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marcos-diazg / musica

MuSiCa - Mutational Signatures in Cancer
https://www.clinicbarcelona.org/en/idibaps/research-areas/liver-digestive-system-and-metabolism/genetic-predisposition-to-gastrointestinal-cancer/tools
MIT License
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musica_env.yml for conda environmet seems to be Mac specific #42

Closed janrehker closed 3 years ago

janrehker commented 3 years ago

Hi,

Could not install musica on my Ubuntu machine due to dependency issues. While changing the entries in musica_env.yml to linux-x64 seemed to resolve al lot of it, some still remain. Is it possible, those packages are MacOS specific?

Best, Jan

marcos-diazg commented 3 years ago

Hi Jan,

So sorry for my late reply. I agree that it's entirely possible that some packages in the musica_env.yml file are macOS-specific, sorry about this. Were you finally able to install the tool? If not, please send me your conda error message and I'll have a look into it.

Thanks so much for your interest!

janrehker commented 3 years ago

Hi Marcos,

Thanks for your reply. Unfortunately I have not solved the issues yet:

Here is my error message:

`conda env create -f musica_env.yml Collecting package metadata (repodata.json): done Solving environment: failed

ResolvePackageNotFound:

Tried to exchange some of the packages but without success.

Best, Jan

marcos-diazg commented 3 years ago

Hi Jan,

Thanks for your interest. Not sure which version of macOS you are using. I'm using macOS Big Sur v11.5.1 with Xcode installed and I was able to install the environment from the yml file without issues.

Anyway, I prepared a setup script specific for macOS. You can follow the instructions in the new README, just running source musica_setup_macos.sh you should be able to install the required environment for MuSiCa.

Please let me know if you have any further issues with the tool. You can also contact me anytime by email at mdiazgay@ucsd.edu. Thanks again!

Best wishes,

Marcos

janrehker commented 3 years ago

Hi Marcos,

Sorry for the misunderstanding. It's the other way around. I am actually on a Ubuntu 20.04 machine and have no access to a Mac. This is probably the reason, packages like gfortran_impl_osx-64==7.3.0=hf4212f2_2 or cctools_osx-64==949.0.1=h5ba7a2e_1 won't install.

So what I would need, would be alternatives for those packages, if possible.

marcos-diazg commented 3 years ago

Hey Jan,

Sorry for my misunderstanding, I read it the other way around. Anyway, I would recommend you to try the same script I prepared for macOS since it is not as specific as before. It should also work on a Ubuntu machine. Let me know if you find any issues and I'll try to find a Ubuntu machine to work on this. Thanks!

marcos-diazg commented 3 years ago

Hi again,

I have just tried on a Ubuntu machine and it works correctly, so the setup script is valid for both macOS and Ubuntu. Please follow the new installation instructions in the updated README file and that should solve your issue. Please let me know if that is not the case. Thanks again for letting me know about this!

janrehker commented 3 years ago

Now it works on my Ubuntu machine and it installed on a remote CentOS 8 (not tested yet for functionality on the latter). Thanks for this nice piece of software by the way!

Best regards, Jan

marcos-diazg commented 3 years ago

Thank you for your interest! Happy to help.

Best regards,

Marcos

janrehker commented 3 years ago

Just tested the installation on CentOS 8 and had to install a few more packages to really get it to work. Functionality was there after the first two, I needed pandoc to store output as pdf.

` conda install -c r r-shinysky

conda install -c conda-forge r-v8

conda install -c conda-forge pandoc ` Thanks, Jan

marcos-diazg commented 3 years ago

Thanks!