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biocom-uib / vpf-tools

Virus Protein Family tools
BSD 3-Clause "New" or "Revised" License
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Yaml file not found #32

Open erichy91 opened 1 year ago

erichy91 commented 1 year ago

Hello,

I first ran docker-entrypoint.sh and now I try to run vpf-tools, and I get the following error message :

stack exec -- vpf-class --data-index ../index.yaml -i vMAGs_unique_mod2.fna -o test-classified error loading data file index: YAML exception: Yaml file not found: ../index.yaml

I tried to move the index.yaml and run the command from other directories, but the program still can't recognize the index.yaml.

Thanks for your help.

bielr commented 1 year ago

Hi,

Which instructions are you following? There are none that I know that require you to run docker-entrypoint.sh.

In addition, if you are using the Docker image there's no need to specify --data-index. If not, it looks like you specified the wrong path to index.yaml.

erichy91 commented 1 year ago

Hi,

I ran docker-entrypoint.sh to download the index.yaml file, the vpf_classification folder and the uvigs_scores folder.

I am not using the Docker image, I have installed stack and compiled vpf-tools. I have tried both giving the full path (/path/to/index.yaml) or from the folder I run the command in (../index.yaml) and I always get the same error message.

bielr commented 1 year ago

That shouldn't happen, but also docker-entrypoint.sh is written with the single purpose of being the Docker entrypoint.

I would recommend downloading and extracting the data yourself and then pointing to the yaml file yourself, as the docker-entrypoint.sh script may have polluted the environment or had permission issues when extracting the data files.