Conda not found when building docker image for Peddy
claudiadast opened this issue · 4 comments
claudiadast commented
I've made the following Docker container for Plink and Peddy, but whenever I try to build the container, I'm getting the following error:
Executing transaction: ...working... WARNING conda.core.envs_manager:register_env(46): Unable to register environment. Path not writable or missing.
environment location: /root/identity_check/anaconda
registry file: /root/.conda/environments.txt
done
installation finished.
Removing intermediate container cdf60f5bf1a5
---> be254b7571be
Step 7/10 : RUN conda update -y conda && conda config --add channels bioconda && conda install -y peddy
---> Running in aa2e91da28b4
/bin/sh: 1: conda: not found
The command '/bin/sh -c conda update -y conda && conda config --add channels bioconda && conda install -y peddy' returned a non-zero code: 127
Dockerfile:
FROM ubuntu:19.04
WORKDIR /identity_check
RUN apt-get update && \
apt-get install -y \
python-pip \
tabix \
wget \
unzip
RUN apt-get update && apt-get install -y sudo && rm -rf /var/lib/apt/lists/* \
&& sudo apt-get -y update \
&& sudo pip install --upgrade pip \
&& sudo pip install awscli --upgrade --user \
&& sudo pip install boto3 \
&& sudo pip install pyyaml \
&& sudo pip install sqlitedict
# Install PLINK
RUN wget http://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20190617.zip \
&& mv plink_linux_x86_64_20190617.zip /usr/local/bin/ \
&& unzip /usr/local/bin/plink_linux_x86_64_20190617.zip
# Install Peddy
RUN INSTALL_PATH=~/anaconda \
&& wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh \
&& bash Miniconda2-latest* -fbp $INSTALL_PATH \
&& PATH=$INSTALL_PATH/bin:$PATH
RUN conda update -y conda \
&& conda config --add channels bioconda \
&& conda install -y peddy
ENV PATH=$PATH:/identity_check/
ADD . /identity_check
CMD bash /identity_check/identity_setup.sh
brentp commented
looks like you need to update the $PATH with:
ENV PATH=~/anaconda/bin:$PATH
just before your block that starts with RUN conda update ...
claudiadast commented
I have tried that as well and I still get the same error
# Install Peddy
RUN INSTALL_PATH=~/anaconda \
&& wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh \
&& bash Miniconda2-latest* -fbp $INSTALL_PATH
ENV PATH=~/anaconda/bin:$PATH
RUN conda update -y conda \
&& conda config --add channels bioconda \
&& conda install -y peddy
brentp commented
this works for me:
FROM ubuntu:19.04
WORKDIR /identity_check
ARG INSTALL_PATH=/anaconda
RUN apt-get update && \
apt-get install -y \
python-pip \
tabix \
wget \
unzip
RUN apt-get update && apt-get install -y && rm -rf /var/lib/apt/lists/* \
&& apt-get -y update \
&& pip install --upgrade pip \
&& pip install awscli --upgrade --user \
&& pip install boto3 \
&& pip install pyyaml \
&& pip install sqlitedict
# Install PLINK
RUN wget -q http://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20190617.zip \
&& mv plink_linux_x86_64_20190617.zip /usr/local/bin/ \
&& unzip /usr/local/bin/plink_linux_x86_64_20190617.zip
# Install Peddy
RUN wget -q http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh \
&& bash Miniconda2-latest* -fbp $INSTALL_PATH && rm Miniconda2-latest-Linux-x86_64.sh
ENV PATH=$PATH:$INSTALL_PATH/bin
RUN conda update -y conda \
&& conda config --add channels bioconda \
&& conda install -y peddy
ENV PATH=$PATH:/identity_check/
ADD . /identity_check
CMD bash /identity_check/identity_setup.sh
brentp commented
closing this as solved. please re-open if the above docker image does not work for you.