Tutorial - How to setup a DivBrowse instance for your data¶

Here we describe the setup of a DivBrowse instance with a VCF file of Homo sapiens step by step.

Please make sure that you have installed DivBrowse properly. See Installation for more information about the installation.

Setup a directory structure for the new instance¶

Create a new project directory for your DivBrowse instance:

$ mkdir ~/divbrowse_instance_homo_sapiens
$ cd ~/divbrowse_instance_homo_sapiens

Create a new directory data within your previously created project directory and switch to this new directory:
```
$ mkdir data
$ cd data
```

Obtaining VCF files from the European Nucleotide Archive¶

Download the VCF files for all chromosomes from the following EBI-ENA web page: https://www.ebi.ac.uk/ena/browser/view/PRJEB30460
Concatenate all 23 VCF files into one combined VCF file with bcftools:

$ bcftools concat --output-type z -o ./ALL.shapeit2_integrated_v1a.GRCh38.20181129.phased.vcf.gz \
ALL.chr1.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz ALL.chr2.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz \
ALL.chr3.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz ALL.chr4.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz \
ALL.chr5.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz ALL.chr6.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz \
ALL.chr7.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz ALL.chr8.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz \
ALL.chr9.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz ALL.chr10.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz \
ALL.chr11.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz ALL.chr12.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz \
ALL.chr13.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz ALL.chr14.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz \
ALL.chr15.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz ALL.chr16.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz \
ALL.chr17.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz ALL.chr18.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz \
ALL.chr19.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz ALL.chr20.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz \
ALL.chr21.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz ALL.chr22.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz \
ALL.chrX.shapeit2_integrated_v1a.GRCh38.20181129.GRCh38.phased.vcf.gz

Convert the concatenated VCF file to a Zarr archive with the DivBrowse CLI:

$ divbrowse vcf2zarr --path-vcf ./ALL.shapeit2_integrated_v1a.GRCh38.20181129.phased.vcf.gz --path-zarr ./ALL.shapeit2_integrated_v1a.GRCh38.20181129.phased.zarr

Obtaining the gene annotation from ensemble.org¶

Download the file Homo_sapiens.GRCh38.107.chr.gff3.gz from: http://ftp.ensembl.org/pub/release-107/gff3/homo_sapiens/
```
$ wget http://ftp.ensembl.org/pub/release-107/gff3/homo_sapiens/Homo_sapiens.GRCh38.107.chr.gff3.gz
```

Uncompress the gzipped file:

$ gzip -d Homo_sapiens.GRCh38.107.chr.gff3.gz

Now you should have ALL.shapeit2_integrated_v1a.GRCh38.20181129.phased.zarr and Homo_sapiens.GRCh38.107.chr.gff3 in the path ~/divbrowse_instance_homo_sapiens/data

Setup configuration file¶

Switch back to the project directory:
```
$ cd ~/divbrowse_instance_homo_sapiens
```

And download the configuration file divbrowse.config.yml from the Github repository:

$ wget https://raw.githubusercontent.com/IPK-BIT/divbrowse/main/examples/homo_sapiens/divbrowse.config.yml

Make sure to adjust the option datadir in the configuration file divbrowse.config.yml to your local conditions:

datadir: /home/myusername/divbrowse_instance_homo_sapiens/data/

Start intergrated web server to serve the instance¶

Now you can start the configured instance by executing the following command:
```
$ divbrowse start
```