I am trying to to run an entrypoint script via docker-compose file. And im getting permission denied error while trying to edit a configuration while. I have tried with root user as well with no luck.
Dockerfile
FROM centos:7 AS ingestbase
RUN mkdir -p ${USER_HOME}/certs ${USER_HOME}/logs
COPY config/* ${USER_HOME}/
RUN useradd -m -d ${USER_HOME} user
RUN chown -R user ${USER_HOME}/
USER user
WORKDIR ${USER_HOME}
ENTRYPOINT ["/entrypoint.sh"]
Entrypoint.sh is as below:
set -x
TRY_LOOP="3"
who
pwd
ls -ltr
sed -i "s#{DB_PASS}#$DB_PASS#g" ${USER_HOME}/config.py
Following are the logs while running enrypoint.sh
+ TRY_LOOP=3
+ who
/usr/local/userhome
+ pwd
+ ls -ltr
total 10
drwxr-xr-x 9 user root 4096 Sep 20 02:51 logs
drwxr-xr-x 1 user root 6 Sep 25 05:59 certs
-rw-r--r-- 1 user root 41558 Sep 25 05:59 config.py
sed: couldn't open temporary file /usr/local/userhome/sedjzy3se: Permission denied
You most likely don't have executable permission on the entrypoint.
Have you tried doing:
RUN chmod +x /entrypoint.sh
ENTRYPOINT [ "/bin/sh", "/entrypoint.sh" ]
I am trying to run a gocd server docker image and facing file permissions issues. Can't seem to figure out what I am missing.
Found out what uid/gid is being used in the container:
]$ sudo docker container run gocd/gocd-server:v21.1.0 id
$ exec /usr/local/sbin/tini -g -- id
uid=1000(go) gid=0(root) groups=0(root)
[centos#ip-10-0-0-168 ~]$
Created a folder on the local host and set ownership:
$ sudo mkdir -p /gocd/data
[centos#ip-10-0-0-168 ~]$ sudo chown -R 1000:0 /gocd/
[centos#ip-10-0-0-168 ~]$
[centos#ip-10-0-0-168 ~]$ ls -l /
total 16
lrwxrwxrwx. 1 root root 7 Feb 29 2020 bin -> usr/bin
:
drwxr-xr-x. 3 centos root 18 Feb 8 15:55 gocd
:
Docker run:
$ sudo docker run -v /gocd/data/:/godata -p 8153:8153 gocd/gocd-server:v21.1.0
/docker-entrypoint.sh: Creating directories and symlinks to hold GoCD configuration, data, and logs
$ mkdir -v -p /godata/artifacts
mkdir: can't create directory '/godata/artifacts': Permission denied
/docker-entrypoint.sh: cannot mkdir -v -p /godata/artifacts
[centos#ip-10-0-0-168 ~]$
Ok, so instead of chown -R 1000:00 /gocd, I switched to chown -R 1000:root and with that I was able to get the container to start.
Though in both cases the output of ls -l shows the same user and group:
drwxr-xr-x. 3 centos root 18 Feb 9 01:36 gocd
This question already has an answer here:
Run docker command in bash file and run using crontab
(1 answer)
Closed 5 years ago.
I use GOGS as a personal Git server (using Docker image). I made a backup script which runs fine when I launch it manually, but when CRON lauches it, seems to malfunction as backups are strictly identical to previous one.
IMPORTANT PRECISION : usual problems like this are related to $PATH that might be incomplete, but script below only uses docker, ls, head or xargs commands which are under /usr/bin or /usr (so in $PATH).
Example results on 3 weeks (CRON once a week) :
root#1:~# ll /path/to/backup/
total 1724864
-rw-r--r-- 1 root root 588742750 janv. 29 11:30 gogs_2018_01_29.zip
-rw-r--r-- 1 root root 588742750 janv. 29 11:30 gogs_2018_02_02.zip
-rw-r--r-- 1 root root 588742750 janv. 29 11:30 gogs_2018_02_09.zip
Even system dates are identical... While date setup by bash are good related on execution. I don't get it.
After manual launch :
-rw-r--r-- 1 root root 588742750 janv. 29 11:30 gogs_2018_01_29.zip
-rw-r--r-- 1 root root 588742750 janv. 29 11:30 gogs_2018_02_02.zip
-rw-r--r-- 1 root root 589503781 févr. 9 11:21 gogs_2018_02_09.zip
Last backup is bigger, dates matches... Worked.
Why do I have this malfunction on CRON launch only?
Script gogs_backup:
#!/bin/bash
# Make backup
docker exec -i -t gogs_1 /app/gogs/gogs backup --target /tmp --archive-name gogs.zip
# Build file name
now=$(date +"%Y_%m_%d")
file="/path/to/backup/gogs_$now.zip"
# Copy file
docker cp gogs_1:/tmp/gogs.zip $file
# Remove everything from /tmp dir
docker exec -i -t gogs_1 rm -rf /tmp/gogs*
# Keep only 3 in destination folder
ls -drt /path/to/backup/* | head -n-3 | xargs rm
CRON line :
0 3 * * 5 bash /path/to/gogs_backup
From the exec documentation
The docker exec command runs a new command in a running container.
And from the cp documentation
The CONTAINER can be a running or stopped container.
So my guess is that docker exec fails because the container is stoped, but cp works because it works on stoped containers.
Check your logs. And check your return values, there are more bugs in this script.
Thanks to #mncl post, I decided to have a look again on docker commands documentation.
I spotted here that I runned docker exec -i -t gogs_1 /app/gogs/gogs backup --target /tmp --archive-name gogs.zip.
-i seemed useless to me, as it is a CRON launch. I removed it and the CRON launched script runned well.
Nonetheless, the Docker doc about -i puzzle me out. Why keeping STDIN attached to command would be a problem in this case?
I am very puzzled by this problem I am having. I am trying to execute a file in Ubuntu 12.04 LTS via command line. I have a script that calls a program to run and write the results in a hard drive. I changed the permissions and ownership of everything to be wxr. Here is the ls -l of my script (called TEST-star):
-rwxrwxrwx 1 root root 950 Nov 15 13:16 TEST-star
Here is the ls -l of the package my script calls:
-rwxrwxrwx 1 root root 1931414 Nov 10 12:37 STAR
Finally the ls -l of the hard drive mounted in /media/CLC"
drwxrwxrwx 1 root root 8192 Nov 15 13:04 CLC
I have been trying to run it since yesterday and always get a message that I don't have permission to write the results:
EXITING because of FATAL ERROR: could not create output file ./_STARtmp//Unmapped.out.mate1.thread14
Solution: check that you have permission to write this file
I thought if I change the permissions to rwx and run my script as root it would not have a problem (using sudo). Right now I run out of options. Any suggestion would be appreciated. Please let me know what other information you would need solve this issue.
Thank you.
Here is the first line of script I am trying to run:
#!/bin/sh
cd /media/CLC/ANOPHELES-STAR-v2.4f1/; mkdir GambFemAnt1 && cd GambFemAnt1; echo $PWD && echo Starting mapping of GambFemAnt1; /home/aedes/Documents/STAR_2.4.0f1/STAR --genomeDir /media/Galaxy/Galaxy_data/Anopheles/STAR/Genome --readFilesIn /media/Galaxy/Galaxy_data/Anopheles/QC/GambFemAnt1/GambFemAnt1.fastq --runThreadN 23 --outFilterMismatchNmax 4 --outFilterMatchNminOverLread 0.75 --seedSearchLmax 30 --seedSearchStartLmax 30 --seedPerReadNmax 100000 --seedPerWindowNmax 100 --alignTranscriptsPerReadNmax 100000 --alignTranscriptsPerWindowNmax 10000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx; mv Aligned.sortedByCoord.out.bam GambFemAnt1.bam; mv Unmapped.out.mate1 GambFemAnt1-unmapped.fastq; cp *.fastq /media/CLC/ANOPHELES-STAR-v2.4f1/UNMAPED-reads/; cd /media/CLC/ANOPHELES-STAR-v2.4f1 && echo $PWD && echo GambFemAnt1 mapping finished;
I also posted a question for the authors of the package.
Turns out all the permissions were set correctly. The problem resigns within the package. I found out that it works using --runThreadN 12 instead of --runThreadN 23.
After yesterday's news of Shocker, it seems like apps inside a Docker container should not be run as root. I tried to update my Dockerfile to create an app user however changing permissions on app files (while still root) doesn't seem to work. I'm guessing this is because some LXC permission is not being granted to the root user maybe?
Here's my Dockerfile:
# Node.js app Docker file
FROM dockerfile/nodejs
MAINTAINER Thom Nichols "thom#thomnichols.org"
RUN useradd -ms /bin/bash node
ADD . /data
# This next line doesn't seem to have any effect:
RUN chown -R node /data
ENV HOME /home/node
USER node
RUN cd /data && npm install
EXPOSE 8888
WORKDIR /data
CMD ["npm", "start"]
Pretty straightforward, but when I ls -l everything is still owned by root:
[ node#ed7ae33e76e1:/data {docker-nonroot-user} ]$ ls -l /data
total 64K
-rw-r--r-- 1 root root 383 Jun 18 20:32 Dockerfile
-rw-r--r-- 1 root root 862 Jun 18 16:23 Gruntfile.js
-rw-r--r-- 1 root root 1.2K Jun 18 15:48 README.md
drwxr-xr-x 4 root root 4.0K May 30 14:24 assets/
-rw-r--r-- 1 root root 416 Jun 3 14:22 bower.json
-rw-r--r-- 1 root root 930 May 30 01:50 config.js
drwxr-xr-x 4 root root 4.0K Jun 18 16:08 lib/
drwxr-xr-x 42 root root 4.0K Jun 18 16:04 node_modules/
-rw-r--r-- 1 root root 2.0K Jun 18 16:04 package.json
-rw-r--r-- 1 root root 118 May 30 18:35 server.js
drwxr-xr-x 3 root root 4.0K May 30 02:17 static/
drwxr-xr-x 3 root root 4.0K Jun 18 20:13 test/
drwxr-xr-x 3 root root 4.0K Jun 3 17:38 views/
My updated dockerfile works great thanks to #creak's clarification of how volumes work. Once the initial files are chowned, npm install is run as the non-root user. And thanks to a postinstall hook, npm runs bower install && grunt assets which takes care of the remaining install steps and avoids any need to npm install -g any node cli tools like bower, grunt or coffeescript.
Check this post: http://www.yegor256.com/2014/08/29/docker-non-root.html In rultor.com we run all builds in their own Docker containers. And every time before running the scripts inside the container, we switch to a non-root user. This is how:
adduser --disabled-password --gecos '' r
adduser r sudo
echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers
su -m r -c /home/r/script.sh
r is the user we're using.
Update 2015-09-28
I have noticed this post getting a bit of attention. A word of advice for anyone who is potentially interested in doing something like this. I would try to use Python or another language as a wrapper for your script executions. Doing native bash scripts I had problems when trying to pass through a variety of arguments to my containers. Specifically there was issues with the interpretation/escaping of " and ' characters by the shell.
I was needing to change the user for a slightly different reason.
I created a docker image housing a full featured install of ImageMagick and Ffmpeg with a desire that I could do transformations on images/videos within my host OS. My problem was that these are command line tools, so it is slightly trickier to execute them via docker and then get the results back into the host OS. I managed to allow for this by mounting a docker volume. This seemed to work okay except that the image/video output was coming out as being owned by root (i.e. the user the docker container was running as), rather than the user whom executed the command.
I looked at the approach that #François Zaninotto mentioned in his answer (you can see the full make script here). It was really cool, but I preferred the option of creating a bash shell script that I would then register on my path. I took some of the concepts from the Makefile approach (specifically the user/group creation) and then I created the shell script.
Here is an example of my dockermagick shell script:
#!/bin/bash
### VARIABLES
DOCKER_IMAGE='acleancoder/imagemagick-full:latest'
CONTAINER_USERNAME='dummy'
CONTAINER_GROUPNAME='dummy'
HOMEDIR='/home/'$CONTAINER_USERNAME
GROUP_ID=$(id -g)
USER_ID=$(id -u)
### FUNCTIONS
create_user_cmd()
{
echo \
groupadd -f -g $GROUP_ID $CONTAINER_GROUPNAME '&&' \
useradd -u $USER_ID -g $CONTAINER_GROUPNAME $CONTAINER_USERNAME '&&' \
mkdir --parent $HOMEDIR '&&' \
chown -R $CONTAINER_USERNAME:$CONTAINER_GROUPNAME $HOMEDIR
}
execute_as_cmd()
{
echo \
sudo -u $CONTAINER_USERNAME HOME=$HOMEDIR
}
full_container_cmd()
{
echo "'$(create_user_cmd) && $(execute_as_cmd) $#'"
}
### MAIN
eval docker run \
--rm=true \
-a stdout \
-v $(pwd):$HOMEDIR \
-w $HOMEDIR \
$DOCKER_IMAGE \
/bin/bash -ci $(full_container_cmd $#)
This script is bound to the 'acleancoder/imagemagick-full' image, but that can be changed by editing the variable at the top of the script.
What it basically does is:
Create a user id and group within the container to match the user who executes the script from the host OS.
Mounts the current working directory of the host OS (using docker volumes) into home directory for the user we create within the executing docker container.
Sets the tmp directory as the working directory for the container.
Passes any arguments that are passed to the script, which will then be executed by the '/bin/bash' of the executing docker container.
Now I am able to run the ImageMagick/Ffmpeg commands against files on my host OS. For example, say I want to convert an image MyImage.jpeg into a PNG file, I could now do the following:
$ cd ~/MyImages
$ ls
MyImage.jpeg
$ dockermagick convert MyImage.jpeg Foo.png
$ ls
Foo.png MyImage.jpeg
I have also attached to the 'stdout' so I could run the ImageMagick identify command to get info on an image on my host, for e.g.:
$ dockermagick identify MyImage.jpeg
MyImage.jpeg JPEG 640x426 640x426+0+0 8-bit DirectClass 78.6KB 0.000u 0:00.000
There are obvious dangers about mounting the current directory and allowing any arbitrary command definition to be passed along for execution. But there are also many ways to make the script more safe/secure. I am executing this in my own non-production personal environment, so these are not of highest concern for me. But I would highly recommend you take the dangers into consideration should you choose to expand upon this script. It's also worth me mentioning that this script doesn't take an OS X host into consideration. The make file that I steal ideas/concepts from does take this into account, so you could extend this script to do so.
Another limitation to note is that I can only refer to files currently in the path for which I am executing the script. This is because of the way I am mounting the volumes, so the following would not work:
$ cd ~/MyImages
$ ls
MyImage.jpeg
$ dockermagick convert ~/DifferentDirectory/AnotherImage.jpeg Foo.png
$ ls
MyImage.jpeg
It's best just to go to the directory containing the image and execute against it directly. Of course I am sure there are ways to get around this limitation too, but for me and my current needs, this will do.
This one is a bit tricky, it is actually due to the image you start from.
If you look at the source, you notice that /data/ is a volume. So everything you do in the Dockerfile will be discarded and overridden at runtime by the volume that gets mounted then.
You can chown at runtime by changing your CMD to something like CMD chown -R node /data && npm start.
Note: I answer here because, given the generic title, this Question pops up in google when you look for a solution to "Running app inside Docker as non-root user". Hope it helps those who are stranded here.
With Alpine Linux you can create a system user like this:
RUN adduser -D -H -S -s /bin/false -u 1000 myuser
Everything in the Dockerfile after this line is executed with myuser.
myuser user has:
no password assigned
no home dir
no login shell
no root access.
This is from adduser --help:
-h DIR Home directory
-g GECOS GECOS field
-s SHELL Login shell
-G GRP Add user to existing group
-S Create a system user
-D Don't assign a password
-H Don't create home directory
-u UID User id
-k SKEL Skeleton directory (/etc/skel)
Note: This answer is given because many people looking for non-root usage will end up here. Beware, this does not address the issue that caused the problem, but is addressing the title and clarification to an answer given by #yegor256, which uses a non-root user inside the container. This answer explains how to accomplish this for non-debian/non-ubuntu use-case. This is not addressing the issue with volumes.
On Red Hat-based systems, such as Fedora and CentOS, this can be done in the following way:
RUN adduser user && \
echo "user ALL=(root) NOPASSWD:ALL" | tee -a /etc/sudoers.d/user && \
chmod 0440 /etc/sudoers.d/user
In your Dockerfile you can run commands as this user by doing:
RUN su - user -c "echo Hello $HOME"
And the command can be run as:
CMD ["su","-","user","-c","/bin/bash"]
An example of this can be found here:
https://github.com/gbraad/docker-dev/commit/644c51002f4b8e6fe5bb745638542a4c3d908b16