Hi Ray
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.
Hans-Rudolf
On 02/18/2016 09:00 AM, Raymond Wan 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It seemed the method written on that page has now been superseded by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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