Hi Hans-Rudolf,
Actually, I'm also feeling a little "old-fashioned" myself and would prefer to edit .loc files, especially given the amount of documentation out there. I know Data Managers are a next step up, but I don't think I'm smart enough to figure out why I was getting a blank page -- perhaps a problem for another day (that I might ignore unless it bothers users :-) ).
By the way, I just got it working -- thank you for your help!
Ray
On Thu, Feb 18, 2016 at 4:10 PM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
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It seemed the method written on that page has now been superseded by Data Managers?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 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