I am trying to run a docker container to automatically set up a sphinx documentation site, but for some reason I get the following error when I try to build
Step 9/11 : RUN make html
---> Running in abd76075d0a0
make: *** No rule to make target 'html'. Stop.
When I run the container and console in, I see that sphinx-quickstart does not seem to have been run since there are no files present at all in /sphinx. Not sure what I have done wrong. Dockerfile is below.
1 # Run this with
2 # docker build .
3 # docker run -dit -p 8000:8000 <image_id>
4 FROM ubuntu:latest
5
6 WORKDIR /sphinx
7 VOLUME /sphinx
8
9 RUN apt-get update -y
10 RUN apt-get install python3 python3-pip vim git -y
11
12 RUN pip3 install -U pip
13 RUN pip3 install sphinx
14
15 RUN sphinx-quickstart . --quiet --project devops --author 'Timothy Pulliam' -v '0.1' --language 'en' --makefile
16 RUN make html
17
18 EXPOSE 8000/tcp
19
20
21 CMD ["python3", "-m", "http.server"]
EDIT:
Using LinPy's suggestion I was able to get it to work. It is still strange that it would not work the other way.
The Dockerfile VOLUME directive mostly only has confusing side effects. Unless you’re 100% clear on what it does and why you want it, you should just delete it.
In particular, one of those confusing side effects is that RUN commands that write into the volume directory just get lost. So when on line 7 you say VOLUME /sphinx, the RUN sphinx-quickstart on line 15 tries to write its output into the current directory, which is a declared volume directory, so the output content isn’t persisted into the image.
(Storing your code in a volume isn’t generally appropriate; build it into the image so it’s reusable later. You can use docker run -v to bind-mount content over any container-side directory regardless of whether or not it’s declared as a VOLUME.)
so you need to set those in one line:
RUN sphinx-quickstart . --quiet --project devops --author 'Timothy Pulliam' -v '0.1' --language 'en' --makefile && make html
I think you can see in the logs , remove intermediate container there for the rule html is not there anymore
You've already resolved the issue with LinPy's helpful comment, but just to add more, doing a quick google search with your error message comes up with this StackOverflow post...
gcc makefile error: "No rule to make target ..."
Perhaps you were accidentally invoking a different command (in this case a GCC command) rather than the .bat file provided by Sphinx.
Hopefully this might shed a bit more light on WHY it was happening. I assume the Ubuntu parent image you're using has GCC pre-installed.
Related
I'm following installation instructions for RedhawkSDR, which rely on having a Centos7 OS. Since my machine uses Ubuntu 22.04, I'm creating a Docker container to run Centos7 then installing RedhawkSDR in that.
One of the RedhawkSDR installation instructions is to create a file with the following command:
cat<<EOF|sed 's#LDIR#'`pwd`'#g'|sudo tee /etc/yum.repos.d/redhawk.repo
[redhawk]
name=REDHAWK Repository
baseurl=file://LDIR/
enabled=1
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-redhawk
EOF
How do I get a Dockerfile to execute this command when creating an image?
(Also, although I can see that this command creates the file /etc/yum.repos.d/redhawk.repo, which consists of the lines from [redhawk] to gpgkey=...., I have no idea how to parse this command and understand exactly why it does that...)
Using the text editor of your choice, create the file on your local system. Remove the word sudo from it; give it an additional first line #!/bin/sh. Make it executable using chmod +x create-redhawk-repo.
Now it is an ordinary shell script, and in your Dockerfile you can just RUN it.
COPY create-redhawk-repo ./
RUN ./create-redhawk-repo
But! If you look at what the script actually does, it just writes a file into /etc/yum.repos.d with a LDIR placeholder replaced with some other directory. The filesystem layout inside a Docker image is fixed, and there's no particular reason to use environment variables or build arguments to hold filesystem paths most of the time. You could use a fixed path in the file
[redhawk]
name=REDHAWK Repository
baseurl=file:///redhawk-yum/
enabled=1
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-redhawk
and in your Dockerfile, just COPY that file in as-is, and make sure the downloaded package archive is in that directory. Adapting the installation instructions:
ARG redhawk_version=3.0.1
RUN wget https://github.com/RedhawkSDR/redhawk/releases/download/$redhawk_version/\
redhawk-yum-$redhawk_version-el7-x86_64.tar.gz \
&& tar xzf redhawk-yum-$redhawk_version-el7-x86_64.tar.gz \
&& rm redhawk-yum-$redhawk_version-el7-x86_64.tar.gz \
&& mv redhawk-yum-$redhawk_version-el7-x86_64 redhawk-yum \
&& rpm -i redhawk-yum/redhawk-release*.rpm
COPY redhawk.repo /etc/yum.repos.d/
Remember that, in a Dockerfile, you are root unless you've switched to another USER (and in that case you can use USER root to switch back); you do not need generally sudo in Docker at all, and can just delete sudo where it appears in these instructions.
How do I get a Dockerfile to execute this command when creating an image?
Just use printf and run this command as single line:
FROM image_name:image_tag
ARG LDIR="/default/folder/if/argument/not/set"
# if container has sudo command and default user is not root
# you should choose this variant
RUN printf '[redhawk]\nname=REDHAWK Repository\nbaseurl=file://%s/\nenabled=1\ngpgcheck=1\ngpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-redhawk\n' "$LDIR" | sudo tee /etc/yum.repos.d/redhawk.repo
# if default container user is root this command without piping may be used
RUN printf '[redhawk]\nname=REDHAWK Repository\nbaseurl=file://%s/\nenabled=1\ngpgcheck=1\ngpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-redhawk\n' "$LDIR" > /etc/yum.repos.d/redhawk.repo
Where LDIR is an argument and docker build process should be run like:
docker build ./ --build-arg LDIR=`pwd`
EDIT: documentation given by the informatic administration was shitty, old version of singularity, now the order of arguments is different and the problem is solved.
To make my tool more portable, and because I have to use it on a cluster, I have to put my bioinformatics tool at disposal for docker. Tool is located here. The docker hub is 007ptar007/metadbgwas, if you want to experience with it. The Dockerfile is in the repo, and to make it easier to everyone :
FROM ubuntu:latest
ENV DEBIAN_FRONTEND=noninteractive
USER root
COPY ./install_docker.sh ./
RUN chmod +x ./install_docker.sh && sh ./install_docker.sh
ENTRYPOINT ["/MetaDBGWAS/metadbgwas.sh"]
ENV PATH="/MetaDBGWAS/:${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 am trying to build using:
FROM mcr.microsoft.com/dotnet/core/sdk:2.1 AS builder
COPY pythonnet/src/ pythonnet/src
WORKDIR /pythonnet/src/runtime
RUN dotnet build -f netstandard2.0 -p:DefineConstants=\"MONO_LINUX\;XPLAT\;PYTHON3\;PYTHON37\;UCS4\;NETSTANDARD\" Python.Runtime.15.csproj
# copy myApp csproj and restore
COPY src/myApp/*.csproj /src/myApp/
WORKDIR /src/myApp
RUN dotnet restore
# now copy everything else as separate docker step
# (copy to staging folder, remove csproj, and copy down - so we don't overwrite project above)
WORKDIR /
COPY src/myApp/ ./staging/src/myApp
RUN rm ./staging/src/myApp/*.csproj \
&& cp -r ./staging/* ./ \
&& rm -rf ./staging
This was working fine, and in Windows 10 still does, but in CentOS 7 I get:
Step 10/40 : RUN rm ./staging/src/myApp/*.csproj && cp -r ./staging/* ./ && rm -rf ./staging
---> Running in 6b17ae0fae89
cp: cannot stat './staging/src/myApp/myApp.csproj': No such file or directory
Using ls instead of cp throws a similar file not found error, so it looks like Docker still knows about myApp.csproj but cannot see it since it has been removed.
Is there a way around this? I have tried using rsync but similar problems.
I simply ignored the issue by tacking on ;exit 0 on the offending lines. Not great, but does the job.
EDIT: This worked for me as I cannot upgrade the version of CemtOS. If you can, check out Alexander Block's answer.
I don't know specifically how to solve this problem as there's a lot of context in the filesystem that you haven't (and probably can't) share with us.
My suggestion on a strategy is that you:
comment out all lines from the failing one 'til the end of the Dockerfile
build the partial image
docker exec -it [image] bash to jump into the image
poke around and figure out what's going wrong
repeat 1-4 until things work as expected
It's not as fun as a perfectly insightful answer of course but this is a relentlessly effective algorithm even if it's tedious and annoying.
EDIT
My wild guess is that somehow, someway the linux machine doesn't have the file where it's expected for some reason and so it doesn't get copied into the image at all and that's why the docker build process can't find it. But there's no way to know without debugging the build process.
cp -r will stop and fail with that cannot stat <file> message whenever the source is a symbolic link and the target of the link does not exist. It will not copy links to non-existent files.
So my guess is that after you run COPY src/myApp/ ./staging/src/myApp your file ./staging/src/myApp/myApp.csproj is a symbolic link to a non-existent file. Why the following RUN rm ./staging/src/*.csproj doesn't remove it and stays silent about that, I don't know the answer to that.
To help demonstrate my theory, see below showing cp failing on a symlink on Centos 7.
[547] $ docker run --rm -it centos:7
Unable to find image 'centos:7' locally
7: Pulling from library/centos
524b0c1e57f8: Pull complete
Digest: sha256:e9ce0b76f29f942502facd849f3e468232492b259b9d9f076f71b392293f1582
Status: Downloaded newer image for centos:7
[root#a47b77cf2800 /]# ln -s /tmp/foo /tmp/bar
[root#a47b77cf2800 /]# ls -l /tmp/foo
ls: cannot access /tmp/foo: No such file or directory
[root#a47b77cf2800 /]# ls -l /tmp/bar
lrwxrwxrwx 1 root root 8 Jul 6 05:44 /tmp/bar -> /tmp/foo
[root#a47b77cf2800 /]# cp /tmp/foo /tmp/1
cp: cannot stat '/tmp/foo': No such file or directory
[root#a47b77cf2800 /]# cp /tmp/bar /tmp/2
cp: cannot stat '/tmp/bar': No such file or directory
Notice how you copy reports that it cannot stat either the source or destination of the symbolic link. It's the exact symptom you are seeing.
If you just want to get past this, you can try tar instead of cp or rsync.
Instead of
cp -r ./staging/* ./
use this instead:
tar -C ./staging -cf - . | tar -xf -
tar will happily copy symlinks that don't exist.
You've very likely encountered a kernel bug that has been fixed a long time ago in more recent kernels. As of https://de.wikipedia.org/wiki/CentOS, CentOS 7 is based on the Linux Kernel 3.10, which is pretty old already and does not have good Docker support in regard to the storage backend (overlay filesystem).
CentOS tried to backport needed fixes and features into 3.10, but seems to not have succeeded fully when it comes to overlay support. There are multiple (slightly different) issues regarding this which you can find when searching for "CentOS 7 overlay driver" on the internet. All of them have in common that removing of files from parent overlays does not work as expected.
For me it looks like rm calls on files return success, even though the files are not fully removed. Directory listings (e.g. by ls or shell expansion as in your case) then still list the file, while accessing the file then fails (no matter if read, write or deletion of the file).
I assume that what you've seen is just another incarnation of these issues. You should either switch to CentOS 8 or upgrade your Kernel (which is not officially supported by CentOS as far as I understand). Or even more radical, switch to a distribution which is used more often in combination with Docker and generally offers more recent Kernels, e.g. Debian or Ubuntu.
I have a Dockerfile describing a container used to build some libs.
Basically, it looks like this:
FROM debian:stretch-slim
COPY somedebianrepo/*.deb \
/basedir/
RUN dpkg -i /basedir/*.deb
When I build the image, I get :
dpkg: dependency problems prevent configuration of [one of my lib] ... depends on [some other lib] however [some other lib] is not installed
Which may sound obvious... but : when I comment the RUN line :
# RUN dpkg -i /basedir/*.deb
then build the image, start the container, and connect to it, I expected the dpkg command to act the same... But actually, when I launch directly the command works fine with no such error.
root#host$ docker exec -it -u root <mycontainer> bash
root#mycontainer $ dpkg -i /basedir/*.deb
root#mycontainer $ (no error)
I also tried with apt-get install, and also encountered such different behaviors.
Since I am quite newbie with Docker, the answer may be quite obvious... but still, it is not to me! I expected the commands executed through "RUN" to act the same way as if executed from within the container..
So if anyone could point out me where I am wrong, she/he is welcome!
EDIT 1 : I have tried to run apt-get update before the dpkg command, though I did not expect it to work : with no success
Edit: Solved- typo
I have a Dockerfile that successfully creates a virtualenv using virtualenvwrapper (along with setting up a heap of "standard" settings/packages in our normal environment). I am using the resulting image as a "base image" for further use. All good so far. However, the following Dockerfile (based of the first image, "base_image_14.04") falls down at the last line:
FROM base_image_14.04
USER root
RUN DEBIAN_FRONTEND=noninteractive \
apt-get update && apt-get install -y \
libproj0 libproj-dev \
libgeos-c1v5 libgeos-dev \
libjpeg62 libjpeg-dev \
zlib1g zlib1g-dev \
libfreetype6 libfreetype6-dev \
libgdal20 libgdal-dev \
&& rm -rf /var/lib/apt/lists
USER webdev
RUN ["/bin/bash", "-ic", "mkproject maproxy"]
EXPOSE 80
WORKDIR $PROJECT_HOME/mapproxy
ADD ./requirements.txt .
RUN ["/bin/bash", "-ic", "workon mapproxy && pip install -r requirements.txt"]
The "mkproject mapproxy" works fine. If I comment out the last line it builds successfully and I can spin up the container and run "workon mapproxy" manually, not a problem. But when I try and build with the last line, it gives a workon error:
ERROR: Environment 'mapproxy' does not exist. Create it with 'mkvirtualenv mapproxy'.
workon is being called, but for some reason it can't find the mapproxy virtualenv.
WORKON_HOME & PROJECT_HOME both exist (defined in the parent image) and point to the correct locations (and are used successfully by "mkproject mapproxy").
So why is workon returning an error when the mapproxy virtualenv exists? The same error happens when I isolate that last line into a third Dockerfile building on the second.
Solved: It was a simple typo. mkproject maproxy instead of mapproxy. :sigh:
I am trying to build a docker image and am running into similar problems.
First question was why use a virtual env in docker? The main reason in a nutshell is to minimize effort to migrate an existing and working approach into a docker container. I will eventually use docker-compose, but I wanted to start by getting my feet wet with it all in a single docker container.
In my first attempt I installed almost everything with apt-get, including uwsgi. I installed my app "globally" with pip3. The app has command line functionality and a separate flask web app, hence the need for uwsgi. The command line functionality works, but when I make a request of the flask app uwsgi / python has a problem with locale: Fatal Python error: Py_Initialize: Unable to get the locale encoding and ImportError: No module named 'encodings
I have stripped away all my app specific additions to narrow down the problem. This is the Dockerfile I'm using:
# Docker image definition for testing
FROM ubuntu:xenial
# Create a user
RUN useradd -G sudo -ms /bin/bash tester
RUN echo 'tester:password' | chpasswd
WORKDIR /home/tester
# Skipping apt-get update to save some build time. Some are kept
# to insure they are the same as on host setup.
RUN apt-get install -y python3 python3-dev python3-pip \
virtualenv virtualenvwrapper sudo nano && \
apt-get clean -qy
# After above, can we use those installed in rest of Dockerfile?
# Yes, but not always, such as with virtualenvwrapper. What about
# virtualenv? How do you "source" the script? Doesn't appear to be
# installed, as bash complains "source needs a single parameter"
ENV VIRTUALENVWRAPPER_PYTHON /usr/bin/python3
ENV VIRTUALENVWRAPPER_VIRTUALENV /usr/bin/virtualenv
RUN ["/bin/bash", "-c", "source", "/usr/share/virtualenvwrapper/virtualenvwrapper.sh"]
# Create a virtualenv so uwsgi can find locale
# RUN mkdir /home/tester/.virtualenv && virtualenv -p`which python3` /home/bts_tools/.virtualenv/bts_tools
RUN mkvirtualenv -p`which python3` bts_tools && \
workon bts_tools && \
pip3 --disable-pip-version-check install --upgrade bts_tools
USER tester
ENTRYPOINT ["/bin/bash"]
CMD ["--login"]
The build fails on the line I try to source the virtualenvwrapper script. Bash complains source needs an argument - the file to be sourced. So I comment out the RUN lines and it builds without error. When I run the resulting container I see all the additions to the ENV that virtualenvwrapper makes (you can see all of them by executing the "set" command without any args), and the script to be sourced is there too.
So my question is why doesn't docker find them? How does the docker build process work if the results of any previous RUNs or ENVs aren't applied for subsequent use in the Dockerfile? I know some things are applied and work, for example if you apt-get nginx you can refer to /etc/nginx or alter things under that folder. You can create a user and set it's password or cd into its home folder for example. If I move the WORKDIR before the RUN useradd -G I see a warning from useradd the home folder already exists. I tried to use the "time" program to time how long it takes to do various things in the Dockerfile and docker complains it can't find 'time'.
So what exactly is going on? I have spent the last 3 days trying to figure this out. It just shouldn't be this difficult. What am I missing?
Parts of the bts_tools flask app worked when I wasn't using virtual envs. Most of the app didn't work, and the issue was this locale problem. Since everything works on the host outside of docker, and after trying to alter the PATH, PYTHONHOME, PYTHONPATH in my uwsgi start script to overcome the dreaded "locale encoding" fatal error, I decided to try to replicate the host setup as closely as possible since that didn't have the locale issue. When I have had that problem before I could run dpkg-reconfigure python3 or fix with changes to PATH or ENV settings. If you google the problem you'll see many people have difficulties with python & locale. It's almost enough reason to avoid using python!
I posted this elsewhere about locale issue, if it helps.