Installation issues that need fixing about scib-pipeline HOT 10 CLOSED

@mumichae happy to support if needed

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@mumichae I will take a look at the README, maybe you could take a look at the first 2 steps

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@mumichae
The below also causes issue for me:

(base) [karin.hrovatin@icb-lisa scib-pipeline]$ pwd
/storage/groups/ml01/code/karin.hrovatin/scib-pipeline
(base) [karin.hrovatin@icb-lisa scib-pipeline]$ . envs/set_vars.sh $HOME/miniconda3/envs/scib-pipeline
dirname: invalid option -- 'b'
Try 'dirname --help' for more information.
cp activate_env_vars.sh /home/icb/karin.hrovatin/miniconda3/envs/scib-pipeline/etc/conda/activate.d/env_vars.sh
cp: cannot stat '/env_vars_activate.sh': No such file or directory
cp deactivate_env_vars.sh /home/icb/karin.hrovatin/miniconda3/envs/scib-pipeline/etc/conda/deactivate.d/env_vars.sh
cp: cannot stat '/env_vars_deactivate.sh': No such file or directory

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@Hrovatin Are you using shell or bash? Maybe try with

bash envs/set_vars.sh $HOME/miniconda3/envs/scib-pipeline

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That worked, thanks.

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libgcc-ng is not a package for macOS so must be removed if using macOS

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Which environment is that from?

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@LuckyMD I just checked the code and calling Seurat via rpy2 is something that is only done in the scib package. Are points 1 and 2 also something you want reflected in the scib package?

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Yes, i think that would be useful.

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rpy2 library loading checking is addressed in scib and all other suggestions have been applied in #20

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