I have made a ubuntu vnc following this question:
Build a full Ubuntu desktop docker image
and then I connected to it by running docker exec -it ubvnc sh. I want to add a folder containing some of my programs to the path, namely myprogs, so I tried adding to my .bashrc file, however that didn't work, so I tried making a script which I could run after connecting that would update my path, but this script is also not updating my path as you can see below:
# whoami
root
# pwd
/root
# ls -ltr myprogs
total 0
-rw-r--r-- 1 root root 0 Jul 5 02:23 someScript.sh
# cat fixPath.sh
export PATH="/root/myprogs:$PATH"
# ./fixPath.sh
# echo $PATH
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
# export PATH="/root/myprogs:$PATH"
# echo $PATH
/root/myprogs:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
#
As you can see in the above, one would expect the path to be updated by running ./fixPath.sh however this doesn't work. I am able however to update the path by running the content of fixpath.sh by pasting it into the terminal and pressing enter (again, as can be seen above). I'd like to know why this is the case and if possible, how to make it so I can update my path by running such a script, or even better, via .bashrc.
Related
I know the proper way to add cron job for the user www-data is to run crontab -u www-data -e
So to do that in dockerfile I should add a line like RUN crontab -u www-data /some_where/crontab.conf
But I found if I do this, it works too (the docker image is based on alpine3.7).
ADD /some_where/crontab /etc/crontabs/www-data
RUN chmod 0644 /etc/crontabs/www-data
But I can't find the document explaining why it works. So why does it work and does this mean if I add another file called www to /etc/crontabs it will make a cronjob for www (assume I have www user) ?
See this:
Multiuser cron
As Unix is a multiuser OS, some of the apps have to be able to support
multiple users, cron is one of these. Each user can have their own crontab
file, which can be created/edited/removed by the command crontab. This
command creates an individual crontab file and although this is a text file,
as the /etc/crontab is, it shouldn't be edited directly. The crontab file is
often stored in /var/spool/cron/crontabs/<user> (Unix/Slackware/BSD),
/var/spool/cron/<user> (RedHat) or /var/cron/tabs/<user> (SuSE),
but might be kept elsewhere depending on what Unx flavor you're running.
And in alpine, it also in /var/spool/cron/crontabs, just /var/spool/cron/crontabs is a symbol link of /etc/crontabs, so you can also put it in /etc/crontabs:
/etc/crontabs # ls -alh /var/spool/cron/crontabs
lrwxrwxrwx 1 root root 13 Jun 19 17:14 /var/spool/cron/crontabs -> /etc/crontabs
I've a simple shell script that executes a docker-exec command inside a container.
The script is located in /var/www/mysite-nginx/nginx-reload.sh and permissions of this file are -rwxrwxr-x
#!/bin/sh
docker exec -it mysite_nginx nginx -s reload
If I execute this script directly from shell, it works. But if I add the script to my crontab with the following line, it doesn't work.
15 4 * * * /var/www/mysite-nginx/nginx-reload.sh
I suppose that cron doesn't execute the command, or what is wrong?
On /var/log/syslog I have:
Jul 23 15:30:01 arrubiu CRON[29511]: (sergej) CMD (/var/www/mysite-nginx/nginx-reload.sh)
[EDIT] Solved in this way: docker exec is not working in cron
The issue seems to be that docker is not found. There are two ways around:
You enter the full paths of all application in your crontab script, you can find that out using e.g. locate docker, so that it looks something like
#!/bin/sh
/usr/bin/docker exec -it mysite_nginx
/usr/bin/nginx -s reload
Alternatively, you can set the $PATH and other environment variables in the same way how they are set for a usual sh-script. To achieve that, first backup what is saved in /etc/environment, and then flush it with the currently available variables by executing:
cp /etc/environment > ~/my_etc_environment_backup
env >> /etc/environment
Related questions on SO
Where can I set environment variables that crontab will use?
I am having some problems trying to make a container that runs a cronjob. I can see cron running using top in the container but it doesn't write to the log file as the below example attempts to. The file stays empty.
I have read answers to the same question here:
How to run a cron job inside a docker container?
Output of `tail -f` at the end of a docker CMD is not showing
But I could not make any of the suggestions work. For example I used the dockerfile from here: https://github.com/Ekito/docker-cron/
FROM ubuntu:latest
MAINTAINER docker#ekito.fr
# Add crontab file in the cron directory
ADD crontab /etc/cron.d/hello-cron
# Give execution rights on the cron job
RUN chmod 0644 /etc/cron.d/hello-cron
# Create the log file to be able to run tail
RUN touch /var/log/cron.log
#Install Cron
RUN apt-get update
RUN apt-get -y install cron
# Run the command on container startup
CMD cron && tail -f /var/log/cron.log
crontab:
* * * * * root echo "Hello world" >> /var/log/cron.log 2>&1
# Don't remove the empty line at the end of this file. It is required to run the cron job
It didn't work on my machine (windows 10). Apparently there seems to be a windows specific issue also reported by someone else: https://github.com/Ekito/docker-cron/issues/3
To test if it was just me doing something wrong I tried to do the same in a virtual machine running ubuntu (so an ubuntu host instead of my windows host) and that worked as expected. The log file is extended as expected.
So what can I do to try to make this work?
I tried writing to a mounted (bind) folder and making a volume to write to. Neither worked.
rferalli's answer on the github issue did the trick for me:
"Had the same issue. Fixed it by changing line ending of the crontab file from CRLF to LF. Hope this helps!"
I have this problem too.
My workaround is to use Task Scheduler to run a .bat file that start a container instead
Using Task Scheduler: https://active-directory-wp.com/docs/Usage/How_to_add_a_cron_job_on_Windows.html
hello.bat
docker run hello-world
TaskScheduler Action
cmd /c hello.bat >> hello.log 2>&1
Hope this help :)
I have run docker run to generate a file
sudo docker run -i --mount type=bind,src=/home/mathed/Simulation/custom_desman/1/Strains/Simulation2/Assembly,target=/home/mathed/Simulation/custom_desman/1/Strains/Simulation2/Assembly 990210oliver/mycc.docker:v1 MyCC.py /home/mathed/Simulation/custom_desman/1/Strains/Simulation2/Assembly/final_contigs_c10K.fa
This is the message I've got after executing.
20181029_0753
4mer
1_rename.py /home/mathed/Simulation/custom_desman/1/Strains/Simulation2/Assembly/final_contigs_c10K.fa 1000
Seqs >= 1000 : 32551
Minimum contig lengh for first stage clustering: 1236
run Prodigal.
/opt/prodigal.linux -i My.fa -a gene.aa -d gene.nuc -f gbk -o output -s potential_genes.txt
run fetchMG.
run UCLUST.
Get Feature.
2_GetFeatures_4mer.py for fisrt stage clustering
2_GetFeatures_4mer.py for second stage clustering
3_GetMatrix.py 1236 for fisrt stage clustering
22896 contigs entering first stage clustering
Clustering...
1_bhsne.py 20
2_ap.py /opt/ap 500 0
Cluster Correction.
to Split and Merge.
1_ClusterCorrection_Split.py 40 2
2_ClusterCorrection_Merge.py 40
Get contig by cluster.
20181029_0811
I now want to get the files generated by MyCC.py to host.
After reading Copying files from Docker container to host, I tried,
sudo docker cp 642ef90103be:/opt /home/mathed/data
But I got an error message
mkdir /home/mathed/data/opt: permission denied
Is there a way to get the files generated to a directory /home/mathed/data?
Thank you.
I assume your dest path does not exist.
Docker cp doc stats that in that case :
SRC_PATH specifies a directory
DEST_PATH does not exist
DEST_PATH is created as a directory and the contents of the source directory are copied into this directory
Thus it is trying to create a directory fro DEST_PATH... and docker must have the rights to do so.
According to the owner of the DEST_PATH top existing directory, you may have to either
create the directory first so that it will not be created by docker and give it the correct rights (looks like it has no rights to do so) using sudo chown {user}:{folder} + chmod +x {folder}
change the rights to the parent existing directory (chown + chmod again),
switch to path where docker is allowed to write.
We are using Docker container and created a Dockerfile. Inside this container we deployed war file using tomcat image
and we can see tomcat logs at console but console logs is not updating
after sending a request to tomcat via URL.
Also we can not see any log file inside tomcat logs folder
Can anyone help me out that how we can see tomcat logs like localhost.logs/catalina.logs/manager.logs etc
MY Dockerfile is :-
FROM openjdk:6-jre
ENV CATALINA_HOME /usr/local/tomcat
ENV PATH $CATALINA_HOME/bin:$PATH
COPY tomcat $CATALINA_HOME
ADD newui.war $CATALINA_HOME/webapps
CMD $CATALINA_HOME/bin/startup.sh && tail -F $CATALINA_HOME/logs/catalina.out
EXPOSE 8080
Used below script to build
$ docker build -t tomcat .
and below used to run tomcat
$ docker run -p 8080:8080 tomcat
Here are a few things wrong with your dockerfile:
You mention that you need java 6, and yet the line FROM java as of this writing is set to use java:8.
You need to replace the FROM line with FROM java:6-jre or as suggested by the official page: FROM openjdk:6-jre if in 2018 you still need java 6, which is dangerous. I would also strongly suggest to use at least FROM tomcat:7 which should be able to run java 6 applets but will include some bug fixes including support for longer Diffie-Hellman primes for HTTPS (if you are serious about your app's security).
Copt tomcat $CATALINA_HOME you either miss-typed the line to SO, or your image should not build at all. It should be COPY tomcat $CATALINA_HOME
Given that you are using the COPY command there is no need to use RUN mkdir -p prior to this, since the COPY command will automatically create all the required folders.
CMD $CATALINA_HOME/bin/startup.sh && tail -f $CATALINA_HOME/logs/catalina.out
First the tail -f part: since you are looking to tail a log file which might be created and recreated during the server's operation instead of following the FD you should be following the path by doing tail -F (capital F)
startup.sh && tail - tail will never start until startup.sh exits. A better approach is to do tail -F $CATALINA_HOME/logs/catalina.out & inside your startup.sh right before you start your tomcat server. That way tail will be running in the background.
Regardless this is a somewhat dangerous approach and you risk zombie processes because bash does not manage its children processes and neither does docker. I would recommend to use supervisord or something similar.
(From https://docs.docker.com/engine/admin/multi-service_container/)
FROM ubuntu:latest
RUN apt-get update && apt-get install -y supervisor
RUN mkdir -p /var/log/supervisor
COPY supervisord.conf /etc/supervisor/conf.d/supervisord.conf
COPY my_first_process my_first_process
COPY my_second_process my_second_process
CMD ["/usr/bin/supervisord"]
Note: this dockerfile sample omits a few of the best practices, e.g. removing the apt cache in the same run command as doing the apt-get update.
Personal favorite is the phusion/baseimage, but it is harder to setup since you'll need to install everything including the java into the image.
If with all of these modifications you still have no luck in seeing the console update, then you'll need to also post the contents of your startup.sh file or other tomcat related configurations.
P.S.: it might be a good idea to do RUN mkdir -p $CATALINA_HOME/logs just to make sure that the logs folder exists for tomcat to write to.
P.P.S.: the java base image is actually using openjdk instead of the oracle one. Just thought I'd point it out
You should check tomcat logging settings. The default logging.properties in the JRE specifies a ConsoleHandler that routes logging to System.err. The default conf/logging.properties in Apache Tomcat also adds several FileHandlers that write to files.
Example logging.properties file to be placed in $CATALINA_BASE/conf:
handlers = 1catalina.org.apache.juli.FileHandler, \
2localhost.org.apache.juli.FileHandler, \
3manager.org.apache.juli.FileHandler, \
java.util.logging.ConsoleHandler
.handlers = 1catalina.org.apache.juli.FileHandler, java.util.logging.ConsoleHandler
############################################################
# Handler specific properties.
# Describes specific configuration info for Handlers.
############################################################
1catalina.org.apache.juli.FileHandler.level = FINE
1catalina.org.apache.juli.FileHandler.directory = ${catalina.base}/logs
1catalina.org.apache.juli.FileHandler.prefix = catalina.
2localhost.org.apache.juli.FileHandler.level = FINE
2localhost.org.apache.juli.FileHandler.directory = ${catalina.base}/logs
2localhost.org.apache.juli.FileHandler.prefix = localhost.
3manager.org.apache.juli.FileHandler.level = FINE
3manager.org.apache.juli.FileHandler.directory = ${catalina.base}/logs
3manager.org.apache.juli.FileHandler.prefix = manager.
3manager.org.apache.juli.FileHandler.bufferSize = 16384
java.util.logging.ConsoleHandler.level = FINE
java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
############################################################
# Facility specific properties.
# Provides extra control for each logger.
############################################################
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].level = INFO
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].handlers = \
2localhost.org.apache.juli.FileHandler
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/manager].level = INFO
org.apache.catalina.core.ContainerBase.[Catalina].[localhost].[/manager].handlers = \
3manager.org.apache.juli.FileHandler
# For example, set the org.apache.catalina.util.LifecycleBase logger to log
# each component that extends LifecycleBase changing state:
#org.apache.catalina.util.LifecycleBase.level = FINE
Example logging.properties for the servlet-examples web application to be placed in WEB-INF/classes inside the web application:
handlers = org.apache.juli.FileHandler, java.util.logging.ConsoleHandler
############################################################
# Handler specific properties.
# Describes specific configuration info for Handlers.
############################################################
org.apache.juli.FileHandler.level = FINE
org.apache.juli.FileHandler.directory = ${catalina.base}/logs
org.apache.juli.FileHandler.prefix = servlet-examples.
java.util.logging.ConsoleHandler.level = FINE
java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
More info at https://tomcat.apache.org/tomcat-6.0-doc/logging.html
we can not see the logs in Docker container until unless we mount it.
To build the Dockerfile:-
docker build -t tomcat
To run the Dockerfile Image:-
docker run -p 8080:8080 tomcat
To copy the logs of tomcat present in docker container to mounted container :-
Run this cmd to mount the container:
1stpath : 2ndpath
docker run \\-d \\-p 8085:8085 \\-v /usr/local/tomcat/logs:/usr/local/tomcat/logs \tomcat
or simply
docker run \\-d \\-v /usr/local/tomcat/logs:/usr/local/tomcat/logs \tomcat
1st:-/usr/local/tomcat/logs: path of root dir: where we want to copy
the logs or destination
2nd:- /usr/local/tomcat/logs: path of tomcat/logs folder present in
docker container
tomcat:-name of image
need to change the port if it is busy
now the container is get mount
to get the list of container run : docker ps -a
now get the container id of latest created container:
docker exec -it < mycontainer > bash
then we can see the logs by
cd /usr/local/tomcat/logs
usr/local/tomcat/logs# less Log Name Here
this to Copy any folder in docker container on root:-
docker cp <containerId>:/file/path/within/container /host/path/target