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.thyssen@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.
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.Thyssen@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.thyssen@ars.usda.gov 504-286-4280
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Dannon Baker -
Thyssen, Gregory - ARS