ERR: error while loading shared libraries: libjulia.so.1: cannot open shared object file [Julia] - Ubuntu 22.04

Question

I'm trying to build a Dockerfile. It has a tool called Atria that utilizes Julia. Since Ubuntu 22.04 does not have Julia package, I had to resort to installing it. The following is the Dockerfile:

FROM ubuntu:22.04
Install tzdata
RUN apt-get update &&

    DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install tzdata
Install Python, Bowtie2 and Java
RUN apt-get install -y python3.10 python3-pip \ 
    openjdk-8-jdk  \ 
    bowtie2 \ 
    wget
RUN  apt-get install --yes --no-install-recommends 

     zlib1g-dev 

     libbz2-dev 

     liblzma-dev
Install RSeQC
RUN pip3 install RSeQC
Install biopython=1.80
RUN pip3 install biopython
#Install Julia
RUN wget https://julialang-s3.julialang.org/bin/linux/x64/1.8/julia-1.8.1-linux-x86_64.tar.gz && 

    tar zxvf julia-1.8.1-linux-x86_64.tar.gz && 

    mv julia-1.8.1/bin/julia /usr/local/bin/julia && 

    chmod +x /usr/local/bin/julia
RUN /sbin/ldconfig -v
Install Atria
RUN wget https://github.com/cihga39871/Atria/releases/download/v3.1.2/atria-3.1.2-linux.tar.gz && 

    tar -zxf atria-3.1.2-linux.tar.gz && 

    mv atria-3.1.2/bin/atria /usr/local/bin/atria && 

    chmod +x /usr/local/bin/atria
#Atria dependencies
RUN  apt-get install pigz pbzip2
Install findtail
RUN wget https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/findtail/findtail_v1.01 && 

     mv findtail_v1.01 /usr/local/bin/findtail_v1.01 && 

     chmod +x /usr/local/bin/findtail_v1.01
Cleanup
RUN apt clean

What I have tried so far is :

1. Julia v1.6.7 and v1.8.4

2. RUN /sbin/ldconfig -v as suggested here

How to fix it? Should I try to install Julia using PPA?

edit- The error:

root@b0f4b17a7c18:/# atria
/usr/local/bin/julia: error while loading shared libraries: libjulia.so.1: cannot open shared object file: No such file or directory

It is recognizing the atria command tho.

Answer 1

You just need to make sure you include the required library files when you install Atria. Since you're not building any software (i.e. using make), the usual way is to simply move the directory under /opt and add the executable(s) to your PATH using the ENV keyword. Note that Julia comes bundled with Atria, so all you need is:

FROM ubuntu:22.04
RUN apt-get update && apt-get install -y 

    bowtie2 

    openjdk-8-jdk 

    pbzip2 

    pigz 

    python3.10 

    python3-pip 

    python3-biopython 

    wget 

    && apt-get clean 

    && rm -rf /var/lib/apt/lists/*
Install RSeQC
RUN pip3 install --no-cache-dir RSeQC
Install Atria
RUN wget -q https://github.com/cihga39871/Atria/releases/download/v3.1.2/atria-3.1.2-linux.tar.gz 

    && tar xf atria-3.1.2-linux.tar.gz 

    && mv atria-3.1.2 /opt/atria
Install findtail
RUN wget -q https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/findtail/findtail_v1.01 

    && chmod +x findtail_v1.01 

    && mv findtail_v1.01 /usr/local/bin/findtail
Add the Atria executable to the PATH
ENV PATH="/opt/atria/bin:${PATH}"

Answer 2

Just to note RUN apt clean ... is much better performed using && apt clean, like in @Steve's approach, recommended for complicated reasons.

Suggestion: what about using the official Julia Docker as the base rather than create it from scratch? There isn't a Ubuntu Julia but there is a Debian base.

docker run -it --rm Julia

or

docker pull julia

or via a Dockerfile,

FROM Julia:buster

or

FROM Julia:latest