On Thu, Jan 8, 2015 at 6:11 PM, Marco Albuquerque <marcoalbuquerque.sfu@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/... Regards, Peter