How to activate GRPC PHP extension via Dockerfile? - docker

I have this Dockerfile. When I try to run it, in the Composer Update line it returns an error, that extensions are not installed.
That is because of GRPC not being activated on the php.ini
My question is, how can I activated it via terminal?
FROM php:7.2-apache
WORKDIR /var/www/html
COPY . ./
RUN apt-get update && apt-get install -y -q nodejs npm curl unzip git rake ruby-ronn zlib1g-dev libpng-dev && apt-get clean
RUN apt-get install php7.2=dev php-pear phpunit
RUN curl -sS https://getcomposer.org/installer | php
RUN mv composer.phar /usr/local/bin/composer
RUN pecl install grpc
RUN docker-php-ext-install mbstring
RUN docker-php-ext-install zip
RUN docker-php-ext-install gd
RUN npm install
RUN npm install -g gulp-cli
RUN composer update
RUN gulp --env=production
EXPOSE 80 443

you forgot to activate the grcp extension ,you can use the code under the comment #install protoc to activated,and you will get message if it has activated or not by RUN php -r "echo extension_loaded('grpc') ? 'yes' : 'no';"
I think this way is better and more concise:
FROM php:7-apache
RUN apt-get update && apt-get install -y -q git rake ruby-ronn zlib1g-dev && apt-get clean
# install composer
RUN cd /usr/local/bin && curl -sS https://getcomposer.org/installer | php
RUN cd /usr/local/bin && mv composer.phar composer
RUN pecl install grpc
#install protoc
RUN mkdir -p /tmp/protoc && \
curl -L https://github.com/google/protobuf/releases/download/v3.2.0/protoc-3.2.0-linux-x86_64.zip > /tmp/protoc/protoc.zip && \
cd /tmp/protoc && \
unzip protoc.zip && \
cp /tmp/protoc/bin/protoc /usr/local/bin && \
cd /tmp && \
rm -r /tmp/protoc && \
docker-php-ext-enable grpc
RUN php -r "echo extension_loaded('grpc') ? 'yes' : 'no';"
WORKDIR /app
COPY . /app
RUN composer install
RUN npm install
RUN npm install -g gulp-cli
RUN gulp --env=production
EXPOSE 8181

Related

GitHub Self Hosted Runner Can't Find Command

I have the following Dockerfile:
FROM ubuntu:20.04
ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update && apt-get -y install curl \
iputils-ping \
apt-transport-https \
tar \
jq \
python && \
curl -sL https://deb.nodesource.com/setup_14.x | bash && \
apt-get install nodejs -yq && \
apt-get clean && apt-get autoremove
RUN npm install -g npm#latest
ARG GH_RUNNER_VERSION="2.283.3"
WORKDIR /actions-runner
RUN curl -o actions.tar.gz --location "https://github.com/actions/runner/releases/download/v${GH_RUNNER_VERSION}/actions-runner-linux-x64-${GH_RUNNER_VERSION}.tar.gz" && \
tar -zxf actions.tar.gz && \
rm -f actions.tar.gz && \
./bin/installdependencies.sh
COPY entrypoint.sh .
RUN chmod +x entrypoint.sh
ENTRYPOINT ["/actions-runner/entrypoint.sh"]
and the following step on the ci:
- name: Create DB
run: npm run dc-up
The output of that step is: npm: command not found.
I added the path using the method the docs suggested, it was done by adding a new step:
- name: add npm to path
run: echo "/usr/bin/npm" >> $GITHUB_PATH
I've checked that node is in the path by printing the path in a separate step inside the CI and the output is:
Run echo "$PATH"
/usr/bin/npm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
I know 100% that NPM is installed into the docker image because when I run it local and only try to interact withit without the ENTRYPOINT then I'm able to print the NPM version and I checked that is it indeed in /usr/bin/npm, but still, inside the steps of the CI it can't find npm for some reason.
And its not only for npm, but for every single installation that I tried to do, I just picked npm for showcase.
Anyone has any idea what can be done?

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

Docker - install nodejs only if it is not installed

dockerfile:
FROM python:3.9
ENV PYTHONUNBUFFERED 1
RUN mkdir /app
WORKDIR /app
RUN apt-get update && apt-get upgrade -y && \
curl -fsSL https://deb.nodesource.com/setup_17.x | bash - && \
apt-get install -y nodejs && \
This will install nodejs every time I build. Can I install nodejs only if it is not installed?
unless you change any of the layers above and including this one or clear docker cache installation would not be reexecuted

Generating PHP library with Dockerized gRPC

I'm trying to build a gRPC PHP Client and gRPC NodeJs Server in docker. But the problem is I can't install protoc-gen-php-grpc to my docker server. When I try to run this run this makefile:
proto_from_within_container:
# PHP
protoc /var/www/protos/smellycat.proto \
--php_out=/var/www/php-client/src \
$(: 👇 generate server interface) \
--php-grpc_out=/var/www/php-client/src \
$(: 👇 generates the client code) \
--grpc_out=/var/www/php-client/src \
--plugin=protoc-gen-grpc=/protobuf/grpc/bins/opt/grpc_php_plugin \
--proto_path /var/www/protos
proto:
powershell rm -r -fo php-client/src -ErrorAction SilentlyContinue
powershell New-Item -ItemType Directory -Path php-client/src -Force -ErrorAction SilentlyContinue
docker-compose run grpc-server make proto_from_within_container
With this command: make proto
Getting this error message after docker containers builded:
protoc /var/www/protos/smellycat.proto \
--php_out=/var/www/php-client/src \
\
--php-grpc_out=/var/www/php-client/src \
\
--grpc_out=/var/www/php-client/src \
--plugin=protoc-gen-grpc=/protobuf/grpc/bins/opt/grpc_php_plugin \
--proto_path /var/www/protos
protoc-gen-php-grpc: program not found or is not executable
Please specify a program using absolute path or make sure the program is available in your PATH system variable
--php-grpc_out: protoc-gen-php-grpc: Plugin failed with status code 1.
Makefile:4: recipe for target 'proto_from_within_container' failed
make: *** [proto_from_within_container] Error 1
This is my docker-compose file
version: "3"
services:
grpc-server:
container_name: grpc-server
build:
context: .
dockerfile: Dockerfile-server
working_dir: /var/www
volumes:
- .:/var/www
grpc-client:
image: php:7.4-cli
container_name: grpc-client
build:
context: .
dockerfile: Dockerfile-client
working_dir: /var/www
volumes:
- .:/var/www
command: bash -c [php php_client.php && composer install]
And this is my grpc-server docker file:
FROM node:latest
ENV DEBIAN_FRONTEND=noninteractive
#Versions
ARG PROTOBUF_VERSION=3.14.0
ARG PHP_GRPC_VERSION=1.34.0
# Utils
RUN apt-get update -yqq \
&& apt-get install -yqq wget unzip zlib1g-dev git autoconf libtool automake build-essential software-properties-common curl zip \
&& rm -rf /var/lib/apt/lists/*
# Protobuf
RUN mkdir -p /protobuf
RUN cd /protobuf \
&& wget https://github.com/protocolbuffers/protobuf/releases/download/v${PROTOBUF_VERSION}/protoc-${PROTOBUF_VERSION}-linux-x86_64.zip -O protobuf.zip \
&& unzip protobuf.zip && rm protobuf.zip
# grpc PHP (generate client)
RUN apt-get update -yqq && apt-get upgrade -yqq
RUN apt-get install php php-dev php-pear phpunit zlib1g-dev -yqq
RUN pecl install grpc-${PHP_GRPC_VERSION}
RUN cd /protobuf && git clone -b v${PHP_GRPC_VERSION} https://github.com/grpc/grpc \
&& cd /protobuf/grpc && git submodule update --init
RUN cd /protobuf/grpc && make grpc_php_plugin
ENV PATH "/protobuf/bin:${PATH}"
ENV PATH "/protobuf/grpc/bins/opt:${PATH}"
# NPM Installation
WORKDIR /var/www
COPY . /var/www
RUN npm install
CMD ["node", "server.js"]
Do you have any advice?
After a lot of search and readings, I finally managed to build a full application that communicates with each other.
The problem was at the Makefile, at this step:
--plugin=protoc-gen-grpc=/protobuf/grpc/bins/opt/grpc_php_plugin
I was assigning the wrong path for grpc_php_plugin.
There is my new dockerfile:
FROM php:7.4-cli
# Environment variables
ENV DEBIAN_FRONTEND=noninteractive
# Utils
RUN apt-get update -yqq && \
apt-get upgrade -yqq && \
apt-get install -y unzip build-essential git software-properties-common curl pkg-config zip zlib1g-dev
# Composer installation
COPY --from=composer:latest /usr/bin/composer /usr/local/bin/composer
# Install grpc and probuf with pecl
RUN pecl install grpc && pecl install protobuf
# Enable grpc and protobuf extensions in php.ini file
RUN echo starting && \
docker-php-ext-enable grpc && \
docker-php-ext-enable protobuf
# Install cmake
RUN apt-get update -yqq && apt-get -y install cmake
# Install grpc_php_plugin and protoc
RUN git clone -b v1.36.2 https://github.com/grpc/grpc && \
cd grpc && git submodule update --init && \
mkdir cmake/build && cd cmake/build && \
cmake ../.. && make protoc grpc_php_plugin
# Setting node, protoc and grpc_php_plugin paths
ENV PATH "/grpc/cmake/build:${PATH}"
ENV PATH "/grpc/cmake/build/third_party/protobuf:${PATH}"
# Moving client folder to vm
WORKDIR /var/www
COPY ./client /var/www
# Packages
RUN composer install
# Generate php libraries from proto file
RUN make proto
CMD [ "php", "./handler.php" ]
For my full application, click.

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.

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