Amplicon and Shotgun Distro Note

Thanks for the great distros!

I have BLAST+ 2.15.0 configured on my Linux system $PATH. When I install the qiime2 amplicon or shotgun distros with mamba I get a shared PATH error, however the installations work well with conda.

The problem to be solved now is getting both these distro conda installations to reference my system Blast+2.15.0 instead of the version 2.14.0, as I assume are part of the distros.

Conda base and qiime2 Tiny are fine but amplicon and shotgun do not respect my system blast installation.

Hello @propolis,

When I install the qiime2 amplicon or shotgun distros with mamba I get a shared PATH error, however the installations work well with conda.

Could you provide a screenshot or copy-paste of this error?

Conda base and qiime2 Tiny are fine but amplicon and shotgun do not respect my system blast installation.

When you activate a conda environment it prepends things to your path and in the case of the amplicon or shotgun distros which include blast as a dependency you end up with their version of blast taking precedence. You can try to install the version you want in the environment you want it in. So, e.g. with your environment activated run conda install blast=2.15.0. However, there is no guarantee this will work because there may be dependency conflicts.

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Thanks for the reply. Conda only installs blast-2.14.1 however I have solved the problem and all of the conda qiime2 environments see my system blast-2.15.0 now.
conda uninstall —force-remove blast
This removes just the single package blast where as if conda uninstall is used it well remove two additional dependencies which need to be kept.

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I have also discovered that if you run conda env remove -n shotgun or amplicon and then try to create these environments again they will fail with shared path errors. The workaround is conda clean —all then recreating either of these two works fine.

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