I added a description and examples of COMMANDS files to https://trac.kbase.us/projects/kbase/wiki/StandardDocuments Please check that I got it right--there was a lot of discussion about the format of this file so I'm not sure whether it changed after the examples I copied were sent out. Are there any other config files that need to be added to https://trac.kbase.us/projects/kbase/wiki/StandardDocuments ? Nomi On Mar 5, 2013, at 3:19 PM, Thomas Brettin <[email protected]> wrote:

Progress on this front. It takes about 120 seconds to create the file. We need this for the production IRIS deployment.

Thanks to everyone that put one into their repo today.

84 17:15 foreach d ( * ) 85 17:15 ls -l $d/COMMANDS >> command.list 86 17:15 end

-rw-r--r-- 1 brettin staff 88 Mar 5 16:59 assembly/COMMANDS -rw-r--r-- 1 brettin staff 72 Mar 5 17:01 communities_api/COMMANDS -rw-r--r-- 1 brettin staff 57 Mar 5 17:01 communities_qc/COMMANDS -rw-r--r-- 1 brettin staff 76 Mar 5 16:59 experiment/COMMANDS -rw-r--r-- 1 brettin staff 103 Mar 5 16:59 genome_annotation/COMMANDS -rw-r--r-- 1 brettin staff 79 Mar 5 17:01 idserver/COMMANDS -rw-r--r-- 1 brettin staff 78 Mar 5 16:59 invocation/COMMANDS -rw-r--r-- 1 brettin staff 83 Mar 5 17:00 jnomics/COMMANDS -rw-r--r-- 1 brettin staff 294 Mar 5 17:01 kb_seed/COMMANDS -rw-r--r-- 1 brettin staff 58 Mar 5 16:59 networks/COMMANDS -rw-r--r-- 1 brettin staff 103 Mar 5 16:59 ontology_service/COMMANDS -rw-r--r-- 1 brettin staff 71 Mar 5 16:58 phispy/COMMANDS -rw-r--r-- 1 brettin staff 64 Mar 5 16:59 plant_expression_service/COMMANDS

MISSING:

feature_selection file_type_service genotype_phenotype_api KBaseFBAModeling microphone otu_correlation prinseq probabilistic_annotation prom_service protein_info_service regprecise sim_service translation trees workspace_service

I'll see what I can find from Bob's work, but anyone owning one of these repos should create their own. I shouldn't be checking these into your repos.

Tom