Hi Anthony,
If the overall goal is to share a reference genome so that others can
also use it in a local Galaxy instance (yours or theirs), you have two
choices (with #2 being the simplest):
1 - share the indexes and .loc files using regular file sharing methods
(outside of Galaxy), then have them install the reference genome in
their instance as a built-in index. This shouldn't involve data
libraries, although I guess you could probably technically use them.
Test first.
The issue with not being able to use the indexes directly from a data
library is not a factor. If the data are indexes, they don't belong in a
history/dataset, as these are set-up files. This wiki covers NGS data
setup, in case you or they need help:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
2 - place just the .fasta version of the reference genome in a data
library then set permissions for the target users. They would then be
able to import the reference genome into a history as a dataset and use
it as a "Custom reference genome" with tools. Or, they could download it
and use it as a base to build their own indexes, loc files, etc. if
running a different Galaxy instance.
When using a custom reference genome, only a .fastsa file is needed, the
indexes are generated at run time. This will utilize more resources in
your instance. More about custom reference genomes:
http://wiki.galaxyproject.org/Support#Custom_reference_genome
Take care,
Jen
Galaxy team
On 12/14/12 2:48 AM, Anthony Bretaudeau wrote:
Hi,
I have a galaxy instance where I would like to make some private data
available to a specific group of users.
The data I would like to make available are some bowtie indexes, so
each index is made of several files with the same prefix.
How can I do this?
I have tried to put these files in a data library, but each file is
seen individually, so it is not usable in the bowtie tool.
I could add it to the bowtie_indices.loc file, but I see no way to
restrict the access to a specific group of user.
Any help would be welcome !
Thanks
Anthony
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Jennifer Jackson
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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
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