Hi,
thanks! Let me clarify myself on the multiple generation question.
When I do command line, I do this:
Bam,Bai -> Prog1 -> Bam,Bai(v2) -> Prog2 -> Bam,Bai(v3)
What I understand, what galaxy is doing ("always overwrite" [1]):
Bam,Bai -> Prog1 -> Bam,Bai(v2) -> Bam(v2) -> Bam,Bai(v2) ->
Prog2 -> Bam,Bai(v3) -> Bam(v3) -> Bam,Bai(v3)
Best,
Alexander
[1]
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py#L314
2015-06-19 1:26 GMT-05:00 Björn Grüning <bjoern.gruen...@gmail.com>:
> Hi Alexander,
>
> Am 19.06.2015 um 01:44 schrieb Alexander Vowinkel:
> > Hi,
> >
> > when I 'produce' a bam file in my output, I can download the bam file
> and a
> > corresponding bai file.
> >
> > I am now wondering where does the bai file come from?
>
> From Galaxy! :)
> Galaxy has a concept of datatypes and metadata. In the case of BAM
> files, Galaxy is producing the index file to every position sorted BAM
> file.
>
> > When is it being generated, what code is used for that?
>
> As soon as the BAM file is created.
>
> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py#L312
>
> > When I do multiple actions with my bam file - is the index generated
> every
> > time? (overhead)
>
> No why should it? The BAM files stays the same right? So if you are
> using the BAM multiple time the one index is used multiple times.
>
> > Where is the bai saved on disk (if it is)?
>
> You can access it with this snipped: $your_bam_file.metadata.bam_index
>
> > I found that in the IUC gatk, a new bai is always generated when a gatk
> > tool is started. This creates quite an overhead. Isn't there a better
> > solution?
>
> Do you have an idea?
> Without Galaxy you also create an index once and reuse it, this is was
> Galaxy is doing. This concept is also used for other datatypes and
> improves the usability dramatically.
>
>
> If this was helpful, please consider to ask this question on Biostar
> again. I think this might be useful for others as well.
>
> Cheers,
> Bjoern
>
> > @ref https://github.com/galaxyproject/tools-iuc/issues/194
> >
> > Best,
> > Alexander
> >
> >
> >
> > ___________________________________________________________
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>
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