ClaidentInstaller

Automatic installer shell scripts for Claident.

To learn how to use Claident, see ClaidentTutorial.

Notice about conda (Anaconda/Miniconda)

Because conda (or the other environment-modifying packages) interferes these installer scripts, conda need to be disabled temporarily when running these installer scripts. Running these installer scripts as newly created user is the best solution.

Notice about UCHIMEDB

This installer no longer install SILVA, RDP Gold, DAIRYdb and UNITE databases because their server often down or require manual registration. Still, I recommend SILVA SSUParc for prokaryotic 16S, eukaryotic mitochondrial 16S and eukaryotic nuclear 18S (SSU), SILVA LSUParc for prokaryotic 23S and eukaryotic nuclear 28S (LSU), Full UNITE+INSD of all eukaryotes for nuclear ITS. In order to install FASTA file as UCHIMEDB to your machine, run the following commands AFTER INSTALLATION OF CLAIDENT.

```

set install prefix (/usr/local by default)

this must be the same as Claident install prefix (see below)

PREFIX=/usr/local

set number of processor cores

NCPU=8

dereplicate sequences

$PREFIX/share/claident/bin/vsearch --fastawidth 0 --notrunclabels --threads $NCPU --strand both --derepfulllength input.fasta --output input_dereplicated.fasta

make reverse-complement sequences

$PREFIX/share/claident/bin/vsearch --fastawidth 0 --notrunclabels --threads $NCPU --labelsuffix revcomp --fastxrevcomp inputdereplicated.fasta --fastaout inputdereplicatedrevcomp.fasta

join FASTA files

cat inputdereplicated.fasta inputdereplicated_revcomp.fasta > DBNAME.fasta

install FASTA file to UCHIMEDB path

mv DBNAME.fasta $PREFIX/share/claident/uchimedb/ || sudo mv DBNAME.fasta $PREFIX/share/claident/uchimedb/ ```

Prerequisites

On Debian GNU/Linux compatible distributions, Debian 11 Bullseye, Ubuntu 20.04LTS or Linux Mint 20 or later is required.

On Red Hat Enterprise Linux compatible distributions, Red Hat Enterprise Linux 8, CentOS 8, AlmaLinux 8 or Rocky Linux 8 is required. Those users need to enable Extra Packages for Enterprise Linux (EPEL) repository before installing Claident. Red Hat Enterprise Linux users also need to enable CodeReady Linux Builder repository. CentOS, AlmaLinux or Rocky Linux users need to enable PowerTools (for v8) / CRB (for v9) repository.

On macOS, macOS 10.14 Mojave or later is required. Mac users need to install Xcode command line tools before installing Claident. Xcode command line tools can be installed by running the following command in the terminal.

xcode-select --install

In addition, mac users also need to install 1 of the following package manager.

• MacPorts
• Homebrew

If you want to generate wordcloud of community composition by using "clplotwordcloud" command, Google Chrome or Chromium is also required. On Debian GNU/Linux compatible distributions, the following commands will install Google Chrome to your machines.

wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb sudo dpkg -i google-chrome-stable_current_amd64.deb sudo apt --fix-broken install sudo dpkg -i google-chrome-stable_current_amd64.deb

On Red Hat Enterprise Linux compatible distributions, use the following commands to install Google Chrome.

wget https://dl.google.com/linux/direct/google-chrome-stable_current_x86_64.rpm sudo dnf localinstall google-chrome-stable_current_x86_64.rpm

On macOS, download installer from Google, install Google Chrome, and execute the following command in the terminal before running "clplotwordcloud" command.

alias google-chrome='/Applications/Google\ Chrome.app/Contents/MacOS/Google\ Chrome'

How to use

```

install Claident and required programs

sh installClaident_Debian.sh

install optional programs

sh installOptions_Debian.sh

install BLAST databases and taxonomy databases

sh installDB_Debian.sh

install reference databases for UCHIME

sh installUCHIMEDB_Debian.sh ```

If you need proxy to access the internet

Type and run the following commands before installation.

export http_proxy=http://server.address:portnumber export https_proxy=http://server.address:portnumber export ftp_proxy=http://server.address:portnumber

If you need username and password to use proxy, use the following commands instead of the above commands.

export http_proxy=http://username:password@server.address:portnumber export https_proxy=http://username:password@server.address:portnumber export ftp_proxy=http://username:password@server.address:portnumber

How to change installation PATH

Set PREFIX environment variable before installation like below.

``` export PREFIX=/path/to/instllation/path

install Claident and required programs

sh installClaident_Debian.sh

install optional programs

sh installOptions_Debian.sh

install BLAST databases and taxonomy databases

sh installDB_Debian.sh

install reference databases for UCHIME

sh installUCHIMEDB_Debian.sh ```

How to update to new version

Run installation scripts in a new working directory.