Qiime2 2023.9 Amplicon Rescript Issue


I have been trying to install rescript in the latest version of Qiime2 2023.9 amplicon version, and I am having trouble with the rescript plugin install within my conda environment. I have used this plugin for training classifiers in old versions of Qiime2 with no issues, but am getting the following errors in the new version related to the q2-types-genomics dependency.

Input code from within active conda environment:

conda install -c conda-forge -c bioconda -c qiime2
-c https ://packages.qiime2.org/qiime2/2023.9/amplicon/released/linux-64
-c defaults xmltodict 'q2-types-genomics>2023.5' ncbi-datasets-pylib

Output error:

PackagesNotFoundError: The following packages are not available from current channels:

  • q2-types-genomics[version='>2023.5']

I have also tried installing the dependencies using mamba, and the only trouble I have is installing the q2-types-genomics


mamba install -c conda-forge -c bioconda -c qiime2
-c released/linux-64
-c defaults xmltodict 'q2-types-genomics>2023.5' ncbi-datasets-pylib

Output error:

Could not solve for environment specs
Encountered problems while solving:

  • nothing provides requested q2-types-genomics >2023.5

Hi @lmjackson,

We are planning on adding rescript to the QIIME 2 Amplicon distribution (hopefully in our upcoming release), but currently only have rescript available within the QIIME 2 Shotgun distribution. There are some dependency conflicts with rescript and q2-types-genomics, which (long story short) is why it's only available in the Shotgun distribution right now.

What I'd recommend doing is installing both distributions from our latest releases (i.e. QIIME 2 2023.9 for both Amplicon and Shotgun) and swapping between environments as needed for your analysis. You may even be able to get away with just using the Shotgun distribution, depending on what actions are needed for your analysis. Here are all of the plugins available within the Shotgun distribution:

  • q2-assembly
  • q2-cutadapt
  • q2-demux
  • q2-diversity
  • q2-diversity-lib
  • q2-emperor
  • q2-feature-classifier
  • q2-feature-table
  • q2-metadata
  • q2-moshpit
  • q2-quality-control
  • q2-quality-filter
  • q2-sample-classifier
  • q2-sapienns
  • q2-taxa
  • q2-types
  • q2-types-genomics
  • rescript

I hope this helps! Cheers :lizard:

1 Like

Just to add to this, if you have both environments installed and mainly running amplicon workflows you can pre-pend conda run -n qiime2-shotgun-2023.9 to the rescript command to save the hassle of swapping to the shotgun environment to run rescript.


You can follow the instructions here: