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Difficulty installing anvio v5 #895
I have anvio v4 installed on my computer, and I tried to install v5 with homebrew, and this is what happened:
I checked to make sure I actually have v4 installed:
And I also checked to make sure I had MCL installed:
I'm not really sure what's going on. Can someone help me fix this?
I was trying to install anvio5 via conda: "conda install -c bioconda -c conda-forge anvio diamond bwa", but the version it installs is anvio4. Specifying anvio=5 also didn't do it. And when I do conda update anvio, also anvio4 it shows as most recent. If I download the source file, and run pip install -r requirements.txt and then python setup.py install, it exits with many errors. Can you help me with this issue?
Yes, I tried, and I get this:
vsc31426@hpc-p-login-2 /vsc-hard-mounts/leuven-data/314/vsc31426/miniconda3/bin 16:55 $ conda install -n anvio5 -c bioconda -c conda-forge anvio=5.1.0 diamond bwa
PackageNotFoundError: Dependency missing in current linux-64 channels:
Close matches found; did you mean one of these?
I now specified explicitly django=2.0.2, which made it work in my case, for an hpc system.
./conda create -y --name anvio5 python=3.6
source activate anvio5
When installing anvio with conda with
it also installed the latest hmmer version which gave the error
when running the self-test.
Downgrading to version 3.1b2 with
solved the problem
Yes, thank you! This ended up working for me (on a Linux VM) too, but I spent a while trying to figure out why anvi'o commands couldn't be found before I saw the 'source activate anvio5' line here. Could this also be included in the installation instructions? :)