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2026 server setup

This is not a module that we have previously run, but is a page that contains instructions for installing all of the programs that we use throughout these tutorials. If you do not plan to run all of the tutorials, you can see which environments are needed for each of the tutorials at the top of the page and install only these.

Introduction

If you have not run through the Introduction to the command line then I highly recommend doing this first! This page assumes that you have all knowledge from there already.

We will be creating conda environments that we have used for each of the tutorial sections and installing the necessary programs to these, as well as any necessary databases.

All of these environment installs will follow the format:

  1. Create environment: conda create -y --name env_name
  2. Activate environment: conda activate env_name
  3. Install required programs: conda install -y package1 package2

I recommend creating and changing into a directory called tools. Many of these will not create any folders in here, but if they do then it is nice to keep them together.

mkdir tools
cd tools

A note on databases
If you are on a shared server, you may wish to designate a spot for all databases to go to avoid storing unnecessary duplicates (especially when these may be several hundred GB in size). On our lab servers, this is typically something like /home/shared/MH2/databases/, but this is something to think about if you are setting up your own server.
We will assume that you will change into this folder before downloading any databases within these tutorials.

Note that here we have tried to note which programs you are using each time, but if you use the same workflow for your own analysis then it is really important to cite all of the tools that you use!

Quality control

This environment has:

Create the environment:

conda create -y --name quality_control

Activate the environment:

conda activate quality_control

Install the programs:

conda install -y bioconda::fastqc bioconda::multiqc

Deactivate the environment (optional):

conda deactivate

QIIME2

This environment has:

First set default channel priority within conda:

conda config --set channel_priority flexible
conda clean --all -y

Create the environment and install QIIME2:

conda env create \
  --name rachis-qiime2-2026.7 \
  --file https://raw.githubusercontent.com/qiime2/distributions/refs/heads/dev/2026.7/qiime2/released/rachis-qiime2-linux-64-conda.yml

Activate the environment:

conda activate rachis-qiime2-2026.7

Test environment:

qiime info

If you run into R errors, you may need to run:

mkdir -p $CONDA_PREFIX/etc/conda/activate.d
mkdir -p $CONDA_PREFIX/etc/conda/deactivate.d
echo 'export R_PROFILE_USER=""' > $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh
echo 'export R_ENVIRON_USER=""' >> $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh
echo 'export RENV_CONFIG_SANDBOX=true' >> $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh
echo 'export R_LIBS_SITE=""' >> $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh
echo 'export R_LIBS_USER=""' >> $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh
echo "R_PROFILE_INITIAL=''" >> $CONDA_PREFIX/lib/R/etc/Renviron
echo "R_LIBS_SITE=''" >> $CONDA_PREFIX/lib/R/etc/Renviron

And then close your terminal window. Reopen a new one and run:

conda activate rachis-qiime2-2026.7
qiime info

Only run these last two steps if you got an error when running qiime info!!

Deactivate the environment (optional):

conda deactivate

Kneaddata

This environment has:

  • Kneaddata (and all dependencies)
  • Bowtie2 version 2.5.4 (we have specified this version because the latest version prints an annoying warning message every time it is run)
  • GNU parallel (a program that allows us to run multiple samples at once)

Create the environment:

conda create -y --name kneaddata-0.12.4

Activate the environment:

conda activate kneaddata-0.12.4

Install the programs:

conda install -y bioconda::kneaddata parallel bioconda::bowtie2=2.5.4
conda install -y -c bioconda -c conda-forge perl-parallel-forkmanager

If you’d like to install the default database, you can do that like so:

kneaddata_database --download human_genome bowtie2 human_bt2db

If you’d like to install a custom database (i.e. for a different host organism) then you can see details on doing that here.

Deactivate the environment (optional):

conda deactivate

Kraken

Note that Kraken is a little more complicated as it seems to need the Github installation to ensure that it all works as expected. But we still make a conda environment and activate it:

conda create -y --name kraken-2.17.1
conda activate kraken-2.17.1

Then, make sure you are in your tools directory that you made above and run the following:

git clone https://github.com/DerrickWood/kraken2
cd kraken2
./install_kraken2.sh .

Now, we want to make sure that the programs we need are added to our environment and can be found:

mkdir $CONDA_PREFIX/bin
cp kraken2{,-build,-inspect} $CONDA_PREFIX/bin/

And install the other programs that we will need:

conda install -y bioconda::bracken parallel

For this step, you will want to change into the directory that you have decided your databases will live in. If this isn’t a shared area, then just somewhere that you can remember.

For Kraken 2, it is important to have the largest database that your server can handle. You can see all available Kraken 2 databases here - note that if you choose a different one than I have, you will need to modify these commands.

Change to the directory that your database will live in:

cd database_directory

Standard smallest database:

wget https://genome-idx.s3.amazonaws.com/kraken/k2_standard_08_GB_20260626.tar.gz
mkdir k2_standard_08_GB_20260626
tar -xvf k2_standard_08_GB_20260626.tar.gz -C k2_standard_08_GB_20260626

If you are happy that the database is downloaded correctly, remove the tar file:

rm k2_standard_08_GB_20260626.tar.gz

Standard plus protozoa and fungi:

wget https://genome-idx.s3.amazonaws.com/kraken/k2_pluspf_20260626.tar.gz
mkdir k2_pluspf_20260626
tar -xvf k2_pluspf_20260626.tar.gz -C k2_pluspf_20260626

If you are happy that the database is downloaded correctly, remove the tar file:

rm k2_pluspf_20260626.tar.gz

Deactivate the environment (optional):

conda deactivate

MetaPhlAn

conda create -y --name metaphlan-4.2.6
conda activate metaphlan-4.2.6
conda install -y bioconda::metaphlan bioconda::bowtie2=2.5.4 parallel

Get the database:

metaphlan --install --db_dir metaphlan_databases

If you - like me - need to try to install these in a shared location that you need sudo access to copy to, you can download them as above to an accessible area and then run the following:

sudo cp -r metaphlan_databases/* /home/shared/MH2/databases/metaphlan_databases/

Note that you may need to specify the database location when you are running MetaPhlAn.

Deactivate the environment (optional):

conda deactivate

Anvi’o

This follows the instructions here.

Create and activate the Anvi’o environment:

conda create -y --name anvio-9 python=3.10
conda activate anvio-9

Install some dependencies:

conda install -y -c conda-forge -c bioconda python=3.10 \
        sqlite=3.46 prodigal idba mcl muscle=3.8.1551 famsa hmmer diamond \
        blast megahit spades bowtie2=2.5.4 bwa graphviz "samtools>=1.9" \
        trimal iqtree trnascan-se fasttree vmatch r-base r-tidyverse \
        r-optparse r-stringi r-magrittr bioconductor-qvalue meme ghostscript \
        nodejs=20.12.2 llvmlite numba
        
conda install -y -c bioconda fastani

Note that if fastani doesn’t install properly then this is likely fine.

Now get and install Anvi’o:

curl -L https://github.com/merenlab/anvio/releases/download/v9/anvio-9.tar.gz \
        --output anvio-9.tar.gz
        
pip install anvio-9.tar.gz

Remove the Anvi’o tar file:

rm anvio-9.tar.gz

Download the SCG taxonomy and NCBI COGs (functional information):

anvi-setup-scg-taxonomy
anvi-setup-ncbi-cogs

Install the binners for clustering contigs:

#CONCOCT
cd tools
git clone https://github.com/merenlab/CONCOCT.git

cd CONCOCT
pip install cython
python setup.py build
python setup.py install

#other binners
conda install -y bioconda::metabat2 bioconda::maxbin2 bioconda::das_tool bioconda::binsanity
#conda install -y -c bioconda metabat2
#conda install -y -c bioconda maxbin2
#conda install -y -c bioconda das_tool
#conda install -y -c bioconda binsanity

Install some specific versions of things:

pip install "setuptools<82"
pip install nose
conda install -y -c bioconda -c conda-forge "scikit-learn==1.1.0" usearch diamond

Test Anvi’o:

anvi-self-test --suite mini --no-interactive

#pip install gffutils - unused

Install a couple of other packages that we will use:

conda install -y -c bioconda gotree
conda install -y parallel

Deactivate the environment (optional):

conda deactivate

Checkm2

Create and activate the environment:

conda create -y --name checkm2-1.1.0
conda activate checkm2-1.1.0

Install CheckM2:

conda install -y bioconda::checkm2

Install the CheckM2 database:

checkm2 database --download --path .

Check that it is working:

checkm2 testrun

Deactivate the environment (optional):

conda deactivate

GTDB-tk

Create and activate the environment:

conda create -y --name gtdbtk-2.7.2
conda activate gtdbtk-2.7.2

Install CheckM2:

conda install -y -c conda-forge -c bioconda gtdbtk=2.7.2

Deactivate the environment (optional):

conda deactivate

GeCoCheck

Download GeCoCheck:

wget https://github.com/R-Wright-1/GeCoCheck/archive/refs/tags/v1.0.1.tar.gz
tar -xvf v1.0.1.tar.gz
cd GeCoCheck-1.0.1

Make the environment and install:

conda env create -f coveragechecker-env.yaml
conda activate GeCoCheck-v1.0.1
pip install --editable .

Deactivate the environment (optional):

conda deactivate

PICRUSt2

Download the package:

wget https://github.com/picrust/picrust2/archive/v2.6.3.tar.gz
tar xvzf  v2.6.3.tar.gz
cd picrust2-2.6.3/

I then modified the picrust2-env.yaml file so that the environment would be called picrust2-v2.6.3 instead of picrust2 - this is up to you, but you will just need to remember to change the environment name when activating this environment later if you don’t do this.

Install:

conda env create -f picrust2-env.yaml
conda activate picrust2
pip install --editable .

Run the tests to verify the installation:

pytest

Deactivate the environment (optional):

conda deactivate

R packages

These will need to be installed in RStudio instead of on the command line! If you have RStudio server then we recommend using this so that you don’t need to copy any files across.

Install necessary R packages:

install.packages("vctrs")
install.packages("dplyr")
install.packages("tidyr")
install.packages("ggplot2")
install.packages("vegan")
install.packages("devtools")
devtools::install_github("biobakery/maaslin3")
install.packages("GUniFrac")
install.packages("ape")
install.packages("data.table", type = "source")

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("phyloseq")
install.packages("taxonomizr")
install.packages("colorspace")
install.packages("RColorBrewer")
install.packages("stringr")

Authors

Author: Robyn Wright
Modifications by: NA
Based on initial versions by: NA

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