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TYMichaelsen / covid19

Bioinformatic pipelines used to assemble SARS-CoV-2 genomes from DK
GNU General Public License v3.0
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Create singularity container for Pentaho BI #16

Open tomersagi opened 4 years ago

tomersagi commented 4 years ago

I want to create a user in the singularity image but do not want to store the password in the .def file for obvious reasons. Should I perhaps create the user without the password and use a public-private keypair to login to it? @KasperSkytte @biocyberman Ideas are welcome.

biocyberman commented 4 years ago

Hi @tomersagi Do you want to use the user for some service? Or how the user will be used?

tomersagi commented 4 years ago

The installation process for pentaho requires a pentaho user to be created to run the service etc. https://help.pentaho.com/Documentation/9.0/Setup/Prepare_your_Linux_environment_for_an_archive_install

KasperSkytte commented 4 years ago

You could pass the -D option to adduser to not assign any password.

tomersagi commented 4 years ago

yeah, that is what I'm doing for now

KasperSkytte commented 4 years ago

Alright. I have never had to add users in a docker image or use any keys/secrets, so I have no experience with it, neither have I tried pentaho. But I guess you could figure it out just as well as me, have a look here. Have you also seen this docker image? Maybe it just works or at least for inspiration.

biocyberman commented 4 years ago

Two ways I think you can try to approach this:

  1. Create custome credentials files and bind them to the container: mkdir credentials touch credentials/{passwd,shadow,group} singularity -B credentails/passwd:/etc/passwd -B credentails/shadow:/etc/shadow -B credentails/group:/etc/group shell <image.sif>. In this way the files can be updated and kept across instances of containers.

  2. Using singularity compose, similar way to docker compose. I haven't tested with singularity, but tried with docker on other server. The idea is to use it to setup variables, users, and orchestrate multiple images. See example for docker. Singularity compose is very similar

tomersagi commented 4 years ago

TBC, will try to use the suggestions above

tomersagi commented 4 years ago

Currently installed in ~/pentaho of my homedir. Configured according to the instructions to connect to a MySQL db. But it is failing to load when accessed at localhost:8080.

Consider https://www.youtube.com/watch?v=SNf2VJjTmd4&list=UUAHejP4v46vrWU-VuAtWeXA&index=28