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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/