newbie here, having trouble with install

[Sheila Reynolds]

Hi all,

I'm very much looking forward to using the biocommons/hgvs module but have been running into trouble related to htslib/pysam in getting it installed.  Can anyone here provide me with a list of apt-get/pip commands that will get me from a barebones VM to successfully using hgvs from python3?  (I'm using a GCE VM, typically Ubuntu)

many thanks!

Sheila

[Reece Hart]

Hi Sheila-

In the future, please send the error that you’re seeing and information about your system (version of ubuntu, python version, how you’re installing hgvs, and anything else that seems relevant).

However, my guess is that you’re missing a few libraries required by pysam. Try this (tested on naive ubuntu 19.04):

$ docker run -it ubuntu:19.04
# apt update
# apt install -y python3-pip gcc make libbz2-dev zlib1g-dev liblzma-dev
# pip3 install --user hgvs
# python3
>>> import hgvs
>>> from hgvs.dataproviders.uta import connect
>>> hdp = connect()
>>> hdp.schema_version()
'1.1'
>>> hdp.get_gene_info("VHL")
['VHL', '3p25.3', 'von Hippel-Lindau tumor suppressor', ...

Good luck,
Reece

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