Hi Hans-Rudolf,

Thank you for getting back to me!

I did take a peak at those files and they seem self-explanatory.  I
think I can do that.  However, I was worried about the message at the
top of:

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

It seemed the method written on that page has now been superseded by
Data Managers?  I was worried editing *.loc files directly with an
editor would break a database and cause more headaches for me.  Is
that not the case or perhaps I can get away with doing it just for the
FASTA files but should still use Data Managers for index generation?

Thank you!

Ray

On Thu, Feb 18, 2016 at 3:54 PM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
> 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.work@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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