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nanoporetech / dorado

Oxford Nanopore's Basecaller
https://nanoporetech.com/
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Issue installing Dorado #895

Closed Narmatha99 closed 3 months ago

Narmatha99 commented 3 months ago

I tried to install Dorado through homebrew on the terminal of the Mac Pro. However I have run into some problems. I started by installing homebrew and installing dependencies (brew install cmake and brew install hdf5). Then I cloned the Dorado repository: git clone https://github.com/nanoporetech/dorado.git > cd dorado. Afterwards I created a virtual environment: python3 -m venv dorado_env > source dorado_env/bin/activate. I tried installing python dependencies by using the following command: pip install -r requirements.txt but I got an error for this:

Screenshot python dependencies error

I continued by trying to install the dependencies through the following command: python -m pip install SomePackage.

Then I continued by building Dorado as followed: mkdir build > cd build > cmake.. This is where I run into trouble because I get the following error:

Screenshot error build Dorado

I hope it is clear what I did (I am new to this so I must have made a mistake). Thanks in advance for any advice

susie-ont commented 3 months ago

Hi @Narmatha99, is there a reason you want to build Dorado yourself? We have prebuilt binaries available here with instructions to install: https://github.com/nanoporetech/dorado?tab=readme-ov-file#installation

Narmatha99 commented 3 months ago

Hi @susie-ont, I tried to do that. I downloaded the installer voor mac os and unzipped this (in the download map where it is placed automatically) but I then struggle with the following command that is given in the instruction manual: $ /path/to/dorado-x.y.z-linux-x64/bin/dorado basecaller hac pod5s/ > calls.bam. I am not too sure how to use this in the terminal? If you could explain it to me that would help me a lot! The method I described is one chatGPT has given me.

susie-ont commented 3 months ago

Hi @Narmatha99, you will need to replace /path/to/dorado-x.y.z-linux-x64/bin/dorado with the path to the download on your machine.

So if dorado-0.7.2-osx-arm64 has been unzipped in your Downloads folder, you can access Dorado by entering the following in the terminal: ~/Downloads/dorado-0.7.2-osx-arm64/bin/dorado

& your commands will look like this: ~/Downloads/dorado-0.7.2-osx-arm64/bin/dorado basecaller hac pod5s/ > calls.bam Note in the above example you will need to replace pod5s/ with the path to the directory or file that you wish to basecall.

Narmatha99 commented 3 months ago

Oh wow, it was that simple then. Thank you very much @susie-ont!