nf-core
Getting No module named 'nf_core' after successfully building the docker image
Hi There,
I successfully built the docker image using the dockerfile given here (https://github.com/nf-core/tools/blob/master/Dockerfile) with slight modifications in the file given below
FROM python:3.8.9-slim
LABEL authors="[email protected],[email protected]" \
description="Docker image containing requirements for the nfcore tools"
# Do not pick up python packages from $HOME
ENV PYTHONNUSERSITE=1
# Update pip to latest version
RUN python -m pip install --upgrade pip
# Install dependencies
COPY requirements.txt requirements.txt
RUN python -m pip install -r requirements.txt
# Install Nextflow dependencies
RUN apt-get update \
&& apt-get upgrade -y \
&& apt-get install -y git \
&& apt-get install -y wget
# Create man dir required for Java installation
# and install Java
RUN mkdir -p /usr/share/man/man1 \
&& apt-get install -y openjdk-11-jre \
&& apt-get clean -y && rm -rf /var/lib/apt/lists/*
# Setup ARG for NXF_VER ENV
ARG NXF_VER=""
ENV NXF_VER ${NXF_VER}
# Install Nextflow
RUN wget https://github.com/nextflow-io/nextflow/releases/download/v21.04.3/nextflow | bash \
&& mv nextflow /usr/local/bin \
&& chmod a+rx /usr/local/bin/nextflow
# Add the nf-core source files to the image
COPY . /usr/src/nf_core
WORKDIR /usr/src/nf_core
# Install nf-core
RUN python -m pip install .
# Set up entrypoint and cmd for easy docker usage
ENTRYPOINT [ "nf-core" ]
CMD [ "." ]
Instead of the curl I have just used the wget and tried to install the nextflow version 21.04.03. Although the Docker image is built successfully as shown below,
cheemaa@kepler:~/all_files/nextflow_docker$ cat logfile
Sending build context to Docker daemon 98.82kB
Step 1/16 : FROM python:3.8.9-slim
---> 5904641efd27
Step 2/16 : LABEL authors="[email protected],[email protected]" description="Docker image containing requirements for the nfcore tools"
---> Using cache
---> 2d43d8ba1cf3
Step 3/16 : ENV PYTHONNUSERSITE=1
---> Using cache
---> 682e6da6c52f
Step 4/16 : RUN python -m pip install --upgrade pip
---> Using cache
---> 64ac09a27790
Step 5/16 : COPY requirements.txt requirements.txt
---> Using cache
---> ea589aba8376
Step 6/16 : RUN python -m pip install -r requirements.txt
---> Using cache
---> da8e612968fa
Step 7/16 : RUN apt-get update && apt-get upgrade -y && apt-get install -y git && apt-get install -y wget
---> Using cache
---> 0e4a8470273f
Step 8/16 : RUN mkdir -p /usr/share/man/man1 && apt-get install -y openjdk-11-jre && apt-get clean -y && rm -rf /var/lib/apt/lists/*
---> Using cache
---> 0d7878e74239
Step 9/16 : ARG NXF_VER=""
---> Using cache
---> e174be554070
Step 10/16 : ENV NXF_VER ${NXF_VER}
---> Using cache
---> f54d7f1b655e
Step 11/16 : RUN wget https://github.com/nextflow-io/nextflow/releases/download/v21.04.3/nextflow | bash && mv nextflow /usr/local/bin && chmod a+rx /usr/local/bin/nextflow
---> Using cache
---> dcecab0fccbe
Step 12/16 : COPY . /usr/src/nf_core
---> Using cache
---> 979b9af529f8
Step 13/16 : WORKDIR /usr/src/nf_core
---> Using cache
---> 968f059514c4
Step 14/16 : RUN python -m pip install .
---> Using cache
---> 6d42a11fcdbd
Step 15/16 : ENTRYPOINT [ "nf-core" ]
---> Using cache
---> 710284d3ef67
Step 16/16 : CMD [ "." ]
---> Using cache
---> 2433748d282b
Successfully built 2433748d282b
Successfully tagged nfcore/tools:latest
cheemaa@kepler:~/all_files/nextflow_docker$
But when I run the nextflow from the docker image I get following errror,
cheemaa@kepler:~/all_files/nextflow_docker$ docker run -it --rm -v /home/cheemaa/all_files/nextflow_docker:/home/cheemaa/all_files/nextflow_docker nfcore/tools:latest nextflow
Traceback (most recent call last):
File "/usr/local/bin/nf-core", line 5, in <module>
from nf_core.__main__ import run_nf_core
ModuleNotFoundError: No module named 'nf_core'
Is there any solution to this problem ?
Thanks,
Note to self, diff for the dockerfile changes:
diff --git a/original.dockerfile b/issue.dockerfile
index 8343e06c..49d485c6 100644
--- a/original.dockerfile
+++ b/issue.dockerfile
@@ -16,7 +16,7 @@ RUN python -m pip install -r requirements.txt
RUN apt-get update \
&& apt-get upgrade -y \
&& apt-get install -y git \
- && apt-get install -y curl
+ && apt-get install -y wget
# Create man dir required for Java installation
# and install Java
@@ -28,7 +28,7 @@ RUN mkdir -p /usr/share/man/man1 \
ARG NXF_VER=""
ENV NXF_VER ${NXF_VER}
# Install Nextflow
-RUN curl -s https://get.nextflow.io | bash \
+RUN wget https://github.com/nextflow-io/nextflow/releases/download/v21.04.3/nextflow | bash \
&& mv nextflow /usr/local/bin \
&& chmod a+rx /usr/local/bin/nextflow
# Add the nf-core source files to the image
Instead of the curl I have just used the wget and tried to install the nextflow version 21.04.03.
@ammarsabircheema how come you're making these modifications? The dockerfile is already set up to allow you to use a specific version of Nextflow if you want (could be better commented / documented). The Nextflow installed listens to the $NXF_VER environment variable which is set with a Dockerfile ARG here. It's blank by default which should get the latest release, but you can customise by running Docker as follows:
docker build . --build-arg NXF_VER=21.04.3
Then you don't need to modify the Dockerfile at all.
Make sure that you're running in the base directory of the cloned nf-core/tools repo, as it expects the code to be in the current working directory:
# Add the nf-core source files to the image
COPY . /usr/src/nf_core
WORKDIR /usr/src/nf_core
This is my guess as to what's not working here, but it's a bit tricky to tell because most of your log output is just cached outputs 😉
Step 14/16 : RUN python -m pip install .
---> Using cache
---> 6d42a11fcdbd
Phil
ps. Docs about Dockerfile ARG stuff: https://docs.docker.com/engine/reference/builder/#arg
Closing as it seems solved, feel free to reopen if you still have problems :)
