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# Configuration file defining biological data to retrieve and install.
# These are stored in an Amazon S3 bucket:
# https://s3.amazonaws.com/biodata
# and retrieved using the data_fabfile Fabric script.
# ## Genome data -- Next generation sequencing and Galaxy
# Details about the genomes you want to include.
# Required genome fields (corresponding to Galaxy's tool_data_table_conf.xml columns):
# dbkey - globally unique identifier for the genome (e.g., hg19)
# name - descriptive name for the given genome (to be displayed in Galaxy, e.g., Hsapiens)
# Optional genome fields (corresponding to Galaxy's tool_data_table_conf.xml columns):
# formats, species, dbkey1, dbkey2, value, path, index
# Additional genome fields specific to data deployment:
# genome_indexes - list of tool indexes specific to the associated genome (overrides global 'genome_indexes')
genomes:
- dbkey: phix
name: phiX174
- dbkey: hg18
name: Human (hg18)
dbsnp: true
- dbkey: hg19
name: Human (hg19)
dbsnp: true
rnaseq: true
- dbkey: GRCh37
name: Human (GRCh37)
dbsnp: true
- dbkey: dm3
name: D melangogaster (dm3)
- dbkey: mm9
name: Mouse (mm9)
rnaseq: true
- dbkey: araTha_tair9
name: Arabidopsis thaliana (TAIR9)
- dbkey: xenTro2
name: X tropicalis (xenTro2)
- dbkey: sacCer2
name: S cerevisiae (sacCer2)
- dbkey: WS210
name: C elegans (WS210)
#custom:
# - dbkey: GRCh37-NA12878-xprize-fosmid
# base: GRCh37
# mask: https://s3.amazonaws.com/chapmanb/xprize/GRCh37-NA12878-xprize-fosmid.bed
# Global set of indexes to include for each genome.
# Available choices are in GENOMES_INDEXES_SUPPORTED in data_fabfile.py
genome_indexes:
- bowtie
- bwa
- novoalign
- ucsc
# Additional data targets
install_liftover: true
install_uniref: false
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