CODEWITHSUNDEEP
pythonpython-3.xsingularity-container
mostlyAsking7179
mostlyAsking7179

Reputation: 204

How do I install python packages inside of a singularity container?

I am trying to install packages with pip on my singularity container, but there seems to be no way of doing so without "borrowing" the packages from my machine. I have heard that I may need to use virtualenv's but even that seems to be a circuitous process. Does anyone know of a tried and true way of using packages from pip on their singularity container?

Upvotes: 1

Views: 14282

Answers (2)

Itamar cohen
Itamar cohen

Reputation: 89

A good workaround is to install the required packages using conda.

BootStrap: docker
From: ubuntu:xenial

%environment
export PATH=/miniconda3/bin:$PATH

%runscript
exec vcontact "$@"

%post
apt-get update && apt-get install -y automake build-essential bzip2 wget git default-jre unzip

# Install miniconda 
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -f -p /miniconda3/
rm Miniconda3-latest-Linux-x86_64.sh

# pull the conda functions in . /miniconda3/etc/profile.d/conda.sh and make pip, etc. available while in %post
export PATH="/miniconda3/bin:$PATH"

# Use conda to install pip, numpy
conda install -y -c conda-forge pip numpy 

# Help conda resolving Python "import" 
conda update --all

Upvotes: 1

rjad
rjad

Reputation: 96

How are you building your container? You should be able to use pip inside the container just like you would installing on an actual machine.

Here is an example:

Bootstrap: docker
From: python:3.7-alpine

%post 
    pip install click

Save this as a file, like test.def, then just build the container:

sudo singularity build test.sif test.def

The build a container document will help.

Upvotes: 2

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