Docker COPY is not copying script - docker

Docker COPY is not copying over the bash script
FROM alpine:latest
#Install Go and Tini - These remain.
RUN apk add --no-cache go build-base gcc go
RUN apk add --no-cache --update ca-certificates redis git && update-ca-certificates
# Set Env Variables for Go and add Go to Path.
ENV GOPATH /go
ENV PATH $GOPATH/bin:/usr/local/go/bin:$PATH
RUN go get github.com/rakyll/hey
RUN echo GOLANG VERSION `go version`
COPY ./bench.sh /root/bench.sh
RUN chmod +x /root/bench.sh
ENTRYPOINT /root/bench.sh
Here is the script -
#!/bin/bash
set -e;
echo "entered";
hey;
I try running the above Dockerfile with
$ docker build -t test-bench .
$ docker run -it test-bench
But I get the error
/bin/sh: /root/bench.sh: not found
The file does exist -
$ docker run --rm -it test-bench sh
/ # ls
bin dev etc go home lib media mnt opt proc root run sbin srv sys tmp usr var
/ # cd root
~ # ls
bench.sh
~ #

Is your docker build successful. When I tried to simulate this, found the following error
---> Running in 96468658cebd
go: missing Git command. See https://golang.org/s/gogetcmd
package github.com/rakyll/hey: exec: "git": executable file not found in $PATH
The command '/bin/sh -c go get github.com/rakyll/hey' returned a non-zero code: 1
Try installing git using Dockerfile RUN apk add --no-cache go build-base gcc go git and run again.
The COPY operation here seems to be correct. Make sure it is present in the directory from where docker build is executed.
Okay, the script is using /bin/bash the bash binary is not available in the alpine image. Either it has to be installed or a /bin/sh shell should be used

Related

Copy file from dockerfile build to host - bandit

I just started learning docker. To teach myself, I managed to containerize bandit (a python code scanner) but I'm not able to see the output of the scan before the container destroys itself. How can I copy the output file from inside the container to the host, or otherwise save it?
Right now i'm just using bandit to scan itself basically :)
Dockerfile
FROM python:3-alpine
WORKDIR /
RUN pip install bandit
RUN apk update && apk upgrade
RUN apk add git
RUN git clone https://github.com/PyCQA/bandit.git ./code-to-scan
CMD [ "python -m bandit -r ./code-to-scan -o bandit.txt" ]
You can mount a volume on you host where you can share the output of bandit.
For example, you can run your container with:
docker run -v $(pwd)/output:/tmp/output -t your_awesome_container:latest
And you in your dockerfile:
...
CMD [ "python -m bandit -r ./code-to-scan -o /tmp/bandit.txt" ]
This way the bandit.txt file will be found in the output folder.
Better place the code in your image not in the root directory.
I did some adjustments to your Dockerfile.
FROM python:3-alpine
WORKDIR /usr/myapp
RUN pip install bandit
RUN apk update && apk upgrade
RUN apk add git
RUN git clone https://github.com/PyCQA/bandit.git .
CMD [ "bandit","-r",".","-o","bandit.txt" ]`
This clones git in your WORKDIR.
Note the CMD, it is an array, so just devide all commands and args as in the Dockerfile about.
I put the the Dockerfile in my D:\test directory (Windows).
docker build -t test .
docker run -v D:/test/:/usr/myapp test
It will generate you bandit.txt in the test folder.
After the code is execute the container exits, as there are nothing else to do.
you can also put --rm to remove the container once it finishs.
docker run --rm -v D:/test/:/usr/myapp test

local uaa docker image container not starting in windows docker

I have built a local uaa docker image and tried to run in local.
But I am getting this error when I am trying to start the docker image.
I built the docker image via this below command and the build is successful too.
docker build -t uaa-local --build-arg uaa_yml_name=local.yml .
when I am trying to run the local uaa docker image, I am getting this below error. What I am doing wrong
Content of DockerFile
FROM openjdk:11-jre
ARG uaa_yml_name=local.yml
ENV UAA_CONFIG_PATH /uaa
ENV CATALINA_HOME /tomcat
ADD run.sh /tmp/
ADD conf/$uaa_yml_name /uaa/uaa.yml
RUN chmod +x /tmp/run.sh
RUN wget -q https://archive.apache.org/dist/tomcat/tomcat-8/v8.5.57/bin/apache-tomcat-8.5.57.tar.gz
RUN tar zxf apache-tomcat-8.5.57.tar.gz
RUN rm apache-tomcat-8.5.57.tar.gz
RUN mkdir /tomcat
RUN mv apache-tomcat-8.5.57/* /tomcat
RUN rm -rf /tomcat/webapps/*
ADD dist/cloudfoundry-identity-uaa-74.22.0.war /tomcat/webapps/
RUN mv /tomcat/webapps/cloudfoundry-identity-uaa-74.22.0.war /tomcat/webapps/ROOT.war
RUN mkdir -p /tomcat/webapps/ROOT && cd /tomcat/webapps/ROOT && unzip ../ROOT.war
ADD conf/log4j2.properties /tomcat/webapps/ROOT/WEB-INF/classes/log4j2.properties
RUN rm -rf /tomcat/webapps/ROOT.war
EXPOSE 8080
CMD ["/tmp/run.sh"]
On further investigation I think it is looking for run.sh file in the /tmp/ folder which is added on line 5 in Dockerfile..but when I checked for the file in /tmp/ folder it is not there..Is it because of that?And how to resolve that? I already have the run.sh in my current folder.

Permission denied error from Docker container in Snakemake

I had built a Docker container from this Dockerfile previously and it worked fine:
FROM perl:5.32
MAINTAINER Matthew Jordan Oldach, moldach686#gmail.com
WORKDIR /usr/local/bin
# Install cpan modules
RUN cpanm install --force Cwd Getopt::Long POSIX File::Basename List::Util Bio::DB::Fasta Bio::Seq Bio::SeqUtils Bio::SeqIO Set::IntervalTree Set::IntSpan
RUN apt-get install tar
# Download CooVar-v0.07
RUN wget http://genome.sfu.ca/projects/coovar/CooVar-0.07.tar.gz
RUN tar xvf CooVar-0.07.tar.gz
RUN cd coovar-0.07; chmod +x scripts/* coovar.pl
# Set WORKDIR to /data -- predefined mount location.
RUN mkdir /data
WORKDIR /data
# Set Entrypoint
ENTRYPOINT ["perl", "/usr/local/bin/coovar-0.07/coovar.pl"]
The only issue was that I found there was a slight difference between what is on the repo and the coovar-0.07 which is on our server (there was slight difference in the extract-cdna.pl script).
In order to reproduce our pipeline I'll need to COPY CooVar locally into the container (rather than wget).
I've therefore tried the following Dockerfile:
FROM perl:5.32
MAINTAINER Matthew Jordan Oldach, moldach686#gmail.com
WORKDIR /usr/local/bin
# Install cpan modules
RUN cpanm install --force Cwd Getopt::Long POSIX File::Basename List::Util Bio::DB::Fasta Bio::Seq Bio::SeqUtils Bio::SeqIO Set::IntervalTree Set::IntSpan
# Download CooVar-v0.07
COPY coovar-0.07 /usr/local/bin/coovar-0.07
RUN cd coovar-0.07; chmod +x scripts/* coovar.pl
# Set WORKDIR to /data -- predefined mount location.
RUN mkdir /data
WORKDIR /data
# Set Entrypoint
ENTRYPOINT ["perl", "/usr/local/bin/coovar-0.07/coovar.pl"]
It appears I could run the main script (coovar.pl) from Docker (no Permission Denied error):
# pull the container
$ sudo docker pull moldach686/coovar-v0.07:latest
# force entry point of `moldach686/coovar-v0.07` to /bin/bash
## in order to investigate file system
$ sudo docker run -it --entrypoint /bin/bash moldach686/coovar-v0.07
root#c7459dbe216a:/data# perl /usr/local/bin/coovar-0.07/coovar.pl
USAGE: ./coovar.pl -e EXONS_GFF -r REFERENCE_FASTA (-t GVS_TAB_FORMAT | -v GVS_VCF_FORMAT) [-o OUTPUT_DIRECTORY] [--circos] [--feature_source] [--feature_type]
Program parameter details provided in file README.
However, when I tried to incorporate this into my Snakemake workflow I get the following Permission Denied error:
Workflow defines that rule get_vep_cache is eligible for caching between workflows (use the --cache argument to enable this).
Building DAG of jobs...
Using shell: /cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job counts:
count jobs
1 coovar
1
[Tue Nov 3 21:56:51 2020]
rule coovar:
input: variant_calling/varscan/MTG470.vcf, refs/c_elegans.PRJNA13758.WS265.genomic.fa
output: annotation/coovar/varscan/MTG470/categorized-gvs.gvf, annotation/coovar/varscan/MTG470.annotated.vcf, annotation/coovar/varscan/filtration/MTG470_keep.tsv, annotation/coovar/varscan/filtration/MTG470_exclude.tsv
jobid: 0
wildcards: sample=MTG470
resources: mem=4000, time=10
Activating singularity image /scratch/moldach/COOVAR/cbc22e3a26af1c31fb0e4fcae240baf8.simg
Can't open perl script "/usr/local/bin/coovar-0.07/coovar.pl": Permission denied
The solution I found to work was adding the following line to the Dockerfile:
RUN echo "user ALL=NOPASSWD: ALL" >> /etc/sudoers
This adds the user to the sudoers file giving permissions:
FROM perl:5.32
MAINTAINER Matthew Jordan Oldach, moldach686#gmail.com
USER root
WORKDIR /usr/local/bin
# Install cpan modules
RUN cpanm install --force Cwd Getopt::Long POSIX File::Basename List::Util Bio::DB::Fasta Bio::Seq Bio::SeqUtils Bio::SeqIO Set::IntervalTree Set::IntSpan
RUN echo "user ALL=NOPASSWD: ALL" >> /etc/sudoers
# Download CooVar-v0.07
COPY coovar-0.07 /usr/local/bin/coovar-0.07
RUN cd coovar-0.07; chmod a+rwx scripts/* coovar.pl
# Download Bedtools 2.27.1
ENV VERSION 2.27.1
ENV NAME bedtools2
ENV URL "https://github.com/arq5x/bedtools2/releases/download/v${VERSION}/bedtools-${VERSION}.tar.gz"
WORKDIR /tmp
RUN wget -q -O - $URL | tar -zxv && \
cd ${NAME} && \
make -j 4 && \
cd .. && \
cp ./${NAME}/bin/bedtools /usr/local/bin/ && \
strip /usr/local/bin/*; true && \
rm -rf ./${NAME}/
# Set WORKDIR to /data -- predefined mount location.
RUN mkdir /data
WORKDIR /data
# Set Entrypoint
ENTRYPOINT ["perl", "/usr/local/bin/coovar-0.07/coovar.pl"]

My custom beat cant find custombeat.yml when I try to run it from a container

So, I have built a beat with mage GenerateCustomBeat and it runs okay, except, now I'm trying to cotainerize it. When I run the image I built, it complains that no customBeat.yml was found.
I have secured that the file exists in the folder by adding a line RUN ls . at the end of my Dockerfile.
The beat name is coletorbeat, so this name appears multiple times inside the Dockerfile.
Upon executing sudo docker run coletorbeat I have the following error message:
Exiting: error loading config file: stat coletorbeat.yml: no such file or directory
If there was a way to specify the coletorbeat.yml file location when I execute the beat, in CMD I think I would solve it, but I have not found how to do so yet.
I'll post the Dockerfile below. I know the code inside the beater folder works fine. I'm guessing I'm making some mistake on the containerization.
Dockerfile:
FROM ubuntu
MAINTAINER myNameHere
ARG ${ip:-"333.333.333.333"}
ARG ${porta:-"4343"}
ARG ${dataInicio:-"2020-01-07"}
ARG ${dataFim:-"2020-01-07"}
ARG ${tipoEquipamento:-"type"}
ARG ${versao:-"2"}
ARG ${nivel:-"0"}
ARG ${instituicao:-"RJ"}
ADD . .
RUN mkdir /etc/coletorbeat
COPY /coletorbeat/coletorbeat.yml /etc/coletorbeat/coletorbeat.yml
RUN apt-get update && \
apt-get install -y wget git
RUN wget https://storage.googleapis.com/golang/go1.14.4.linux-amd64.tar.gz
RUN tar -zxvf go1.14.*.linux-amd64.tar.gz -C /usr/local
RUN mkdir /go
ENV GOROOT /usr/local/go
ENV GOPATH $HOME/go
ENV PATH $PATH:$GOROOT/bin:$GOPATH/bin
RUN echo $PATH
RUN go get -u -d github.com/magefile/mage
RUN cd $GOPATH/src/github.com/magefile/mage && \
go run bootstrap.go
RUN apt-get install -y python3-venv
RUN apt-get install -y build-essential
RUN cd /coletorbeat && chmod go-w coletorbeat.yml && ./coletorbeat setup
RUN cd /coletorbeat && ./coletorbeat test config -c /coletorbeat/coletorbeat.yml && ls .
CMD ./coletorbeat/coletorbeat -E 'coletorbeat.ip=${ip}'
You are adding the yml file into the /etc dir
COPY /coletorbeat/coletorbeat.yml /etc/coletorbeat/coletorbeat.yml
But then running commands on /coletorbeat without using etc.
On CMD line in the Dockerfile, I added the command cd /mybeatfolder and it worked. Libbeat searches the current folder for the config file as default, so moving to the right directory before executing my beat solved it.

Docker : oci runtime error: exec: "/bin/bash": stat /bin in windows 7

I am using windows 7. In my home folder I made a new directory Docker. And inside that I made new directory rails.
This is my docker file: (Docker/rails/Dockerfile)
FROM alpine:3.2
MAINTAINER xxx <xxx#xxx.in>
ENV BUILD_PACKAGES bash curl-dev ruby-dev build-base
ENV RUBY_PACKAGES ruby ruby-io-console ruby-bundler
# Update and install all of the required packages.
# At the end, remove the apk cache
RUN apk update && \
apk upgrade && \
apk add $BUILD_PACKAGES && \
apk add $RUBY_PACKAGES && \
rm -rf /var/cache/apk/*
RUN mkdir /usr/app
WORKDIR /usr/app
COPY Gemfile /usr/app/
COPY Gemfile.lock /usr/app/
RUN bundle install
COPY . /usr/app
And then I changed directory to Docker. On ls it shows rails.
Then I typed this command:
docker build rails
Now the image name is alpine. I made a tag to rails like this:
docker tag <imageid> myname/rails
Problem:
The image is successfully build and I have a repository rails and pushed it successfully. I am able to pull it as well.
Till now everything is fine, but then I run this command:
docker run -i -t xxx/rails /bin/bash
It gives me this error:
C:\Program Files\Docker Toolbox\docker.exe: Error response from daemon: oci runtime error: exec: "/bin/bash": stat /bin/bash: no such file or directory.
So I am stuck there.
My Objective:
I want to run this command successfully:
rails -v
To run that command I need to install the image, and I don't know how to install the image, I have been following up numerous tutorials since last week.
I am new to docker. This is my first docker image.
Edit:
docker exec -it sh
Alpine does not come with bash by default, only /bin/sh so you should change your command to:
docker run -i -t vikaran/rails sh
Also worth noting you can run:
docker build -t myname/rails rails
To automatically tag the image when building it.

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