CIRIquant.utils.ConfigError: Tool: java need to be specified

[adarsh-pp]

Hi,

I am trying to run CIRIquant using the official biocontainer image:

quay.io/biocontainers/ciriquant:1.1.3--pyhdfd78af_0

I am using the Docker image because I do not have permission to manually install software and dependencies on my university HPC system.

Command used:

docker run -v /storage/st326d:/storage/st326d \
quay.io/biocontainers/ciriquant:1.1.3--pyhdfd78af_0 \
CIRIquant \
-t 16 \
-1 /path_to_file/SRR9623676_1_val_1.fq.gz \
-2 /path_to_file/SRR9623676_2_val_2.fq.gz \
--config /path_to_file/config.yml \
-o /path_to_file/ciriquant/ \
-p SRR9623676 \
--circ SRR9623676_ciri.tsv \
--tool CIRI2

However, I get the following error:

CIRIquant.utils.ConfigError: Tool: java need to be specified

I expected the container image to already include Java and related dependencies.

Questions:

1. Does the config.yml still require explicit paths to tools even when using the official Docker image?
2. If yes, what should be the correct Java path inside the container?
3. Is there an example config.yml specifically for Docker/biocontainer usage?

Thank you.

[Kevinzjy]

Hi @adarsh-pp , the biocontainer image is not maintained by us, so we may not be able to provide reliable support for docker-related issues.

Coud you try installing CIRIquant following the recommended installation instructions here?