Hi Ray

If you already have the reference data (as you have written in your first e-mail), then I suggest you manually add those files (file paths) to


~/tool-data/bowtie2_indices.loc
~/tool-data/bowtie_indices.loc

This way you prevent duplication of your reference data


Regards, Hans-Rudolf



Dear all,

I have gotten a bit further and was able to install the Data Managers
this time.  Previously, I was having problems accessing the ToolShed
web site and some Python errors in the log file, but fine ... sort of
(I get some intermittent errors accessing the Tool Shed site; maybe
it's a problem on my side).

However, with the FASTA fetch tool installed from the Galaxy Main Tool
Shed, I selected "Local Data" from the Administrator panel.  Under
"Run Data Manager Tools", I now have "Bowtie index", "Reference
Genome", etc.  When I click on any of the options under "Run Data
Manager Tools", though, I get a blank page.  I mean, I get a
user-level menu on the left, history on the right, a menu along the
top.  But the center is blank.  Is there something else I need to do?

If I go to "View Data Manager Jobs", "Reference Genome", though, I get
a message that says there are "There are no jobs for this data
manager.".

If possible, I would like to upload FASTA files myself to our local
Galaxy instance.  For reasons which I'm still working on (and which is
unrelated to Galaxy), download times are very long.  Since I have the
FASTA file already, it might be easier to upload one myself; but if
that's not something Data Managers can do, I guess I can just start
the download and set it aside...

Thank you!

Ray



On Thu, Feb 18, 2016 at 8:36 AM, Raymond Wan <rwan.w...@gmail.com> wrote:
Dear all,

I'm a bit new at being a Galaxy administrator, so apologies for the
basic question.

I need to install some bowtie and bowtie2 indices.  I have the indices
already but came across this page:

https://wiki.galaxyproject.org/Admin/DataPreparation

which says the steps mentioned on that page have been replaced with
Data Managers.  I'm having problems with installing Data Managers
(accessing ToolShed right now and some errors which I guess I need to
sort out later) and was wondering if there was a way to bypass Data
Managers?

Are Data Managers the only way of installing reference data?  With the
indices already pre-calculated, can I install them without having to
go through re-calculating them within Galaxy?

Thank you!

Ray
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