Don't install metawrap via metawrap-mg

[yqy6611]

This is a suggestion.

metawrap-mg is totally outdated. Moreover, all of dependencies can actually work with python 3 without revising module scripts of metawrap.

Prepare a cleaner conda environment with python 3 and manually install those dependencies except for prokka and salmon can solve majority problems. For prokka and salmon, prepare separate environments for each of them and redirect the locations in scripts.

For some small auxiliary python 2 scripts we can prepare another python 2 environment and redirect python interpreter in those scripts. Of course it will be better if you can revise those scripts using python 3.

[bachelot34]

When you say do not use metawrap-mg, are you saying we should follow this step described in the installation document:

Note: ordering is important

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
conda config --add channels ursky

conda install biopython blas=2.5 blast=2.6.0 bmtagger bowtie2 bwa checkm-genome fastqc kraken=1.1 krona=2.7 matplotlib maxbin2 megahit metabat2 pandas quast r-ggplot2 r-recommended samtools=1.9 seaborn spades trim-galore

and then add prokka and salmon afterwards?

Thank you

[yqy6611]

When you say do not use metawrap-mg, are you saying we should follow this step described in the installation document:

Note: ordering is important

conda config --add channels defaults

conda config --add channels conda-forge

conda config --add channels bioconda

conda config --add channels ursky

conda install biopython blas=2.5 blast=2.6.0 bmtagger bowtie2 bwa checkm-genome fastqc kraken=1.1 krona=2.7 matplotlib maxbin2 megahit metabat2 pandas quast r-ggplot2 r-recommended samtools=1.9 seaborn spades trim-galore

and then add prokka and salmon afterwards?

Thank you

Yes and no need to add ursky channel. And don't add spades 4.0.0 in this environment due to compatibility issues. If you really hope to use it, install it in a separate environment like prokka and salmon.

[bachelot34]

Thank you! When you say I will have to adapt the scripts after creating new environments for salmon and prokka, which scripts are you referring to? Some of the metawrap scripts, or my own scripts?