Hi,
Is it possible to access data on the filesystem without uploading it. i.e. I install galaxy locally, and then want to refer to some huge fasta file on disk. At the moment, I can upload it, which is slow and creates two copies. Can I just point galaxy at it somehow?
thanks, James
Hello James,
The current Galaxy distribution does not allow for accessing data on the file system without uploading it. However, Galaxy will soon include support for what we are calling "dataset libraries", which will provide this behavior. Using dataset libraries, a Galaxy administrator will upload datasets into a library ( a subdirectory of datasets to which Galaxy points ), and users will be able to access the datasets by "uploading" them into their histories. This "uploading" process will not make a copy of the dataset, however, but will be a sort of pointer to the dataset on disk. This approach will allow for multiple users to have access to a single dataset on disk. We are well into the implementation of these new features, and they should be available in the Galaxy distribution within the next few weeks.
Greg Von Kuster Galaxy Development Team
James Casbon wrote:
Hi,
Is it possible to access data on the filesystem without uploading it. i.e. I install galaxy locally, and then want to refer to some huge fasta file on disk. At the moment, I can upload it, which is slow and creates two copies. Can I just point galaxy at it somehow?
thanks, James _______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
Hi Greg,
Thanks for your answer. It looks as if you are on top of my requirements. Do let me know if you need any help testing the code,
cheers, James
2008/9/29 Greg Von Kuster ghv2@psu.edu:
Hello James,
The current Galaxy distribution does not allow for accessing data on the file system without uploading it. However, Galaxy will soon include support for what we are calling "dataset libraries", which will provide this behavior. Using dataset libraries, a Galaxy administrator will upload datasets into a library ( a subdirectory of datasets to which Galaxy points ), and users will be able to access the datasets by "uploading" them into their histories. This "uploading" process will not make a copy of the dataset, however, but will be a sort of pointer to the dataset on disk. This approach will allow for multiple users to have access to a single dataset on disk. We are well into the implementation of these new features, and they should be available in the Galaxy distribution within the next few weeks.
Greg Von Kuster Galaxy Development Team
James Casbon wrote:
Hi,
Is it possible to access data on the filesystem without uploading it. i.e. I install galaxy locally, and then want to refer to some huge fasta file on disk. At the moment, I can upload it, which is slow and creates two copies. Can I just point galaxy at it somehow?
thanks, James _______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
This approach will allow for multiple users to have access to a single dataset on disk.
Will it also be possible for a single user to "upload" a dataset into more than one history of their own? That would be tremendously helpful to me.
Michael
-----Original Message----- From: galaxy-user-bounces@bx.psu.edu [mailto:galaxy-user- bounces@bx.psu.edu] On Behalf Of Greg Von Kuster Sent: Monday, September 29, 2008 8:30 AM To: James Casbon Cc: galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] accessing data from the filesystem
Hello James,
The current Galaxy distribution does not allow for accessing data on the file system without uploading it. However, Galaxy will soon include support for what we are calling "dataset libraries", which will provide this behavior. Using dataset libraries, a Galaxy administrator will upload datasets into a library ( a subdirectory of datasets to which Galaxy points ), and users will be able to access the datasets by "uploading" them into their histories. This "uploading" process will not make a copy of the dataset, however, but will be a sort of pointer to the dataset on disk. This approach will allow for multiple users to have access to a single dataset on disk. We are well into the implementation of these new features, and they should be available in the Galaxy distribution within the next few weeks.
Greg Von Kuster Galaxy Development Team
James Casbon wrote:
Hi,
Is it possible to access data on the filesystem without uploading it. i.e. I install galaxy locally, and then want to refer to some huge fasta file on disk. At the moment, I can upload it, which is slow and creates two copies. Can I just point galaxy at it somehow?
thanks, James _______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
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Michael Rusch