Question about composite blast datatypes

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Question about composite blast datatypes

Eric Rasche
Hi Peter,
 
I'm working on composite datatypes now (for PacBio SMRT cells). In the datatype I know I'll have files with variable names (e.g. .1, .2, .3) and after using the blast datattype as reference material, I noticed that you had commented out files with variable names from the datatype. Is there rationale behind that? Are we ensured that the entire directory will always be transferred so it's not a problem to not specify files as part of the datatype?
 
 
Cheers,
Eric
 
--
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M Univesity
College Station, TX 77843
Ph: <a href="http://tel:4046922048">4046922048
 
 

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Re: Question about composite blast datatypes

Peter Cock
On Wed, Aug 13, 2014 at 7:22 PM, Eric Rasche <[hidden email]> wrote:

> Hi Peter,
>
> I'm working on composite datatypes now (for PacBio SMRT cells). In the
> datatype I know I'll have files with variable names (e.g. .1, .2, .3) and
> after using the blast datattype as reference material, I noticed that you
> had commented out files with variable names from the datatype. Is there
> rationale behind that? Are we ensured that the entire directory will always
> be transferred so it's not a problem to not specify files as part of the
> datatype?
>
> Reference:
> https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatypes/blast.py#L232
>
> Cheers,
> Eric

Hi Eric,

Edward Kirton wrote the original BLAST DB datatypes - I'm not sure
how to nicely define open ended file lists for datatypes, but also the
makeblastdb wrapper output does not have this problem (yet).
If and when we try to support partitioned BLAST databases (with a
*.nal or *.pal alias file) then this would be needed.

I would think that the HTML composite datatype might be a better
guide here, since you will order get lots of child files (images etc).

My guess is the whole directory may be transferred anyway, but
having "undefined" files could be a problem at some point...

Regards,

Peter
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Re: Question about composite blast datatypes

Eric Rasche
14.08.2014, 10:01, "Peter Cock" <[hidden email]>:

On Wed, Aug 13, 2014 at 7:22 PM, Eric Rasche <[hidden email]> wrote:

 Hi Peter,

 I'm working on composite datatypes now (for PacBio SMRT cells). In the
 datatype I know I'll have files with variable names (e.g. .1, .2, .3) and
 after using the blast datattype as reference material, I noticed that you
 had commented out files with variable names from the datatype. Is there
 rationale behind that? Are we ensured that the entire directory will always
 be transferred so it's not a problem to not specify files as part of the
 datatype?

 Reference:
 https://github.com/peterjc/galaxy_blast/blob/master/datatypes/blast_datatypes/blast.py#L232

 Cheers,
 Eric

Hi Eric,

Edward Kirton wrote the original BLAST DB datatypes - I'm not sure
how to nicely define open ended file lists for datatypes, but also the
makeblastdb wrapper output does not have this problem (yet).
If and when we try to support partitioned BLAST databases (with a
*.nal or *.pal alias file) then this would be needed.

I would think that the HTML composite datatype might be a better
guide here, since you will order get lots of child files (images etc).

My guess is the whole directory may be transferred anyway, but
having "undefined" files could be a problem at some point...

Regards,

Peter

Hi Peter,
 
Okay, that generally answers that, I'm using the HTML datatype now, hopefully it'll accomplish what I want it to. Thanks for this information!
 
Cheers,
Eric
 
--
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M Univesity
College Station, TX 77843
Ph: <a href="http://tel:4046922048">4046922048
 
 

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