building the .sif file

[humanpaingeneticslab]

Dear Oleksandr,

I've cloned the rep, then tried to build the .sif file. Any help appreciated!

Unfortunately, I get an error:

10 58.88 Building dependency tree...

10 59.41 Reading state information...

10 59.51 E: Version '1:2.25.1-1ubuntu3.12' for 'git' was not found

10 59.52 update-alternatives: error: alternative path /usr/bin/python3 doesn't exist

==>> It's probably chocking @ "#10 59.51"...?

$ ls -al /usr/bin/python3 lrwxrwxrwx 1 root root 9 Oct 27 2020 /usr/bin/python3 -> python3.8 $ uname -a Linux X-X-X 5.15.0-107-generic #117~20.04.1-Ubuntu

I found this other rep here: https://github.com/comorment/mixer From which I cloned, and found the mixer.sif file to work (the one distributed in the rep)! BUT, that version of mixer doesn't implement some functions; e.g.: mixer.py: error: invalid choice: 'split_sumstats'

Interesting, so there's two parallel versions of mixer?

Many Thanks!

[espenhgn]

Hi @humanpaingeneticslab, This repository contains the material for GSA-Mixer which was recently published: https://www.nature.com/articles/s41588-024-01771-1

If this is what you want, then you can omit to build the Docker or Singularity image locally, but fetch them from https://github.com/orgs/precimed/packages?repo_name=gsa-mixer

It looks like @ofrei didn't update the documentation for this in this repository. You may look at the similar procedure in the old MiXeR container repository here and update URLs accordingly.

If you are inclined to rebuild either way; apt packages such as git are version-pinned and may sometimes need updating to whatever is current at packages.ubuntu.com

As for the MiXeR development tree, yes, there are indeed multiple parallel projects in different tracks in this GitHub organization; uni/bivariate MiXeR, trivariate MiXeR, MiXeR-pred

[humanpaingeneticslab]

Thank you @espenhgn for your prompt response!

I followed the instructions there, but alas:

$ docker pull ghcr.io/precimed/gsa-mixer_sif:latest unsupported media type application/vnd.oci.empty.v1+json

$ singularity pull docker://ghcr.io/precimed/gsa-mixer_sif:latest FATAL: While making image from oci registry: error fetching image to cache: while building SIF from layers: packer failed to pack: while unpacking tmpfs: error unpacking rootfs: unpack rootfs: config blob is not correct mediatype application/vnd.oci.image.config.v1+json: application/vnd.oci.empty.v1+json

I think I can get it from here: https://github.com/norment/ofrei_repo/blob/main/2024_01_06/mixer.sif YES, this one seems to work on the tutorial...

[espenhgn]

Hi again, @humanpaingeneticslab, Unfortunately, we cannot seem to update the GHCR.io autogenerated pulling instructions. For the "_sif" suffix package you need the Oras client, as explained in the other instructions I linked to. Either should work (replace <tag> with latest or some other tag):

apptainer pull docker://ghcr.io/comorment/gsa-mixer:<tag>  # or
singularity pull docker://ghcr.io/comorment/gsa-mixer:<tag> # or 
oras pull ghcr.io/comorment/gsa-mixer_sif:<tag>

Practically, these are likely similar to the mixer.sif file you obtained, however.

[ofrei]

@humanpaingeneticslab sorry for my slow response on this! I now fixed Docker and singulrity builds (this was the fix), and updated the README file with instructions on how to pull Docker and Singularity versions of the GSA-MiXeR. Using the latest images (I've tested both Docker and Singularity) I tested the instructions from Getting Started Example the README.md, and they run without errors. I'll possibly need to make some small changes to make real-world example run smoothly. I'll get back on this in #5 . Thanks for submitting the tickets!

I'm closing this one as building Docker / singulartiy images should be working fine at this point.