Question: Bowtie Index In Data Libraries
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gravatar for Anthony Bretaudeau
5.8 years ago by
Anthony Bretaudeau10 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
alignment bowtie • 724 views
ADD COMMENTlink modified 5.8 years ago by Jennifer Hillman Jackson25k • written 5.8 years ago by Anthony Bretaudeau10
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gravatar for Jennifer Hillman Jackson
5.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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 -- Jennifer Jackson http://galaxyproject.org
ADD COMMENTlink written 5.8 years ago by Jennifer Hillman Jackson25k
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