Re: [galaxy-dev] Tool Development DELLY

2015-01-12 Thread 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 
marcoalbuquerque@gmail.com 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 p.j.a.c...@googlemail.com
 javascript:; 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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Re: [galaxy-dev] Tool Development DELLY

2015-01-09 Thread Peter Cock
On Thu, Jan 8, 2015 at 6:11 PM, Marco Albuquerque
marcoalbuquerque@gmail.com 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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