cron service not starting post docker run and container is getting exit - docker

tried running cron through dockerfile but when running the container its getting exit. Below is my dockerfile and error. Any help would be really appreciated
Error:
docker: Error response from daemon: OCI runtime create failed: container_linux.go:380: starting container process caused: exec: "cron": executable file not found in $PATH: unknown.
Dockerfile:
# Pull base image.
FROM amazonlinux:2
ARG TERRAFORM_VERSION=1.2.6
RUN \
yum update -y && \
yum install unzip -y && \
yum install wget -y && \
yum install vim -y \
yum install bash -y
################################
# Install Terraform
################################
# Download terraform for linux
RUN wget https://releases.hashicorp.com/terraform/${TERRAFORM_VERSION}/terraform_${TERRAFORM_VERSION}_linux_amd64.zip
RUN unzip terraform_${TERRAFORM_VERSION}_linux_amd64.zip
RUN mv terraform /usr/local/bin/
################################
# Install python
################################
RUN yum install -y python3-pip
RUN pip3 install --upgrade pip
################################
# Install AWS CLI
################################
RUN pip install awscli --upgrade --user
# add aws cli location to path
ENV PATH=~/.local/bin:$PATH
RUN mkdir ~/.aws && touch ~/.aws/credentials
################################
# Install Cron
################################
RUN yum -y install ca-certificates shadow-utils cronie && yum -y clean all
# Creating crontab
COPY ./automation.sh /var/automation.sh
# Giving executable permission to script file.
RUN chmod +x /var/automation.sh \
&& echo "* * * * * /bin/bash /var/automation.sh" >> /var/crontab
# Ensure sudo group users are not asked for a password
RUN echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> \
/etc/sudoers
#run cron process through cmd
CMD ["cron", "-f"]

Update the CMD to this:
CMD ["/usr/bin/crontab", "/var/crontab"]

Anyone looking for answer to this, I had to change the approach a bit of running cron and it worked finally. Here is the dockerfile with updated approach.
# Pull base image.
FROM amazonlinux:2
ARG TERRAFORM_VERSION=1.2.6
################################
# Install Dependencies
################################
RUN yum update -y && yum -y install unzip wget vim bash procps python3-pip jq git && pip3 install --upgrade pip
################################
# Install AWS CLI
################################
RUN pip install awscli --upgrade --user
# add aws cli location to path
ENV PATH=~/.local/bin:$PATH
RUN mkdir ~/.aws && touch ~/.aws/credentials
################################
# Install Terraform
################################
# Download terraform for linux
RUN wget https://releases.hashicorp.com/terraform/${TERRAFORM_VERSION}/terraform_${TERRAFORM_VERSION}_linux_amd64.zip
RUN unzip terraform_${TERRAFORM_VERSION}_linux_amd64.zip
RUN mv terraform /usr/local/bin/
################################
# Install Cron
################################
RUN yum -y install ca-certificates shadow-utils cronie && yum -y clean all
# Creating crontab
COPY ./automation.sh /var/automation.sh
# Giving executable permission to script file.
RUN chmod +x /var/automation.sh \
&& echo "* * * * * /bin/bash /var/automation.sh" >> /var/crontab
RUN crontab /var/crontab
# Ensure sudo group users are not asked for a password
RUN echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> \
/etc/sudoers
#run cron process through cmd
CMD ["/usr/sbin/crond", "-n"]

Related

save plotly images from Rstudio in docker, get error ! System command 'orca' failed

I have RStudio in docker, and am trying to save a plotly image using orca. I installed orca following Docker and Plotly.
I build and start successfully, and to check if I can save an image I run:
library(plotly)
library(processx)
fig <- plot_ly(z = ~volcano) %>% add_surface()
orca(fig,"t.png")
Whereupon I receive the following error:
Error in `processx::run("orca", "-h")`:
! System command 'orca' failed
---
Exit status: 127
Stderr: <empty>
---
Type .Last.error to see the more details.
Warning message:
'orca' is deprecated.
Use 'kaleido' instead.
See help("Deprecated")
> .Last.error
<system_command_status_error/rlib_error_3_0/rlib_error/error>
Error in `processx::run("orca", "-h")`:
! System command 'orca' failed
---
Exit status: 127
Stderr: <empty>
---
Backtrace:
1. plotly::orca(fig, "t.png")
2. plotly:::orca_available()
3. plotly:::correct_orca()
4. processx::run("orca", "-h")
5. processx:::throw(new_process_error(res, call = sys.call(), echo = echo, …
>
Is there another way to install orca, or save a plotly image in RStudio running in docker?
My full dockerfile:
FROM rocker/verse
ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update && apt-get install -y --no-install-recommends build-essential libpq-dev python3.9 python3-pip python3-setuptools python3-dev
RUN pip3 install --upgrade pip
ADD . ./home/rstudio
ADD requirements.txt .
ADD install_packages.r .
# Miniconda and dependencies
RUN cd /tmp/ && \
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh && \
bash Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda3 && \
/root/miniconda3/condabin/conda install -y python=3.7
ENV PATH=$PATH:/root/miniconda3/bin
#RUN npm install phantomjs-prebuilt --phantomjs_cdnurl=http://cnpmjs.org/downloads
# installing python libraries
RUN pip3 install -r requirements.txt
# installing r libraries
RUN Rscript install_packages.r
RUN if ! [[ "16.04 18.04 20.04 21.04 21.10" == *"$(lsb_release -rs)"* ]]; \
then \
echo "Ubuntu $(lsb_release -rs) is not currently supported."; \
exit; \
fi
RUN sudo su
RUN apt-get update && apt-get install -y gnupg2
RUN curl https://packages.microsoft.com/keys/microsoft.asc | apt-key add -
RUN curl https://packages.microsoft.com/config/ubuntu/$(lsb_release -rs)/prod.list > /etc/apt/sources.list.d/mssql-release.list
RUN exit
RUN sudo apt-get update
RUN sudo ACCEPT_EULA=Y apt-get install -y msodbcsql17
RUN chmod -R 777 /home/rstudio
# Download orca AppImage, extract it, and make it executable under xvfb
RUN apt-get install --yes xvfb libgconf-2-4
RUN wget https://github.com/plotly/orca/releases/download/v1.1.1/orca-1.1.1-x86_64.AppImage -P /home
RUN chmod 777 /home/orca-1.1.1-x86_64.AppImage
# To avoid the need for FUSE, extract the AppImage into a directory (name squashfs-root by default)
RUN cd /home && /home/orca-1.1.1-x86_64.AppImage --appimage-extract
RUN printf '#!/bin/bash \nxvfb-run --auto-servernum --server-args "-screen 0 640x480x24" /home/squashfs-root/app/orca "$#"' > /usr/bin/orca
RUN chmod 777 /usr/bin/orca
RUN chmod -R 777 /home/squashfs-root/

Errors Installing singularity inside dockerfile

I am trying to run a nextflow pipeline which uses an older version of nextflow (21.04.3) and java version 8. Since I have to use this pipeline on a remote server, therefore I can only use singularity.
As this nextflow pipeline also uses singularity pull calls therefore I need the singularity installed inside the docker image as well. Then, I can convert this image docker image to a singularity image and then I can move it to the remote server.
I am trying to install singularity inside dockerfile but I am getting errors,
This is the dockerfile that I am using,
FROM python:3.8.9-slim
LABEL authors="phil.ewels#scilifelab.se,erik.danielsson#scilifelab.se" \
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/*
# Install Singularity
RUN wget -O- http://neuro.debian.net/lists/xenial.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list && \ apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 && \ apt-get update
RUN apt-get install -y singularity-container
# 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
CMD [ "." ]
These are the errors I am getting
Step 9/17 : RUN wget -O- http://neuro.debian.net/lists/xenial.us-ca.full | tee
/etc/apt/sources.list.d/neurodebian.sources.list && \ apt-key adv --recv-keys --
keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 && \ apt-get update
---> Running in afc3dcbbd1ee
--2022-03-17 17:40:19-- http://neuro.debian.net/lists/xenial.us-ca.full
Resolving neuro.debian.net (neuro.debian.net)... 129.170.233.11
Connecting to neuro.debian.net (neuro.debian.net)|129.170.233.11|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 262
Saving to: ‘STDOUT’
0K 100% 18.4M=0s
deb http://neurodeb.pirsquared.org data main contrib non-free
#deb-src http://neurodeb.pirsquared.org data main contrib non-free
deb http://neurodeb.pirsquared.org xenial main contrib non-free
#deb-src http://neurodeb.pirsquared.org xenial main contrib non-free
2022-03-17 17:40:19 (18.4 MB/s) - written to stdout [262/262]
/bin/sh: 1: apt-key: not found
The command '/bin/sh -c wget -O- http://neuro.debian.net/lists/xenial.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list && \ apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9 && \ apt-get update'
returned a non-zero code: 127
I there a way to install singularity using a dockerfile ?
Thanks
I made some changes in the dockerfile based on the method to install singularity in linux given here.
The complete dockerfile with which I was able to run successfully nextflow, java and singularity within singularity is given below,
FROM python:3.8.9-slim
LABEL
authors="phil.ewels#scilifelab.se,erik.danielsson#scilifelab.se" \
description="Docker image containing requirements for the nfcore tools"
# Do not pick up python packages from $HOME
ENV PYTHONNUSERSITE=1
# Update pip to latest version
RUN python -m pip install --upgrade pip
# Install dependencies
COPY requirements.txt requirements.txt
RUN python -m pip install -r requirements.txt
# Install Nextflow dependencies
RUN apt-get update \
&& apt-get upgrade -y \
&& apt-get install -y git \
&& apt-get install -y wget
# Create man dir required for Java installation
# and install Java
RUN mkdir -p /usr/share/man/man1 \
&& apt-get install -y openjdk-11-jre \
&& apt-get clean -y && rm -rf /var/lib/apt/lists/*
# Install Singularity
RUN apt-get update && apt-get install -y \
build-essential \
libssl-dev \
uuid-dev \
libgpgme11-dev \
squashfs-tools \
libseccomp-dev \
wget \
pkg-config \
procps
# Download Go source version 1.16.3, install them and modify the PATH
ENV VERSION=1.16.3
ENV OS=linux
ENV ARCH=amd64
RUN wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz && \
tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz && \
rm go$VERSION.$OS-$ARCH.tar.gz && \
echo 'export PATH=$PATH:/usr/local/go/bin' | tee -a /etc/profile
# Download Singularity from version 3.7.3 (security version)
ENV VERSION=3.7.3
RUN wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-${VERSION}.tar.gz && \
tar -xzf singularity-${VERSION}.tar.gz
# Compile Singularity sources and install it
RUN export PATH=$PATH:/usr/local/go/bin && \
cd singularity && \
./mconfig --without-suid && \
make -C ./builddir && \
make -C ./builddir install
# 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
CMD [ "." ]
The file named requirements.txt used in the above dockerfile is given below,
click
GitPython
jinja2
jsonschema
packaging
prompt_toolkit>=3.0.3
pyyaml
pytest-workflow
questionary>=1.8.0
requests_cache
requests
rich>=10.0.0
tabulate

Entrypoint not found when deployed to Fargate. Locally works

I have the following Dockerfile, currently working locally in my device:
FROM python:3.7-slim-buster
WORKDIR /app
COPY . /app
VOLUME /app
RUN chmod +x /app/cat/sitemap_download.py
COPY entrypoint.sh /app/entrypoint.sh
RUN chmod +x /app/entrypoint.sh
ARG VERSION=3.7.4
RUN apt update && \
apt install -y bash wget && \
wget -O /tmp/nordrepo.deb https://repo.nordvpn.com/deb/nordvpn/debian/pool/main/nordvpn-release_1.0.0_all.deb && \
apt install -y /tmp/nordrepo.deb && \
apt update && \
apt install -y nordvpn=$VERSION && \
apt remove -y wget nordvpn-release
RUN apt-get clean \
&& apt-get -y update
RUN apt-get -y install python3-dev \
python3-psycopg2 \
&& apt-get -y install build-essential
RUN pip install --upgrade pip
RUN pip install -r cat/requirements.txt
RUN pip install awscli
ENTRYPOINT ["sh", "-c", "./entrypoint.sh"]
But when I deploy it to Fargate, the container stops before reaching the steady state with:
sh: 1: ./entrypoint.sh: not found
Edit: Adding entrypoint.sh file for clarification:
#!/bin/env sh
# start process, but it should exit once the file is in S3
/app/cat/sitemap_download.py
# Once the process is done, we are good to scale down the service
aws ecs update-service --cluster cluster_name --region eu-west-1 --service service-name --desired-count 0
I have tried modifying ENTRYPOINT to use it as exec form, or with full path but always get the same issue. Any ideas on what am I doing wrong?
I've managed to fix it now.
Changing the Dockerfile to look as follows solves the issue:
COPY . /app
VOLUME /app
RUN chmod +x /app/cat/sitemap_download.py
COPY entrypoint.sh /app/entrypoint.sh
RUN chmod +x /app/entrypoint.sh
ARG VERSION=3.7.4
RUN apt update && \
apt install -y bash wget && \
wget -O /tmp/nordrepo.deb https://repo.nordvpn.com/deb/nordvpn/debian/pool/main/nordvpn-release_1.0.0_all.deb && \
apt install -y /tmp/nordrepo.deb && \
apt update && \
apt install -y nordvpn=$VERSION && \
apt remove -y wget nordvpn-release
RUN apt-get clean \
&& apt-get -y update
RUN apt-get -y install python3-dev \
python3-psycopg2 \
&& apt-get -y install build-essential
RUN pip install --upgrade pip
RUN pip install -r cat/requirements.txt
RUN pip install awscli
ENTRYPOINT ["/bin/bash"]
CMD ["./entrypoint.sh"]
I tried this after reading: What is the difference between CMD and ENTRYPOINT in a Dockerfile?
I believe this syntax fixes it because with entrypoint I'm indicating bash to be run at start, and then passing the script as parameter.

Dockerfile: Python3 not found

I am trying to convert a bash script to a Dockerfile since we are going the containerization route with AWS Batch
Basically I install CPLEX (an optimization library) and Anaconda, install some related packages, check if my environment it good to go, and then kick off a shell script to run the batch job.
Here is a snippet of my Dockerfile:
FROM amazonlinux:latest
# Download packages for container
RUN yum update -y
RUN yum -y install which unzip aws-cli \
RUN yum install -y tar.x86_64
RUN yum install gzip -y
RUN yum install ncompress -y
RUN yum -y install wget
RUN yum install -y nano
# Set working directory
WORKDIR /setup
#: Copy CPLEX installer binary and installation script.
COPY cplex_odee1210.linux-x86-64.bin /setup/
COPY cplex_installer_input.sh /setup/
#: Install CPLEX and update .bashrc
RUN chmod +x /setup/cplex_odee1210.linux-x86-64.bin
RUN chmod +x cplex_installer_input.sh
RUN ./cplex_installer_input.sh | bash cplex_odee1210.linux-x86-64.bin
RUN echo 'export PATH=$PATH:/opt/ibm/ILOG/CPLEX_Optimizer1210/cplex/bin/x86-64_linux' >>/root/.bashrc \
&& /bin/bash -c "source ~/.bashrc"
ENV PATH $PATH:/opt/ibm/ILOG/CPLEX_Optimizer1210/cplex/bin/x86-64_linux
#: Download Anaconda
COPY Anaconda3-2019.10-Linux-x86_64.sh /setup/
RUN bash Anaconda3-2019.10-Linux-x86_64.sh -b -p /home/ec2-user/anaconda3
RUN echo 'export PATH=$PATH:/home/ec2-user/anaconda3/bin' >>/root/.bashrc \
&& /bin/bash -c "source ~/.bashrc"
ENV PATH $PATH:/home/ec2-user/anaconda3/bin
RUN conda install pandas -y \
&& conda install numpy -y \
&& conda install ujson -y \
&& pip install docplex \
&& pip install boto3 \
&& pip install grpcio \
&& pip install grpcio-tools
RUN python3 -m docplex.mp.environment
ADD fetch_and_run.sh /usr/local/bin/fetch_and_run.sh
ENTRYPOINT ["/usr/local/bin/fetch_and_run.sh"]
From there, I kick off a bash script
#!/bin/bash
date
echo "Args: $#"
env
echo "script_path: $1"
echo "script_name: $2"
echo "path_prefix: $3"
echo "jobID: $AWS_BATCH_JOB_ID"
echo "jobQueue: $AWS_BATCH_JQ_NAME"
echo "computeEnvironment: $AWS_BATCH_CE_NAME"
echo "current directory: $(pwd)"
mkdir /tmp/scripts/
aws s3 cp $1 /tmp/scripts/$2
python3 /tmp/scripts/${#:2}
But for some reason, I keep getting
/tmp/tmp.hQlWYBEFs/batch-file-temp: line 20: python3: command not found
Do I need to change some PATH variables? Why isn't Docker picking up my Python 3 version?
The image needs to have python3 installed. Building images works off of files and programs that exist in the container. The python3 you have installed on your own system is not available.

Conda not found when trying to build Docker image

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
I've tried changing the INSTALL_PATH and seeing if that makes a difference and even launched a virtual machine to test out these installation steps manually and it works fine. I don't understand why conda isn't found.
# 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
The last part of the above updates a PATH variable that will only exist in the shell running the command. That shell exits immediately after setting the PATH variable, and the temporary container used to execute the RUN command exits. The result of the RUN command is to gather the filesystem changes into a layer of the docker image being created. Any environment variable changes, background processes launched, or anything else not part of the container filesystem is lost.
Instead, you'll want to update the image environment with:
# Install Peddy
RUN INSTALL_PATH=~/anaconda \
&& wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh \
&& bash Miniconda2-latest* -fbp $INSTALL_PATH \
ENV PATH=/root/anaconda/bin:$PATH
If the software permits it, I would avoid installing in the /root home directory and instead install it somewhere like /usr/local/bin, making it available if you change the container to run as a different user.

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