> [curtish@cheaha galaxy]$ find . -name "*.py"  | xargs grep sam_fa_indices.loc
> ./tools/samtools/    seqFile = '%s/sam_fa_indices.loc' % 
> ./tools/ngs_rna/        
> cached_seqs_pointer_file = os.path.join( options.index_dir, 
> 'sam_fa_indices.loc' )
> Is there any place in galaxy-core where such a core service lives and could 
> be used by all these adaptors, rather than replicating the code everywhere?

Not yet, but this is definitely needed. However, tools and Galaxy must remain 
independent , so the location of needed indices should be passed to the tool 
via the command line rather than having tools call into Galaxy.
> As a related question, for fasta genomes from the current history, these 
> wrappers compute the .fai file on the fly, in TMP, then throw it away, every 
> time. Has there been any discussion about storing such derived indices in the 
> dataset’s metadata (like the .bai file on a .bam data set), so it gets 
> computed once, then re-used?

Converted datasets, which subsume indices-as-metadata, can store dataset 
indices. Extending converted datasets to store indices created on the fly is 
also very much needed.

Any community contributions that address these issues would be most welcome.

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