chapmanb/cloudbiolinux

UCSC 2bit needed for GATK4 parallel BQSR

Ensures ggd-recipes checked even if seq directory already present.
Avoid double downloads and ensure all faidx indexes passed.

Complements #244, adding update for hg19 and including additional
genomes for hg38.

Includes hg38 viral genomes from TCGA prepared with bwa indexes

Improve GGD messages with details about genome and version running.
Add vcfanno downloads for hg38 GEMINI support.

Work towards GEMINI support for hg38 (chapmanb/bcbio-nextgen#1573)

- Move installation of configuration files from bcbio logic to
  a recipe.
- Add gemini GRCh37/hg19 config for vcfanno/vcf2db support.
- Standardize RADAR file naming so consistent for hg19/GRCh37 to avoid
  needing two recipes for vcfanno.

mirbase.org is currently down. Fixes chapmanb/bcbio-nextgen#1716
Fixes chapmanb/bcbio-nextgen#1718

dbNSFP installation moved to ggd-recipes. Fixes
chapmanb/bcbio-nextgen#1702

…xtgen#1688

- Add effect transcripts for cancer canonical adjustments from defaults
- Enable effect_transcripts and genesplicer installs
- Fixes for genesplicer recipe
- Forces latest version of snpEff (4.3g). conda resolves 4.3 > 4.3g so
  gives an older version.

Provide automated downloads of capture regions for inclusion in bcbio

mirbase.org is offline, causing failures to retrieve resources:
https://twitter.com/mirbase/status/789406368901980165

Fixes chapmanb/bcbio-nextgen#1605

Includes addition of NA24631 validation set

Just needed to point at the new URL.

Update with new Genome in a Bottle v3.2 truth sets and add NA24385
reference material calls.

readme:
https://github.com/lpantano/custom_genome_annotation

here we are! @ohofmann

RADAR download at Stanford is currently offline. We need to create a
cached version for installation. Fixes chapmanb/bcbio-nextgen#1388

- All transcript installs for RNA-seq are GGD recipes.
- Update biodata to provide additional install targets and annotation
  groups for custom data installation from bcbio
- Use commandline picard for indexing instead of jar directory.
- Fixes for RADAR and mirbase GGD recipes during testing

Removes custom dbsnp biodata code in favor for GGD recipes for all
input genomes. Building block to allow custom setting of annotations.

Moves installation of dbSNP and associated variation targets into
individual GGD recipes instead of biodata.py script. Initial step
towards providing a configurable installation procedure.