I have made singulaty image and run that. it works perfectly because when I look at the container using this command:
singularity shell image_name
I can see the output. so the question is that, how can I copy the files from the container into the local directory?
This will get your image's file in the current working directory:
singularity exec <image path or url> cp <file in container> .
By default your home and current working directory are mounted into the image, so you can copy the desired files directly to either of those directories.
Related
Background
I have a singularity container that was created from a docker image. The docker image has files that are meant to be in the user's home directory (e.g. in $HOME/.files). Because I don't know what the username will be, I put the files in /opt in the container and want to set the user's home to /opt.
I would like to be able to run the container with /opt as the home directory, OR somehow be able to run the container so that the home directory contains the files that already exist within the container
What I have tried:
use the --home flag : This maps a folder on the host as the home directory, rather than a folder in the container.
try overriding the $HOME environment variable with --env HOME=/opt : I get the error Overriding HOME environment variable with SINGULARITYENV_HOME is not permitted
Other questions
this question is related, but interested in mapping the container's home folder to a folder on the host machine
You can use the $HOME shell environment variable when you bind the two directories.
singularity exec -B $HOME:/opt example_container.sif touch /opt/file
Here is the documentation on singularity's bind feature
Fed up with struggling with lib install/dependencies problems, I'm starting working with Singularity.
Though, I'm not sure I understand precisely how it works regarding files management in the sandbox mode (not data, programs).
For example, I designed a very simple definition file that is just a "naked" Debian:
Bootstrap: library
From: debian
%post
apt-get update
I create a sandbox with this to add stuff:
sudo singularity build --sandbox Test/ naked_Debian.def
And I try to install a program. But what I don't understand is that I managed to do it, removed the sandbox directory but I think there are still files that were created during the sandbox life (in /dev, /run, /root, etc.). For example, the program that I cloned from git is now in /root of my local (independently of any container).
From what I understood, everything was in the container and should disappear if I remove the sandbox directory. Otherwise, I'm gonna leave a lot of mess with all the tests? And then I can't port the container from system to another.
If I create any new sandbox directory, the program is already there.
Cheers,
Mathieu
By default, singularity mounts $HOME to the container and uses that path as the working directory for singularity shell / exec. Since you're running the sandbox with sudo, /root is being mounted in and that's where any repos you cloned would end up if you didn't cd to a different directory. /tmp is also automatically mounted in, though that is unlikely to cause an issue since it's just temp files.
You have a few options to avoid files ending up in places you don't expect.
Disable automount of home: singularity shell --no-home ...
The default working directory is now / instead of $HOME and files are created directly in sandbox (as opposed to a mounted in directory)
If you want to get files out of the sandbox, you'll either need to copy to /tmp inside the container, and on the host OS from /tmp to the desired location
Set a different location to use as home: singularity shell --home $PWD ...
This mounts in and uses the current directory as $HOME instead of the user's $HOME on the host OS
Simpler to move files between host OS and container, but still creates files in the host OS
Don't mount system directories at all: singularity shell --contain --workdir /some/dir ...
Directories for /tmp and /var/tmp are created inside /some/dir instead of using /tmp and /var/tmp on the host. $HOME has the same path as the host and is used as the working directory, but it is empty and separate from the host OS
Complete separation from host OS, while still allowing some access between container and OS
Additional details on these options can be found in the documentation.
For snakemakev5.27+
Is there a way to run snakemake with the container directive that points to a local image? E.g. if I store the Docker containers on Dockerhub, and I also have a copy locally, when running snakemake, I don't want the rule to pull a singularity image copy from DockerHub if there already exists the exact copy locally. Makes for faster runs.
Sure, just pass a relative or absolute file path to the directive.
Even though the snakemake manual doesn't explicitly state it, it is possible to use a local singularity image using the containerized directive.
So instead of the example in the link above:
containerized: "docker://username/myworkflow:1.0.0"
You can point to the singularity sif file path (which contains the image)
containerized: "/path/to/myimage.sif"
Make sure you use --use-singularity when running snakemake.
How to build the singularity (sif) image:
You can build the sif image in various ways as described here, bug as for your question, you can build it from a local docker image.
I.e. you can list your local images by docker images and pick one to build the local sif file like so:
SINGULARITY_NOHTTPS=1 singularity build /path/to/myimage.sif docker-daemon://mydockerimage:latest
Note, it doesn't seem to work straight from local docker container, i.e. I would have expected this to work:
containerized: "docker-daemon://scpipe_docker:latest"
... but it didn't as of snakemake version 6.10.0
I use singularity images that do not require any binding of the desired host path, i.e.
singularity exec image.simg IMAGE_COMMAND -i $PWD/input_file -o ./output_dir
simply works like any other command on the "input_file" in my host system, also using relative paths as in "-o".
I'm not comfortable enough with Singularity and its jargon to understand how this is made.
Is a configuration done in singularity.conf?
How is this feature called? (is it "MOUNT HOSTFS"?)
By default, both your home and current directories are mounted/bound into the image for you. You can modify this in singularity.conf. Details on the settings are available in the admin documentation.
The MOUNT HOSTFS in the config is a toggle to automatically mount all host filesystems into the image. MOUNT HOME is the corresponding setting for auto-mounting the user's HOME directory.
You can see which files/directories are currently being mounted by using the --verbose option with your singularity command.
I want to know whether if there is any method to remove the ROOT folder within the tomcat /webapps folder after its being deployed by a Docker image.
The reason that I want to achieve this is that I want to run my .war file as the root. I have already renamed my war file as ROOT.war. But when I run my Docker image with the tomcat base image, a ROOT folder is also created by default within the container's tomcat/webapps folder which doesn't allow me to access my ROOT.war file as the root.
My Dockerfile
# Pull base image
FROM tomcat:8.0.30-jre7
# Copy to images tomcat path
COPY /ROOT.war /usr/local/tomcat/webapps/
Sure. You can just delete the already existing ROOT folder as part of your Dockerfile:
# Pull base image
FROM tomcat:8.0.30-jre7
# Delete existing ROOT folder
RUN rm -rf /usr/local/tomcat/webapps/ROOT
# Copy to images tomcat path
COPY ROOT.war /usr/local/tomcat/webapps/