On 18/07/2021 14:19, Beatrice Torracca wrote:
[...] Is the qiime installation via bioconda going to clash with the qiime from the Debian testing repository I installed via apt?
Hi, Beatrice.No, Bioconda provides a separate isolated environment in which to run QIIME. The advantage is that you can still use APT-managed packages from within a Bioconda environment, but anything you install within Bioconda is stored separately to the APT-managed packages and accessed using a PATH that prioritises Bioconda versions over APT-managed versions.
In a very real sense, you get the best of both worlds. However, there is one catch: Don't allow the "miniconda" bootstrap to 'initialise' your shell or it *will* conflict with APT-managed packages by prioritising Bioconda versions over Ubuntu/Debian-Med versions. You can solve this by using my Bioconda 'wrapper'.
HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis@minke-informatics.co.uk
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