outputs (either to stdout or the output file) what you'd like to see. begin:vcard fn:Ryan Golhar, Ph.D. n:Golhar;Ryan org:The Cancer Institute of NJ;Cancer Informatics Core/Bioinformatics adr:5th floor;;120 Albany St;New Brunswick;NJ;08901;USA email;internet:golha...@umdnj.edu title:NGS Bioinformatics Specialist tel;work:(732) 235-6613 tel;fax:(732) 235-6267 tel;cell:(732) 236-1176 x-mozilla-html:FALSE url:http://www.cinj.org version:2.1 end:vcard ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
