I'm new to Travis and getting this error in the build output:
Setting environment variables from .travis.yml
$ export DOCKER_COMPOSE_VERSION=1.23.1
0.01s$ source ~/virtualenv/python3.6/bin/activate
$ python --version
Python 3.6.3
$ pip --version
pip 9.0.1 from /home/travis/virtualenv/python3.6.3/lib/python3.6/site-packages (python 3.6)
before_install.1
0.01s$ sudo rm /usr/local/bin/docker-compose
before_install.2
0.13s$ curl -L https://github.com/docker/compose/releases/download/${DOCKER_COMPOSE_VERSION}/docker-compose-'uname -s'-'uname -m' > docker-compose
before_install.3
0.00s$ chmod +x docker-compose
before_install.4
0.01s$ sudo mv docker-compose /usr/local/bin
install
10.72s$ pip install -r requirements.txt
0.02s$ docker-compose up -d --build
/usr/local/bin/docker-compose: line 1: syntax error near unexpected token `<'
This is strange because there is < nowhere in my docker-compose files. Why am I seeing this error ?
The problem doesn't come from your docker-compose.yml project file but from from the docker-compose file itself, which has not been properly downloaded; namely it is not a binary, but a HTML file (hence the < character you got):
$ export DOCKER_COMPOSE_VERSION=1.24.1
$ curl -L https://github.com/docker/compose/releases/download\
/${DOCKER_COMPOSE_VERSION}/docker-compose-'uname -s'-'uname -m' > docker-compose
$ file docker-compose
docker-compose: HTML document, ASCII text, with CRLF line terminators
$ head docker-compose
<!DOCTYPE html><title>Malformed request</title>
<body>We didn't receive a proper request from your browser. Please contact us if the problem persists.</body>
</html>
To solve this, you should fix your script by using the command substitution $(uname -s), instead of 'uname -s':
$ curl -L https://github.com/docker/compose/releases/download\
/${DOCKER_COMPOSE_VERSION}/docker-compose-$(uname -s)-$(uname -m) > docker-compose
$ file docker-compose
docker-compose: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (...)
Related
I have built an image with Dockerfile, it looks like this:
FROM node:12.18.1
USER root
RUN apt-get -y update
RUN apt-get -y install curl
RUN npm install
ENTRYPOINT ["curl"]
Now I can see that curl is installed, but how can I check on Node?
Every time I am trying to see the version I get an error:
'node'/'npm' is not recognized as an internal or external command,
I also tried this:
docker run -it --rm node /bin/bash -c 'node --version'
but ended up with this:
--version': -c: line 1: unexpected EOF while looking for matching `''
--version': -c: line 2: syntax error: unexpected end of file
EDIT: documentation given by the informatic administration was shitty, old version of singularity, now the order of arguments is different and the problem is solved.
To make my tool more portable, and because I have to use it on a cluster, I have to put my bioinformatics tool at disposal for docker. Tool is located here. The docker hub is 007ptar007/metadbgwas, if you want to experience with it. The Dockerfile is in the repo, and to make it easier to everyone :
FROM ubuntu:latest
ENV DEBIAN_FRONTEND=noninteractive
USER root
COPY ./install_docker.sh ./
RUN chmod +x ./install_docker.sh && sh ./install_docker.sh
ENTRYPOINT ["/MetaDBGWAS/metadbgwas.sh"]
ENV PATH="/MetaDBGWAS/:${PATH}"
And the install_docker.sh script contains :
apt-get update
apt install -y libgatbcore-dev libhdf5-dev libboost-all-dev libpstreams-dev zlib1g-dev g++ cmake git r-base-core
Rscript -e "install.packages(c('ape', 'phangorn'))"
Rscript -e "install.packages('https://raw.githubusercontent.com/sgearle/bugwas/master/build/bugwas_1.0.tar.gz', repos=NULL, type='source')"
git clone --recursive https://github.com/Louis-MG/MetaDBGWAS.git
cd MetaDBGWAS
sed -i "51i#include <limits>" ./REINDEER/blight/robin_hood.h #temporary fix for REINDEER compilation
sh install.sh
The problem :
My tool parses the command line, and needs a verbose (-v, or --verbose) argument. It also needs to reject unknown arguments; anything that isn't used by the tool causes the help message to be printed in the standard output and exits. To use the tool, I need to mount volumes were the data is; using -v /path/to/files:/input option:
singularity run docker://007ptar007/metadbgwas --volumes '/path/to/data:/inputd/:/input' --files /input --strains /input/strains --threads 8 --output ~/output
But my tool sees this as a bad -v option value or the --volume as an unknown option. I can't change this on my tool. How do I solve this conflict ?
You need to put any arguments intended for singularity - such as the volume mounting - before the name of the image you want to run (e.g. the docker image you specify in your command):
singularity run -v '/path/to/data:/input' docker://007ptar007/metadbgwas --files /input --strains /input/strains --threads 8 --output ~/output
I run these command:
docker run -ti --rm alpine
apk add --no-cache curl
curl https://registry.npmjs.org/monaco-editor/-/monaco-editor-0.15.6.tgz | tar xvz --strip 1 package/min
and got error tar: package/min: not found in archive.
I run the same command (curl | tar) in Mac terminal and docker ubuntu, all of them are success.
The tar included in Alpine isn't the usual (GNU) tar, but a component of BusyBox:
/scratch # tar --version
tar (busybox) 1.28.4
Apparently, this version of tar generates a (bogus) error message when run with
tar xvz --strip 1 package/min
(however, at first glance, it created the target directory just fine, so ignoring the error message might be ok).
To get rid of the annoying error, you should install GNU tar and use that:
/scratch # apk add --no-cache tar
fetch http://dl-cdn.alpinelinux.org/alpine/v3.8/main/x86_64/APKINDEX.tar.gz
fetch http://dl-cdn.alpinelinux.org/alpine/v3.8/community/x86_64/APKINDEX.tar.gz
(1/1) Installing tar (1.31-r0)
Executing busybox-1.28.4-r2.trigger
OK: 7 MiB in 19 packages
/scratch # tar --version
tar (GNU tar) 1.31
<rest of message omitted>
Afterwards, running your original command works without any error messages.
I'm trying to build a Docker image based on oracle/database:11.2.0.2-xe (which is based on Oracle Linux based on RHEL) and want to change the system locale in this image (using some RUN command inside a Dockerfile).
According to this guide I should use localectl set-locale <MYLOCALE> but this command is failing with Failed to create bus connection: No such file or directory message. This is a known Docker issue for commands that require SystemD to be launched.
I tried to start the SystemD anyway (using /usr/sbin/init as first process as well as using -v /sys/fs/cgroup:/sys/fs/cgroup:ro -v /run thanks to this help) but then the localectl set-locale failed with Could not get properties: Connection timed out message.
So I'm now trying to avoid the usage of localectl to change my system globale locale, how could I do this?
According to this good guide on setting locale on Linux, I should use
localedef -c -i fr_FR -f ISO-8859-15 fr_FR.ISO-8859-15
But this command failed with
cannot read character map directory `/usr/share/i18n/charmaps': No such file or directory`
This SO reply indicated one could use yum reinstall glibc-common -y to fix this and it worked.
So my final working Dockerfile is:
RUN yum reinstall glibc-common -y && \
localedef -c -i fr_FR -f ISO-8859-15 fr_FR.ISO-8859-15 && \
echo "LANG=fr_FR.ISO-8859-15" > /etc/locale.conf
ENV LANG fr_FR.ISO-8859-15
I have a project running on Docker with docker-compose for dev environment.
I want to get it running on GitLabCI with a gitlab-ci-multi-runner "Docker mode" instance.
Here is my .gitlab-ci.yml file:
image: soullivaneuh/docker-bash
before_script:
- apk add --update bash curl
- curl --silent --location https://github.com/docker/compose/releases/download/1.5.2/docker-compose-`uname -s`-`uname -m` > /usr/local/bin/docker-compose
- chmod +x /usr/local/bin/docker-compose
- ./configure
- docker-compose up -d
Note that soullivaneuh/docker-bash image is just a docker image with bash installed.
The script fails on docker-compose up -d command:
gitlab-ci-multi-runner 0.7.2 (998cf5d)
Using Docker executor with image soullivaneuh/docker-bash ...
Pulling docker image soullivaneuh/docker-bash:latest ...
Running on runner-1ee5079f-project-3-concurrent-1 via sd-59984...
Fetching changes...
Removing app/config/parameters.yml
Removing docker-compose.env
HEAD is now at 5c5e7ff remove docker service
From https://git.dummy.net/project/project
5c5e7ff..45e643d docker-ci -> origin/docker-ci
Checking out 45e643dd as docker-ci...
Previous HEAD position was 5c5e7ff... remove docker service
HEAD is now at 45e643d... Remove docker info commands
$ apk add --update bash curl
fetch http://dl-4.alpinelinux.org/alpine/v3.2/main/x86_64/APKINDEX.tar.gz
OK: 10 MiB in 28 packages
$ curl --silent --location https://github.com/docker/compose/releases/download/1.5.2/docker-compose-`uname -s`-`uname -m` > /usr/local/bin/docker-compose
$ chmod +x /usr/local/bin/docker-compose
$ ./configure
$ docker-compose up -d
bash: line 30: /usr/local/bin/docker-compose: No such file or directory
ERROR: Build failed with: exit code 1
I have absolutly no idea why this is failing.
Thanks for help.
The No such file or directory is misleading. I've received that many times while trying to run dynamically linked binaries using alpine linux (which it appears you are using).
The problem (as I understand it) is that the binary was compiled and linked against glibc, but alpine uses musl, not glibc.
You could use ldd /usr/local/bin/docker-compose to tell you which libraries are missing (or run it with strace if all else fails).
To get it working, it might be easier to install from python source (https://docs.docker.com/compose/install/#install-using-pip), which is what the official compose image does (https://github.com/docker/compose/blob/master/Dockerfile.run).
Or you could use an image built on debian or some other distro that uses glibc.