GenomicsDB-Go

Experimental golang bindings to the native GenomicsDB library. Only queries are supported for now. For importing vcf files into GenomicsDB, use the command line tools - vcf2genomicsdb or gatk GenomicsDBImport.

For users

Installation : Only Linux and MacOS are supported

Step 1 - Prerequisites

This step is required to install native genomicsdb if it is not available.

• system prerequisites for native genomicsdb are minimal, openssl/curl/zlib.
• verify that $GOPATH is included in the $PATH environment variable
• go install github.com/GenomicsDB/GenomicsDB-Go/install-genomicsdb@latest
• Invoke $GOPATH/bin/install-genomicsdb
  • By default, the genomicsdb shared library is installed in /usr/local and may require sudo access. Set environment variable GENOMICSDB_INSTALL_DIR to any custom location before invoking InstallGenomicsDB for installing to locations other than /usr/local.
  • Generates a helper genomicdb.env file that exports PKG_CONFIG_PATH for building and DYLD/LD_LIBRARY_PATH for usage. This file can be sourced if the native GenomicsDB was installed in a custom location.

Step 2 - Building

• If a custom location was used for installing GenomicsDB in Step 1, either
  • source genomicsdb.env or
  • set environment variable PKG_CONFIG_PATH to $GENOMICSDB_INSTALL_DIR/lib/pkgconfig/genomicsdb.pc
• go get -u github.com/GenomicsDB/GenomicsDB-Go/bindings from a go module

Example Usage

If a custom location was used for installing GenomicsDB in Step 1, either

• source genomicsdb.env or
• set environment variable DYLD_LIBRARY_PATH for MacOS or LD_LIBRARY_PATH for Linux to include $GENOMICSDB_INSTALL_DIR/lib.

#!/bin/bash
mkdir example-genomicsdb-go
pushd example-genomicsdb-go
go mod init example/example-genomicsdb-go
go get -u github.com/GenomicsDB/GenomicsDB-Go/bindings
cat > main.go << EOF
package main

import (
  "log"

  gdb "github.com/GenomicsDB/GenomicsDB-Go/bindings"
)

func main() {
  log.Println("Got GenomicsDB version: ", gdb.GetVersion())
}
EOF
go build
go run .
popd

For release

GenomicsDB-Go/bindings and GenomicsDB-Go/install_genomicsdb are separate modules, so both bindings and install_genomicsdb folders have to be git tagged separately for go install and go get to function. For example, create bindings/v0.0.1 and install_genomicsdb/v0.0.1 git tags to get the steps for users outlined above to work. Note: If only one of the modules is updated, bump the version only associated with that module.