Conda not found when building docker image for Peddy

[Claudia Dastmalchi]

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 

[Brent Pedersen]

looks like you need to update the $PATH with:

ENV PATH=~/anaconda/bin:$PATH

just before your block that starts with RUN conda update ...

[Claudia Dastmalchi]

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

[Brent Pedersen]

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 

[Brent Pedersen]

closing this as solved. please re-open if the above docker image does not work for you.