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oschwengers / asap

A scalable bacterial genome assembly, annotation and analysis pipeline
https://doi.org/10.1371/journal.pcbi.1007134
GNU General Public License v3.0
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how to avoid sudo privileges while using the docker container? #7

Closed MostafaYA closed 4 years ago

MostafaYA commented 4 years ago

Hi Oliver, a bit silly question, how to avoid sudo privileges while using the docker container? I am on contos 7 and do not have sudo rights.
thanks,

oschwengers commented 4 years ago

Hi @MostafaYA , not a silly question at all! TL;DR It's currently not possible. You could try Podman or Singularity but I haven't tried them yet and unfortunately have no experience to guide you through this.

Of course, you always need proper sudo permissions to start a Docker container. As some users asked if it's possible to have the result files have user affiliations instead of root I changed the asap-docker.sh script in a way, that you should execute it without sudo, so it can automatically extract your user name/group and pass this information into the Docker container. To execute the container, the script will then prompt for sudo permissions just before the container execution. I hope this helps. Maybe you could ask your admin to provide you with a VM so you could execute ASA³P as sudo?

Best regards!

jp589 commented 1 week ago

Hello @MostafaYA and @oschwengers,

Perhaps I am a bit late to the party, but I only recently discovered the ASA3P pipeline. I also ran into this same issue because I wanted to run this pipeline on my university's HPC grid, but I don't have root privileges there.

I recently built a Singularity image for the pipeline based on the ASA3P pipeline Dockerfile and made some modifications to several of the pipeline files in order to make the the pipeline run inside a single container. The pipeline successfully ran the example files as well as some of my own files.

If you or anyone reading this is interested in the singularity image, please visit https://github.com/jp589/ASA3P_Singularity/ for files and instructions on how to build the image and update the appropriate files.