search

ohmeta / metapi

A general metagenomics data mining system focus on robust microbiome research
https://ohmeta.github.io
GNU General Public License v3.0
56 stars 17 forks source link

Need to install those software before running? #40

Closed wangjiaxuan666 closed 2 years ago

wangjiaxuan666 commented 2 years ago

Thank you for providing such good software which can analysis the meta workflow.

when I run 

metapi mag_wf all --use-conda --run-local

and I get the config.yml

Before I run the workflow ,need I download those software which in requirement? and export to the env path?

alienzj commented 2 years ago

Thanks for reporting this issues.

Most of rules in metapi have been configured using conda env. But there are still some software not yet. In the near future, I will update all to use conda env.

Currently, For conda env part, you can run:

metapi mag_wf all --use-conda --cores 8 --conda-create-envs-only # only create envrionments
# or 
metapi mag_wf all --use-conda --cores 8 --run-local # create environments and run it

then snakeamke will call mamba to create environment automatically. After setup the environment, snakemake will activate it and run the specific cmd declared in the metapi rule. Don't worry about the environment, when you run metapi again, sankemake will find it. If the envs file updated, snakemake will create environment again.

For non conda env part, maybe you should install some softwares if it hasn't been installed yet.

mamba install fastp bwa bowtie2 megahit spades multiqc fastqc seqkit samtools

Hope it can help you.

alienzj commented 2 years ago

Dear @wangjiaxuan666, Now, https://github.com/ohmeta/metapi/releases/tag/v2.3.0 support running metapi without installing any software manually, just run it with parameter --use-conda.