dbkeys_list_test.yaml

api_key: 
galaxy_instance: 54.161..97
# Each dbkey should posses keys and values for all DMs that require
# arguments other than the dbkey itself
dbkeys:
# - dbkey: sacCer2
#   genome_version: EquCab2.70
# - dbkey: sacCer1
#   genome_version: EquCab2.70
# - dbkey: phiX
  # genome_version: 176
# - dbkey: eschCol_K12
#   genome_version:
# - dbkey: dm3
  # genome_version:
# - dbkey: ce10
#   genome_version:
- dbkey: mm10
#   genome_version:
# - dbkey: mm9
#   genome_version:
# - dbkey: hg19
#   genome_version:
# - dbkey: hg38
#   genome_version:

# List of DMs to run for listed dbkeys
data_managers:
- id: data_manager_fetch_genome_all_fasta #This works
# - id: data_manager_snpeff_download #This works #Needs genome version
# - id: bwa_index_builder_data_manager #This works
# - id: sam_fasta_index_builder
# - id: data_manager_fetch_genome_all_fasta_dbkey
- id: bowtie2_index_builder_data_manager # This works
# - id: bwa_mem_index_builder_data_manager #This works
# - id: picard_index_builder_data_manager

Jen to-do: order of index building

1. fetch genome
2. sam
   -- most of the rest depend on these both and can be run in any order
3. picard
4. 2bit
5. bowtie2/tophat2
6. bwa
7. bwa-mem
8. snpeff
   ..
   add others