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.
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:
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:
On 12/14/12 2:48 AM, Anthony Bretaudeau wrote:
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 !
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