10:59 a.m.
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
1:30 p.m.
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
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2:24 p.m.
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(a)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(a)bx.psu.edu
> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
>
>
>
3:54 p.m.
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(a)bx.psu.edu [mailto:galaxy-user-
bounces(a)bx.psu.edu] On Behalf Of Greg Von Kuster
Sent: Monday, September 29, 2008 8:30 AM
To: James Casbon
Cc: galaxy-user(a)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(a)bx.psu.edu
> http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
>
>
>
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4 comments
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participants (3)
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Greg Von Kuster -
James Casbon -
Michael Rusch