How to use ImmClassifier on the remote linux system？

[GuohuaZhu]

Thanks for your good algorithm on the lymphocytes classifier. Howerver，when I attempt to install the package on my remotes Linux, I can't get a 'docker', while 'singularity' instead. And further, while I attempt to acquire an image from the docker website ( https://hub.docker.com/search?q=ImmClassifier&type=image) and used it through 'singularity', the 404 error was reported. Could you help me with this question? Thanks a lot.

[xliu-uth]

Hi,

The 404 error is likely due to the IT issues. You can build it locally instead of pulling from the website.
git clone https://github.com/xliu-uth/ImmClassifier.git
cd ImmClassifier
docker build . -t imm-classifier

[GuohuaZhu]

Hi,

The 404 error is likely due to the IT issues. You can build it locally instead of pulling from the website. git clone https://github.com/xliu-uth/ImmClassifier.git cd ImmClassifier docker build . -t imm-classifier

Thanks for your timely answer. when I ran docker build . -t immclassifier at the dir (cellassign) PS E:\ImmClassifier> on my anaconda3 shell.
The error was reported
error during connect: This error may indicate that the docker daemon is not running.: Post "http://%2F%2F.%2Fpipe%2Fdocker_engine/v1.24/build?buildargs=%7B%7D&cachefrom=%5B%5D&cgroupparent=&cpuperiod=0&cpuquota=0&cpusetcpus=&cpusetmems=&cpushares=0&dockerfile=Dockerfile&labels=%7B%7D&memory=0&memswap=0&networkmode=default&rm=1&shmsize=0&t=imm-classifier&target=&ulimits=null&version=1": open //./pipe/docker_engine: The system cannot find the file specified.

Perhaps my docker was not correctly installed.

[xliu-uth]

It looks like the docker has not started yet.

[GuohuaZhu]

It was my first to use the docker. I had search the error report online, and tried the methods that the others provided. However, it didn’t work. I should learn more about the docker for accessing to the 'ImmClassfier' package.

[jefftc]

What kind of errors are you seeing with Docker? Do you see this with other containers, or just this one? Jeff

…

On Dec 8, 2021, at 9:21 PM, GuohuaZhu ***@***.***> wrote: It was my first to use the docker. I had search the error report online, and tried the methods that the others provided. However, it didn’t work. I should learn more about the docker for accessing to the 'ImmClassfier' package. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

[XYZuo]

Hi,
I'm also trying to use the package on my remotes Linux (centos 7), but I have no root privileges.
Is there any way to install ImmClassifier without using a docker container? Thanks.

[xliu-uth]

Hi Dr. Zuo,

There are a few ways to get around:

1. Docker supports Non-root user. Here's an example, https://www.tutorialspoint.com/running-docker-container-as-a-non-root-user.
2. Use singularity instead docker.
3. Use a local computer instead.

Please let me know if you have any question.

Xuan