The bioBakery help forum

Conda: How to specify specific kneaddata version with biobakery workflow?

I am trying to conda install a specific version of kneaddata to fit into the conda install of the biobaker_workflow. The current workflow seems to have issues with the kneaddata it defaults to - the current biobakery_workflow issue where kneaddata gives it a --run-trf command that is outdated, so the workflow throws an error and exits the processing.

Here is the code:

conda create -n metagenome 
conda activate metagenome
pip install networkx==1.11
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels biobakery
conda install -c biobakery biobakery_workflows
conda install -c biobakery leveldb 
conda install -c bioconda/label/cf201901 kneaddata

Currently, the final line does not resolve (conda says Solving Environment with no end). Is there another way to download and integrate a specific kneaddata version into the workflow?

Hello, You can specify a package version with conda by including the version in the install command (eg. $ conda install biobakery kneaddata=0.7.0). Alternatively we have released a new version of Kneaddata that includes the --run-trf option so it is backwards compatible with the biobakery workflows. If you run $ pip install kneaddata==0.10.0 you should have a kneaddata version with all the flags required by the version of the workflows you have installed.

Thank you,