I'm fairly new to this, and have been following the tutorial in the Biostar handbook. I've gotten to the section on k-mers, which is actually very relevant to what I want to do (count CAG units in some amplicon data), but I'm having trouble getting jellyfish to work.
https://www.biostarhandbook.com/sequence-kmers.html
It's showing as installed in my 'bioinfo' conda environment
> micromamba list
jellyfish 1.0.3 py310h0e083fb_0 conda-forge
However, when I try to call it I get an error:
$ micromamba activate bioinfo
$ jellyfish count -C -m 10 -s10M KU182908.fa
-bash: jellyfish: command not found
What's going on?
(PS yes I have activated the environment)
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michael.flower.14 •
You have to install the kmer-jellyfish package
micromamba install kmer-jellyfish
Perfect that's sorted it thanks! Why does it need that version out of interest?
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maybe simple question, have you activated the enviroment first?
What is the output of
which jellyfishandwhich micromamba?Would also be useful to know the various conda environment variables
It seems there's no filepath for the jellyfish binary.
You could try
type jellyfishjust to double check, but looks like it might need reinstalling. Was there an error message or similar during installation you could have missed?Someone more familiar with conda envs might know better than me though
Thanks, I've tried removing and reinstalling jellyfish within the bioinfo environment. Still no joy
Did you have a successfull installation? You probably need to look into the messages during installation, maybe there is an error related to some dependencies.
Yes seems fine:
Don't you need the bioconda
jellyfish? You currently have the conda-forgejellyfish.Sounds sensible, how do you do that?
conda install bioconda::jellyfish, see here: https://anaconda.org/bioconda/jellyfishThanks but getting error messages with that: