medaka command and medaka_consensus errors

[eprileson]

Hi, I am having issues running the basic medaka_consensus command on Linux environment (no GPU)

I installed the latest version of medaka v1.7.2 following the GitHub source instructions: git clone https://github.com/nanoporetech/medaka.git cd medaka make install . ./venv/bin/activate

which installed successfully I believe as all directories installed in my directories match those from the GitHub directories. However, when I try to run the medaka_consensus program: medaka_consensus -i ${BASECALLS} -d ${DRAFT} -o ${OUTDIR} -t ${NPROC} -m r941_min_high_g303 it gives the same error each time: /home/egp43/medaka/scripts/medaka_consensus: line 12: medaka: command not found On the medaka_consensus script at line 12, the command throwing the error is the (medaka --version) command.

It seems like there is a general issue with either installation or missing packages that I'm not aware of as the same error is thrown trying to run any medaka command on the command line, eg. medaka -h This is despite the medaka environment being activated.

Any help towards this would be appreciated! Thanks,

[cjw85]

Hi @eprileson,

Is there a particular reason you want to compile and use the code from source. The preferred method is to use simply the packages from PyPI.

[eprileson]

Hi @cjw85, thanks for your reply; The reason we want to use the code from source is that we're using a MacOS system and receive the error:

error: subprocess-exited-with-error

and so we decided to use the GitHub source

[eprileson]

Following up on this, the same error occurred with the packages installed from PyPI:

medaka_consensus: line 12: medaka: command not found

[cjw85]

Can you provide detailed of you OS and environment setup and describe precisely what you have done to install medaka to lead to this error?

[eprileson]

I am running a Markov interactive desktop (Xfce) through our University's HPC ondemand portal with a Linux system. I installed the latest version of medaka v1.7.2 following the pip install instructions:

virtualenv medaka --python=python3 --prompt "(medaka) "
. medaka/bin/activate
pip install medaka

which installed the software successfully I believe. However, when I try to run the medaka_consensus program:

medaka_consensus -i ${BASECALLS} -d ${DRAFT} -o ${OUTDIR} -t ${NPROC} -m r941_min_high_g303

it gives the same error from before: /home/egp43/medaka/scripts/medaka_consensus: line 12: medaka: command not found On the medaka_consensus script at line 12, the command throwing the error is the (medaka --version) command.

[cjw85]

I apologise for the lack of reply here.

However I don't know that I have much more to add. It strange that medaka_consensus is on your PATH but not medaka. They are both installed into the virtual environment together. Can you run medaka directly?