Well, I guess, you can call me 'old-fashioned' ;)
we still solely rely on manually editing the '*loc' files. The main
reason we do that: Most of our reference data is first prepared (by
others) for people using it on the command line, and only in a second
step we make it available via Galaxy.
On 02/18/2016 09:00 AM, Raymond Wan wrote:
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
It seemed the method written on that page has now been superseded by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?
On Thu, Feb 18, 2016 at 3:54 PM, Hans-Rudolf Hotz <hrh(a)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
> 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",
>> 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
>> 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!
>> On Thu, Feb 18, 2016 at 8:36 AM, Raymond Wan <rwan.work(a)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:
>>> 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
>>> 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!
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