install error about hap.py

[pkrusche]

To run all tests successfully you need to download a hg19 reference FASTA file. If you don't have one, this script downloads it: https://github.com/Illumina/hap.py/blob/master/src/sh/make_hg19.sh

Before running install.py, point hap.py to this file as follows:

export HGREF=<path-to-your-hg19.fa>
export HG19=<path-to-your-hg19.fa>

python install.py ~/hap.py-install

Also I don't think you'll need sudo permissions to install into your home directory if all Python requirements are installed already.

Hope this helps!

[splaisan]

Thanks Peter, you were right, it now worked out (stupid sudo error of mine)

BTW, can I use hap.py with a more recent reference?
Should I simply point the two ref variables to it or is there something in hap.py that is specific to hg19.
I had in mind the latest ensembl GRCh38.p10 with all KIXXXXXX.1 records.
Thanks

[pkrusche]

The environment variables are only needed for running the subset of the tests that are based on hg19.

When running an installed version of hap.py you may point it to any reference Fasta using the -r command line option. Note that the reference Fasta file must match the truth and query VCFs, as well as all other bed files that were passed, otherwise errors may occur.

Both Platinum Genomes and Genome in a Bottle provide separate hg38 reference files, either should be fine to use with hap.py.