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I am trying to download Kallisto in a Docker container. When I run

apt-get update
apt-get install kallisto

interactively in the container, I get:

Reading package lists... Done
Building dependency tree       
Reading state information... Done
E: Unable to locate package kallisto

That being said, I have kallisto installed on my machine outside the container. When I do sudo apt-get install kallisto outside the container, I can successfully install it. Thus, I looked what package repo it can be found in by running apt-cache policy kallisto:

kallisto:
  Installed: 0.46.1+dfsg-2build1
  Candidate: 0.46.1+dfsg-2build1
  Version table:
 *** 0.46.1+dfsg-2build1 500
        500 http://us.archive.ubuntu.com/ubuntu focal/universe amd64 Packages
        100 /var/lib/dpkg/status

So in the container, I tried:

apt-get install software-properties-common
apt-add-repository http://us.archive.ubuntu.com/ubuntu
apt-get update
apt-get install kallisto

but I still get the same error. What should I do?

An Ignorant Wanderer
  • 797

1 Answers1

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To create Docker container with kallisto we need to create a Dockerfile with the following contents:

FROM ubuntu:20.04
RUN apt-get update
RUN apt-get install -y kallisto
CMD which kallisto

then build it by

docker build . -t focal-kallisto

and run

docker run -it focal-kallisto

as the result it will show /usr/bin/kallisto, so it is actually installed inside the container.

N0rbert
  • 99,918