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(a)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 It seemed the method written on that page has now been superseded by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(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
>>
>> ~/tool-data/bowtie2_indices.loc
>> ~/tool-data/bowtie_indices.loc
>>
>> This way you prevent duplication of your reference data
>>
>>
>> Regards, Hans-Rudolf
>>
>>