Tool Development DELLY

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Tool Development DELLY

marcoalbuquerque
Hello Galaxy,

I'm currently working on adding some tools and am having an issue with DELLY.

So, I am under the impression that BAM indexing happens automatically when a BAM is uploaded. However there is no associated dataset_i.dat.bai file in the file location in my local instance of galaxy.

There is however metadata which seems to be created but they are not being linked together. What I mean to say is DELLY errors with cannot find Bam Index.

I was curious if there is a specific way developers are suppose to work around this? Basically we want to avoid having to provide both the BAM and BAM index and symbolically linking a new dataset because we know you have already created a better implementation, we just want to use it and don't know how.

Any help is greatly appreciated,

Marco

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Re: Tool Development DELLY

Peter Cock
On Thu, Jan 8, 2015 at 6:11 PM, Marco Albuquerque
<[hidden email]> wrote:

> Hello Galaxy,
>
> I'm currently working on adding some tools and am having an issue with
> DELLY.
>
> So, I am under the impression that BAM indexing happens automatically when a
> BAM is uploaded. However there is no associated dataset_i.dat.bai file in
> the file location in my local instance of galaxy.
>
> There is however metadata which seems to be created but they are not being
> linked together. What I mean to say is DELLY errors with cannot find Bam
> Index.
>
> I was curious if there is a specific way developers are suppose to work
> around this? Basically we want to avoid having to provide both the BAM and
> BAM index and symbolically linking a new dataset because we know you have
> already created a better implementation, we just want to use it and don't
> know how.
>
> Any help is greatly appreciated,
>
> Marco

I think the symlink approach is best, see for example the Python
wrapper script I used here for "samtools idxstats",
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats

However, you can make the link in the XML directly, see Dave's
reworking of this wrapper:
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_idxstats

Regards,

Peter
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Re: Tool Development DELLY

Peter Cock
Hi Marco,

No problem - I originally copied the metadata access
trick from one of the Galaxy dev-team's tool anyway.

Maybe we need to add this to the wiki...

Peter

On Tuesday, January 13, 2015, Marco Albuquerque <[hidden email]> wrote:
Hi Peter,

I was unaware of how to access metadata, that seemed to be my issue. The
tool works now though!

Thanks so much,

Marco




On 2015-01-09 7:13 PM, "Peter Cock" <<a href="javascript:;" onclick="_e(event, &#39;cvml&#39;, &#39;p.j.a.cock@googlemail.com&#39;)">p.j.a.cock@...> wrote:
>
>I think the symlink approach is best, see for example the Python
>wrapper script I used here for "samtools idxstats",
>https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats
>
>However, you can make the link in the XML directly, see Dave's
>reworking of this wrapper:
>https://github.com/galaxyproject/tools-devteam/tree/master/tool_collection
>s/samtools/samtools_idxstats
>
>Regards,
>
>Peter



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