[mira_talk] Re: Run MIRA in Galaxy....
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Wed, 21 Dec 2011 01:22:29 +0100
On Dec 20, 2011, at 11:51 , Peter Cock wrote:
> Now the question is why isn't there a wiggle file? Since you
> sent me the stdout log, I can see that MIRA deliberately
> didn't write it:
> [...]
> Perhaps I didn't notice this before, but it appears MIRA doesn't
> write out a wiggle file by default in EST mode.
Depending a bit on the usefulness of different files in different scenarios, I
configure MIRA to write / not write certain files. Note that this is bound to
change slightly over time, reflecting the need for certain files. E.g., the
next versions of MIRA will have ACE switched off by default.
At the moment, CAF, MAF, FASTA are on by default (that will stay so for the
next versions 3.9 and 4.0 at least) and I will add SAM (when implemented) to
that list. Maybe also the files which are quick to write or do not take up much
space (WIG comes to mind), but I am undecided there.
> Would it be
> useful to you? I can change the command line to explicitly
> request this (and the other files I try to collect).
I would advise against asking MIRA to write out by default almost every
possible file format it knows. Under many scenarios this just eats up disk
space for nothing. What you could do is have MIRA write out only MAF
(preferably, or CAF as fallback though it is larger on disk) and then, after a
successful MIRA run, have a converter task convert the file into what a user
needs. Would make it more flexible too, I think.
B.
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