chapmanb/cloudbiolinux

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Jul 16, 2013 Re-add accidentally removed biodata.yaml config file. Fixes chapmanb/…
	1	---
	2	# Configuration file defining biological data to retrieve and install.
	3	# These are stored in an Amazon S3 bucket:
	4	# https://s3.amazonaws.com/biodata
	5	# and retrieved using the data_fabfile Fabric script.
	6
	7	# ## Genome data -- Next generation sequencing and Galaxy
	8
	9	# Details about the genomes you want to include.
	10	# Required genome fields (corresponding to Galaxy's tool_data_table_conf.xml columns):
	11	# dbkey - globally unique identifier for the genome (e.g., hg19)
	12	# name - descriptive name for the given genome (to be displayed in Galaxy, e.g., Hsapiens)
	13	# Optional genome fields (corresponding to Galaxy's tool_data_table_conf.xml columns):
	14	# formats, species, dbkey1, dbkey2, value, path, index
Nov 5, 2014 Re-enable mm9 support.
Nov 5, 2014 Re-enable mm9 support.	15	# Additional genome fields specific to data deployment:
Jul 16, 2013 Re-add accidentally removed biodata.yaml config file. Fixes chapmanb/…
	16	# genome_indexes - list of tool indexes specific to the associated genome (overrides global 'genome_indexes')
	17	genomes:
	18	- dbkey: phix
	19	name: phiX174
	20	- dbkey: hg19
	21	name: Human (hg19)
Jul 28, 2017 Add twobit indexes for human builds
Jul 28, 2017 Add twobit indexes for human builds	22	indexes: [seq, twobit]
Dec 2, 2016 Add standard exome capture regions
	23	annotations: [GA4GH_problem_regions, capture_regions,
	24	MIG, prioritize, dbsnp, hapmap, 1000g_omni_snps, 1000g_snps,
Dec 9, 2016 Add effect transcript recipe and enable genesplicer
	25	mills_indels, cosmic, ancestral, clinvar, qsignature, ACMG56_genes, transcripts, RADAR, mirbase,
Feb 8, 2017 Add viral references to hg19/GRCh37
Feb 8, 2017 Add viral references to hg19/GRCh37	26	genesplicer, effects_transcripts, vcfanno, viral]
Dec 15, 2016 added dbscSNV as available annotation
Dec 15, 2016 added dbscSNV as available annotation	27	annotations_available: [battenberg, dbnsfp, dbscsnv]
Sep 12, 2016 Update Genome in a Bottle to 3.3 release
Sep 12, 2016 Update Genome in a Bottle to 3.3 release	28	validation: [giab-NA12878, platinum-genome-NA12878, giab-NA24385, giab-NA24631]
Jul 16, 2013 Re-add accidentally removed biodata.yaml config file. Fixes chapmanb/…
	29	- dbkey: GRCh37
	30	name: Human (GRCh37)
Jul 28, 2017 Add twobit indexes for human builds
Jul 28, 2017 Add twobit indexes for human builds	31	indexes: [seq, twobit]
Dec 2, 2016 Add standard exome capture regions
	32	annotations: [GA4GH_problem_regions, capture_regions,
	33	MIG, prioritize, dbsnp, hapmap, 1000g_omni_snps, 1000g_snps,
Dec 9, 2016 Add effect transcript recipe and enable genesplicer
	34	mills_indels, cosmic, ancestral, clinvar, qsignature, ACMG56_genes, transcripts, RADAR, mirbase,
Feb 8, 2017 Add viral references to hg19/GRCh37
Feb 8, 2017 Add viral references to hg19/GRCh37	35	genesplicer, effects_transcripts, vcfanno, viral]
Dec 18, 2016 Remove old dbNSFP install causing fabric issues
	36	annotations_available: [battenberg, dbnsfp, dbscsnv]
Sep 12, 2016 Update Genome in a Bottle to 3.3 release
Sep 12, 2016 Update Genome in a Bottle to 3.3 release	37	validation: [giab-NA12878, giab-NA24385, giab-NA24631, dream-syn3, dream-syn4]
May 1, 2015 Support download of hg38 full genome. Use build with HLAs from 1000 g…
	38	- dbkey: hg38
	39	name: Human (hg38) full
Jul 28, 2017 Add twobit indexes for human builds
Jul 28, 2017 Add twobit indexes for human builds	40	indexes: [seq, twobit, bwa, hisat2]
Feb 23, 2016 Transition RNA-seq installs to GGD recipes
Feb 23, 2016 Transition RNA-seq installs to GGD recipes	41	annotations: [coverage, prioritize, dbsnp, hapmap_snps, 1000g_omni_snps, 1000g_snps,
Dec 9, 2016 Add effect transcript recipe and enable genesplicer
	42	1000g_indels, mills_indels, clinvar, qsignature, ACMG56_genes, transcripts,
Feb 6, 2017 Install hg38 viral genomes for infection detection
	43	genesplicer, effects_transcripts, vcfanno, esp, exac, viral]
Dec 18, 2016 Remove old dbNSFP install causing fabric issues
	44	annotations_available: [dbnsfp, dbscsnv]
Feb 22, 2017 Finalize GiaB 3.3.2 update: hg19, hg38
	45	validation: [giab-NA12878, giab-NA24385, giab-NA24631,
	46	platinum-genome-NA12878, giab-NA12878-remap, giab-NA12878-crossmap,
May 24, 2016 Fix installation tag for ACMG56 in hg38
May 24, 2016 Fix installation tag for ACMG56 in hg38	47	dream-syn4-crossmap, dream-syn3-crossmap]
Apr 21, 2015 Hook GGD-based download and installation into standard deployments an…
	48	- dbkey: hg38-noalt
	49	name: Human (hg38) without alternative alleles
Feb 23, 2016 Transition RNA-seq installs to GGD recipes
	50	annotations: [coverage, dbsnp, hapmap_snps, 1000g_omni_snps, 1000g_snps,
	51	1000g_indels, mills_indels, clinvar, transcripts]
Dec 18, 2016 Remove old dbNSFP install causing fabric issues
	52	annotations_available: [dbnsfp, dbscsnv]
Nov 5, 2014 Re-enable mm9 support.
	53	- dbkey: mm9
	54	name: Mouse (mm9)
Sep 12, 2013 Add dbSNP preparation and download for mouse mm10 genome. Work toward…
	55	- dbkey: mm10
	56	name: Mouse (mm10)
Oct 31, 2016 Re-enable mirbase now that mirbase.org is back
Oct 31, 2016 Re-enable mirbase now that mirbase.org is back	57	annotations: [problem_regions, dbsnp, transcripts, mirbase]
May 17, 2014 Add support for latest Zebrafish genome build: Zv9
	58	- dbkey: rn5
	59	name: Rat (rn5)
Jul 23, 2015 Add support for latest rat (rn6) and chicken (galGal4) genomes.
	60	- dbkey: rn6
	61	name: Rat (rn6)
Nov 3, 2016 Add rn6 mirbase ann file to config file
Nov 3, 2016 Add rn6 mirbase ann file to config file	62	annotations: [transcripts, mirbase]
May 17, 2014 Add support for latest Zebrafish genome build: Zv9
	63	- dbkey: canFam3
	64	name: Dog (canFam3)
Feb 23, 2016 Transition RNA-seq installs to GGD recipes
Feb 23, 2016 Transition RNA-seq installs to GGD recipes	65	annotations: [dbsnp, transcripts]
Jul 23, 2015 Add support for latest rat (rn6) and chicken (galGal4) genomes.
	66	- dbkey: galGal4
	67	name: Chicken (galGal4)
Jul 16, 2013 Re-add accidentally removed biodata.yaml config file. Fixes chapmanb/…
	68	- dbkey: dm3
	69	name: D melangogaster (dm3)
Jul 25, 2014 Update Arabidopsis and C elegans support to recent versions: TAIR10 a…
	70	- dbkey: TAIR10
	71	name: Arabidopsis thaliana (TAIR10)
Oct 31, 2016 Re-enable mirbase now that mirbase.org is back
Oct 31, 2016 Re-enable mirbase now that mirbase.org is back	72	annotations: [mirbase]
Jul 1, 2014 Update X tropicalis build version to xenTro3
	73	- dbkey: xenTro3
	74	name: X tropicalis (xenTro3)
Jul 25, 2015 Add biodata install for Zebrafish GRCz10
	75	- dbkey: GRCz10
	76	name: Zebrafish (GRCz10)
May 17, 2014 Add support for latest Zebrafish genome build: Zv9
	77	- dbkey: Zv9
	78	name: Zebrafish (Zv9)
Jun 11, 2014 updated yaml; sacCer2 => sacCer3
	79	- dbkey: sacCer3
	80	name: S cerevisiae (sacCer3)
Jul 25, 2014 Update Arabidopsis and C elegans support to recent versions: TAIR10 a…
	81	- dbkey: WBcel235
	82	name: C elegans (WBcel235)
Sep 13, 2014 Support Psuedomonas genome build
	83	- dbkey: pseudomonas_aeruginosa_ucbpp_pa14
	84	name: Pseudomonas aeruginosa UCBPP-PA14
Jul 16, 2013 Re-add accidentally removed biodata.yaml config file. Fixes chapmanb/…
	85
Feb 23, 2016 Transition RNA-seq installs to GGD recipes
	86	# High level targets for specifying annotations
	87	annotation_groups:
Dec 2, 2016 Add standard exome capture regions
Dec 2, 2016 Add standard exome capture regions	88	variation: [problem_regions, GA4GH_problem_regions, capture_regions, MIG, coverage, prioritize, dbsnp,
Jun 29, 2016 Install ACMG56 genes as part of variant install
	89	hapmap, hapmap_snps, 1000g_omni_snps, ACMG56_genes,
Dec 9, 2016 Add effect transcript recipe and enable genesplicer
	90	1000g_snps, mills_indels, 1000g_indels, clinvar, cosmic, ancestral, qsignature,
Feb 6, 2017 Install hg38 viral genomes for infection detection
	91	genesplicer, effects_transcripts, vcfanno, viral]
Dec 29, 2016 Disable srnaseq recipe until mirbase back up
Dec 29, 2016 Disable srnaseq recipe until mirbase back up	92	rnaseq: [transcripts, RADAR]
Jan 5, 2017 Generalize installation of vcfanno config files
Jan 5, 2017 Generalize installation of vcfanno config files	93	smallrna: [mirbase]
Jan 8, 2017 hg38: GGD recipes for ESP and ExAC
Jan 8, 2017 hg38: GGD recipes for ESP and ExAC	94	gemini: [esp, exac]
Feb 23, 2016 Transition RNA-seq installs to GGD recipes
Feb 23, 2016 Transition RNA-seq installs to GGD recipes	95
Jul 16, 2013 Re-add accidentally removed biodata.yaml config file. Fixes chapmanb/…
	96	# Global set of indexes to include for each genome.
	97	# Available choices are in GENOMES_INDEXES_SUPPORTED in cloudbio/biodata/genomes.py
	98	genome_indexes:
	99	- bwa
Jul 28, 2017 Add twobit indexes for human builds
Jul 28, 2017 Add twobit indexes for human builds	100	- twobit
Jul 16, 2013 Re-add accidentally removed biodata.yaml config file. Fixes chapmanb/…
	101
	102	# Additional data targets
Feb 19, 2016 Migrate GRCh37, camFam3, mm10 to ggd recipes
Feb 19, 2016 Migrate GRCh37, camFam3, mm10 to ggd recipes	103	install_liftover: false
Jul 16, 2013 Re-add accidentally removed biodata.yaml config file. Fixes chapmanb/…
	104	install_uniref: false