installing magpy

[mars188]

Hi,

MAGpy seems to be the perfect tool for my metagenomic data analysis but I am unable to even install it. The manual says that after installing conda I should do the following: conda env create -f envs/install.yaml

However, the install.yaml file doesn't contain all the tools needed to run the analysis hence I get the error. My install.yaml file looks like this: `name: magpy_install channels:

• conda-forge
• bioconda
• defaults dependencies:
• snakemake
• mamba`

Another thing that MAGpy/envs folder contains several files basic2.yaml basic3.yaml bioperl.yaml checkm.yaml diamond.yaml ete3.yaml install.yaml MAGpy-2.7.yaml MAGpy-3.5.yaml pfam_scan.yaml phylophlan.yaml prodigal.yaml setup.yaml sourmash.yaml

Should I install all of them? Is it possible to have them together in one file so I could install everything in one run?

Please let me know if I am missing something. Many thanks!

[mw55309]

Hello

Can you tell me what error you get when you run

conda env create -f envs/install.yaml

??

Cheers Mick

[mars188]

When I run conda env create -f envs/install.yaml I don't get any error and environment is created successfully. However, when I activate the environment and run snakemake -rp -s MAGpy --cores 1 --use-conda test it gives the following error: `Building DAG of jobs... Creating conda environment envs/sourmash.yaml... Downloading and installing remote packages. CreateCondaEnvironmentException: Could not create conda environment from /scratch/gencore/ma5877/MAGs/MAGpy/envs/sourmash.yaml: Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Encountered problems while solving:

• package sourmash-4.1.1-hdfd78af_0 requires sourmash-minimal 4.1.1.*, but none of the providers can be installed`

[mw55309]

Just to confirm that the magpy_install and test commands ran to completion for me yesterday with no problems

This may be a problem with your conda setup....