Trying to build a Docker Image from Ubuntu 18.04 base image but gets stuck at "Configuring tzdata"

pubsurfted

12/30/23, 12:32 PM

I'm trying to build a docker image from the following dockerfile:

FROM ubuntu:18.04

# Install Python
RUN apt-get update && apt-get install -y python3.10 python3-pip

# Install Java
RUN apt-get update && apt-get install -y openjdk-8-jdk

# Install Bowtie2
RUN apt-get update && apt-get install -y bowtie2

RUN apt-get update && \
apt-get install --yes --no-install-recommends \
zlib1g-dev \
libbz2-dev \
liblzma-dev \
&& rm -rf /var/lib/apt/lists/*

# Install RSeQC
RUN apt-get update && apt-get install -y python-pip
RUN pip install RSeQC

# Install biopython=1.80
RUN pip install biopython

# Install Atria
RUN apt-get update && apt-get install -y wget
RUN wget https://github.com/cihga39871/Atria/releases/download/v3.1.2/atria-3.1.2-linux.tar.gz
RUN tar -zxf atria-3.1.2-linux.tar.gz
RUN mv atria-3.1.2/bin/atria /usr/local/bin/atria
RUN chmod +x /usr/local/bin/atria

##Atria dependencies
RUN apt-get update && apt-get install pigz pbzip2

# Install findtail
RUN apt-get update && apt-get install -y wget
RUN wget https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/findtail/findtail_v1.01
RUN mv findtail_v1.01 /usr/local/bin/findtail_v1.01
RUN chmod +x /usr/local/bin/findtail_v1.01

When I try to build the image, it gets stuck at:

Configuring tzdata
------------------

Please select the geographic area in which you live. Subsequent configuration
questions will narrow this down by presenting a list of cities, representing
the time zones in which they are located.

  1. Africa      4. Australia  7. Atlantic  10. Pacific  13. Etc
  2. America     5. Arctic     8. Europe    11. SystemV
  3. Antarctica  6. Asia       9. Indian    12. US
Geographic area: 6

It remains stuck there forever until I ctrl+c. Any idea why this is happening?

951

1 + 0

docker

Score:1

Ubuntu

dummyuser

12/30/23, 2:09 PM

You need to modify your Dockerfile slightly. An apt update needs to be done once at the beginning. Tzdata is installed as a dependency and configuration does not work. Use the line

RUN DEBIAN_FRONTEND=noninteractive TZ=Etc/UTC apt-get -y install tzdata.

You need to adopt the timezone.

Finally your dockerfile may look like:

FROM ubuntu:20.04

# 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 pip install RSeQC

# Install biopython=1.80
RUN pip install biopython

# 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

and credit goes to how-to-install-tzdata-on-a-ubuntu-docker-image

+ 6

pubsurfted

12/30/23, 2:49 PM

Thank you so much! @dummyuser

dummyuser

12/30/23, 2:54 PM

there seems to be another issue with `RUN pip install biopython` and pyton versions. out of scope of this question.

pubsurfted

12/30/23, 2:58 PM

Yeah i just encountered that issue and made a post about it. Where is the error coming from?

dummyuser

12/30/23, 3:33 PM

the python version in ubuntu 18.04 seems to be too old. why do you use 18.04 ?

pubsurfted

12/30/23, 3:46 PM

Corrected and it worked. Thank you.

dummyuser

12/30/23, 3:49 PM

I edited my resonse. 1) line 1 use `20.04` and 2) Line 19: `python-pip` is not needed - removed. docker build works.

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