Unable to use conda to install software or update itself?

Question

I am trying to use conda to install some bioinformatic software such as cufflinks:

conda install -c bioconda cufflinks

But I get this error:

Error: Invalid index file: r/linux-64/repodata.json.bz2

And it is the same error for any command using conda, somebody knows how to fix it? it looks like I have to uninstall everything and start from cero.

Answer 1

Bioconda requires the conda package manager.

If we have Anaconda installation, by default it is already available in it.

For Bioconda, Python 3 version is recommended.

We need to add the bioconda channel as well as the other channels bioconda depends on.

as

conda config --add channels defaults

conda config --add channels conda-forge

conda config --add channels bioconda

Now try installing

       conda install -c bioconda cufflinks

Installation will get completed successfully.

Reference : https://bioconda.github.io/