zktuong/dandelion

Installation error using Singularity: FATAL: While getting image info: error decoding image: invalid ObjectId in JSON

hoonghim opened this issue · 1 comments

hoonghim commented

Description of the question

Dear Dr. Tuong,

Hello, thank you for pvoviding your wonderful scVDJ-seq analysis tool, Dandelion.

I have trouble installing Dandelion using Singularity.

I am working on the server in mylab and here is the information of the server and Singularity.

$ singularity --version
singularity version 3.2.0-1

$ cat /etc/os-release

PRETTY_NAME="Ubuntu 22.04.1 LTS"`
NAME="Ubuntu"`
VERSION_ID="22.04"
VERSION="22.04.1 LTS (Jammy Jellyfish)"
VERSION_CODENAME=jammy
ID=ubuntu
ID_LIKE=debian

I had no problems installing scanpy, graph-tool and sc-dandelion using conda and pip.

I was unable to update Singularity because this was installed in our server and used by other lab members.

Minimal example

singularity pull library://kt16/default/sc-dandelion:latest

Any error message produced by the code above

FATAL:   While getting image info: error decoding image: invalid ObjectId in JSON: "kt16/default/sc-dandelion:sha256.afdaf7ca5a9183a771ae3030542b6d57b846d5db8087c158e03ef0e2eb133c81"

OS information

Ubuntu 22.04.1 LTS

Version information

ddl.logging.print_versions()
dandelion==0.3.2 pandas==2.0.2 numpy==1.24.3 matplotlib==3.7.1 networkx==3.1 scipy==1.5.3

Additional context

If there is a guideline to follow the tutorial without Singularity, or solution to solve the above issue, it would be very helpful to my research.

Sincerely,

Seunghoon

zktuong commented

hi @hoonghim, thank you for the interest in dandelion.

I think your singularity version is too old. the image was build using v3.6.1 and i suspect between v3.2.0-1 to v.3.6.1, there could be some differences in how singularity may be trying to download the image.

Simply providing you the current image as a stand alone file won't likely work as i recall trying it with someone else. Seems like an an older singularity can't handle a new image but i'm happy to give it a try. send me an email at z.tuong@uq.edu.au and i'll send you a link to download the image manually.

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