Hi Ray

Data Managers are designed to co-exist with manually editing the .loc
files. So don't worry, edit away.

Peter

On 18 February 2016 at 10:00, Raymond Wan <rwan.w...@gmail.com> wrote:

> 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 It seemed the method written on that page has now been superseded by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 <h...@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.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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