Unable to compile GFA_connector

[Benjamin-Lee]

I have tried compiling both SKESA and GFA_connector specifically using this Dockerfile:

# Base image
FROM ubuntu:18.04

# Install SKESA
RUN apt-get update && apt-get -y -qq install git build-essential bison libxml2 libboost-all-dev libz-dev && \
    git clone https://github.com/ncbi/SKESA && \
    cd SKESA && \
    make gfa_connector

However, I'm getting error codes from deep within Docker that give me no indication why the actual compilation if failing. Do you have any pointers (pun certainly intended) on whether I'm compiling GFA_connector correctly?

[souvorov]

I'm not sure, but try to add boost and bc:
apt-get install libboost-all-dev bc

[tseemann]

What is bc used for? Isn't that a calculator tool?

I managed to compile it ok. But i set BOOST_PATH= manually and used Makefile.nongs

[souvorov]

It is a calculator tool. Apparently it is used by some docker scripts, or at least I was told so by somebody who built a docker for skesa. I haven't tried it myself.

[tseemann]

Ah i see - so for docker not for Skesa. That makes a lot more sense. Still weird though :)