On Apr 4, 2012, at 11:03 AM, Langhorst, Brad wrote:

> Maybe more a more specific example including all the files in the directory, 
> the input data, and the specific tool that will do the analysis would make 
> this clearer.

One particular tool is running pplacer (https://github.com/matsen/pplacer) 
given an input alignment and reference package. The invocation, taken from our 
public example (https://github.com/fhcrc/microbiome-demo) resembles:

> pplacer -c vaginal_16s.refpkg src/p4z1r36.fasta


The reference package is laid out like so:

> $ ls -l vaginal_16s.refpkg 
> total 7936
> -rwxr-xr-x  1 habnabit  staff      987 Feb  8 16:46 CONTENTS.json
> -rwxr-xr-x  1 habnabit  staff     3911 Feb  8 16:46 RAxML_info.bv_refs_aln
> -rwxr-xr-x  1 habnabit  staff    37984 Feb  8 16:46 RAxML_result.bv_refs_aln
> -rwxr-xr-x  1 habnabit  staff   514875 Feb  8 16:46 bacteria16S_508_mod5.cm
> -rwxr-xr-x  1 habnabit  staff    79661 Feb  8 16:46 bv_refdata.csv
> -rwxr-xr-x  1 habnabit  staff  1912382 Feb  8 16:46 bv_refs.sto
> -rwxr-xr-x  1 habnabit  staff  1450284 Feb  8 16:46 bv_refs_aln.fasta
> -rwxr-xr-x  1 habnabit  staff      397 Feb 13 15:33 phylo_model.json
> -rwxr-xr-x  1 habnabit  staff    41259 Feb  8 16:46 tax_table.csv


Tools, including pplacer, read the CONTENTS.json file, which is a manifest that 
describes the other files contained in the directory. In most tools, there's no 
way of specifying these things other than passing the entire reference package 
directory. We'd never had any issues previously with passing around directories.

~Aaron


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