Go Get Data (GGD) is a genomics data management system that provides access to processed and curated genomic data files. It allows users to create "data recipes" that define genomic data files and their metadata. These recipes are used to generate data packages that can be installed and their files accessed via environment variables. GGD also supports finding, installing, uninstalling, and listing installed data packages.

1. Go Get Data (GGD)
July 7th 2021
1

2. Go Get Data
“Conda” for data: A genomics
data management system that
provides access to processed
and curated genomic data files
2

3. Installation
Current version only works with Python 3.6 (not 3.8)
conda create --name ggd_env python=3.6
conda activate ggd_env
conda install -c bioconda ggd
3

4. Data recipe
ggd make-recipe --species Homo_sapiens
--genome-build hg19
--authors <your name>
--package-version 1
--data-version 27-Apr-2009
--data-provider UCSC
--coordinate-base "0-based-inclusive"
--summary "cpg islands from UCSC"
--dependency htslib
--dependency gsort
--keyword CpG
--keyword region
--name cpg-islands
cpg.sh
cpg.sh
genome=https://raw.githubusercontent.com/gogetdata/ggd-
recipes/genomes/hg19/hg19.genome
wget -O - http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/cpgIslandExt.txt.gz
| gzip -dc
| cut -f 2-5
| gsort /dev/stdin $genome
| bgzip -c > cpg.bed.gz
tabix cpg.bed.gz
4

5. Data recipe
ggd make-recipe --species Homo_sapiens
--genome-build hg19
--authors <your name>
--package-version 1
--data-version 27-Apr-2009
--data-provider UCSC
--coordinate-base "0-based-inclusive"
--summary "cpg islands from UCSC"
--dependency htslib
--dependency gsort
--keyword CpG
--keyword region
--name cpg-islands
cpg.sh
cpg.sh
genome=https://raw.githubusercontent.com/gogetdata/ggd-
recipes/genomes/hg19/hg19.genome
wget -O - http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/cpgIslandExt.txt.gz
| gzip -dc
| cut -f 2-5
| gsort /dev/stdin $genome
| bgzip -c > cpg.bed.gz
tabix cpg.bed.gz
Data package -> hg19-cpg-islands-ucsc-v1
5

6. Data packages
Search a package
$ ggd search genome
$ ggd search grch38 reference genome
Install a package $ ggd install grch38-reference-genome-ensembl-v1
Uninstall a package $ ggd uninstall grch38-reference-genome-ensembl-v1
List installed packages $ ggd list
6

7. Data environment variable
$ ggd install grch38-reference-genome-ensembl-v1
$ ls $ggd_grch38_reference_genome_ensemble_v1_dir
$ cd $ggd_grch38_reference_genome_ensemble_v1_dir
bwa mem $ggd_grch38_reference_genome_ensemble_v1_file reads.fq > aln.sam
7

8. Other features
Meta recipes
GGD + workflow (Snakemake)
Available data packages: https://gogetdata.github.io/recipes.html
- No epigenomic data
8