Re: [galaxy-dev] Why upload to Local Instance rather than import?
Hi Greg, I believe that you do not need to actually copy the data to your workstation (although you could ...) - instead, symbolically link it from the external drive to your workstation so that it appears local. Then upload from that path. The data library upload by path option will follow a single symbolic link to data. This is explained in much more detail in our wiki, please see the section Upload directory of files: http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles Sorry for the late reply - this email got sorted incorrectly - it really is best to either send replies back to the mailing list or to start over with a new thread (brand new message to list only, not just a reply with a new subject line). This ensures we get your question tagged and tracked - and you benefit from all the helpful developers on this list that know more than I about many technical things Galaxy. If anyway else has suggestions for Greg, please feel free to add to the post, Jen Galaxy team On 2/4/13 12:53 PM, Thyssen, Gregory - ARS wrote: Hi Jen, I have a local instance of Galaxy running on my workstation. I have external hard drives full of fastq sequencing files. I want to make them available to myself as data libraries. I am the Admin and sole user at this point. The “upload” data libraries seems to pass the data through the (slow) network, even though my workstation and external hard drives are linked by USB. What is the fastest way to import my files into my galaxy instance? Can I copy them into some folder on the workstation’s hard drive? Since everything is physically connected, I don’t think I should be limited by my network speed. Thanks, Greg Thyssen -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.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/
[galaxy-dev] Why upload to Local Instance rather than import?
I have a local instance of Galaxy running on my workstation. I have external hard drives full of fastq sequencing files. I want to make them available to myself as data libraries. I am the Admin and sole user at this point. The upload data libraries seems to pass the data through the (slow) network, even though my workstation and external hard drives are linked by USB. What is the fastest way to import my files into my galaxy instance? Can I copy them into some folder on the workstation's hard drive? Since everything is physically connected, I don't think I should be limited by my network speed. Thanks, Greg Thyssen Gregory Thyssen, PhD Molecular Biologist Cotton Fiber Bioscience USDA-ARS-Southern Regional Research Center 1100 Robert E Lee Blvd New Orleans, LA 70124 gregory.thys...@ars.usda.gov 504-286-4280 This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. ___ 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] Why upload to Local Instance rather than import?
The absolute fastest method would be to enable filepath upload for data libraries (in universe_wsgi.ini -- allow_library_path_paste = True). Once that's set, you can paste the absolute file path into the upload box, and check the box for not copying the data. This will leave the data where it is on the external drive, though it will make it available in the Data Library. Obviously if you use this method, you'll need to have that external drive attached (and always at the same mount point) to use the data. If you actually *do* want to copy this data off the external drive, simply don't check that 'no copy' checkbox and the data will be copied directly through the filesystem and not uploaded. -Dannon On Feb 4, 2013, at 5:36 PM, Thyssen, Gregory - ARS gregory.thys...@ars.usda.gov wrote: I have a local instance of Galaxy running on my workstation. I have external hard drives full of fastq sequencing files. I want to make them available to myself as data libraries. I am the Admin and sole user at this point. The “upload” data libraries seems to pass the data through the (slow) network, even though my workstation and external hard drives are linked by USB. What is the fastest way to import my files into my galaxy instance? Can I copy them into some folder on the workstation’s hard drive? Since everything is physically connected, I don’t think I should be limited by my network speed. Thanks, Greg Thyssen Gregory Thyssen, PhD Molecular Biologist Cotton Fiber Bioscience USDA-ARS-Southern Regional Research Center 1100 Robert E Lee Blvd New Orleans, LA 70124 gregory.thys...@ars.usda.gov 504-286-4280 This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately. ___ 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/
