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Saskia-Oosterbroek / decona

fastq to polished sequenses: pipeline suitable for mixed samples and long (Nanopore) reads
MIT License
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Can't find decona command/ installation issue #21

Closed juanboja closed 2 years ago

juanboja commented 2 years ago

Hi Saskai,

I have installed decona on a linux machine with Ubuntu using Conda 4.11 following the detailed instructions. However, after activating deconda environment the following error message appears when I run the command decona -d -l 800 -m 1200 -q 10 -c 0.80 -n 100 -M :

decona: command not found

I am sure I must be missing something and any advice would be greatly appreciated.

Thanks,

Julio

Saskia-Oosterbroek commented 2 years ago

Hi Julio,

There might be an issue with the installer file, which I don't think includes conda 4.11. You can try copying the files from the .tar file yourself (which is basically what the installer script does). When you extract the tar file you should end up with a few folders amongst which a decona/bin/ folder. The files in that folder should be moved to your conda environment bin/.

You can run conda env list to find out where your Decona environment is located. Usually something like: /home/user/conda/envs/decona. There you should also be able to find your bin: /home/user/conda/envs/decona/bin.

Copying them should be straight forward: cp location_of_unpacked_tar/decona/bin/* /home/user/conda/envs/decona/bin

Let me know it this works, Saskia

juanboja commented 2 years ago

Thank you Saskia, it worked! I can use decona now.