Install the library and the binary with opam install igvxml.
To build from source:
make deps # If you don't have them yet
# sosa nonstd cmdliner xmlm
make # Results in a ./igvxml binary.You can use it like so:
igvxml --help
NAME
igvxml - Create an IGV session file.
SYNOPSIS
igvxml [OPTION]...
OPTIONS
-G VAL, --genome=VAL
Genome used. b37decoy or mm10.
--help[=FMT] (default=pager)
Show this help in format FMT (pager, plain or groff).
-N VAL, --normal-bam=VAL
Path to Normal BAM.
-O VAL, --output=VAL
XML session file to be written.
-R VAL, --rna-bam=VAL
Path to RNA BAM. (optional)
--run-id=VAL
Patient/Run ID.
-T VAL, --tumor-bam=VAL
Path to Tumor BAM.
-V VAL, --vcfs=VAL
List (comma-separated) of name=path VCFs.
--version
Show version information.
Description
Create an IGV.xml session file from the specified arguments.igvxml is built for somatic paired BAMs and multiple VCFs, with optional RNA
seq data.
Contributions welcome for making this more general.