Installation

The simplest way to install Captus is to create an isolated software environment using conda, if you don’t have conda we recommend to install miniconda from https://docs.conda.io/en/latest/miniconda.html. Once you have conda installed in your system you need to configure your channels:

conda config --prepend channels bioconda
conda config --prepend channels conda-forge
conda config --show channels

The last command should show your current channels, the order matters:

channels:
  - conda-forge
  - bioconda
  - defaults

Now we are ready to create a separate environment for Captus:

conda create -n captus captus

conda sometimes takes too long to find and configure dependencies, if that happens we recommend installing mamba first, and installing Captus with it:

conda install mamba
mamba create -n captus captus

Once Captus is installed in its own environment, let’s activate it:

conda activate captus

And that is all! Notice that the beginning of your prompt should have changed from(base)$ to (captus)$ as we activate the environment.

Just to verify it is correctly installed try typing captus_assembly --help, if everything went OK you should see the following output in the terminal:

usage: captus_assembly command [options]

Captus 1.0.0: Assembly of Phylogenomic Datasets from High-Throughput Sequencing data

Captus-assembly commands:
  command     Program commands (in typical order of execution)
                clean = Trim adaptors and quality filter reads with BBTools, run
                        FastQC on the raw and cleaned reads
                assemble = Perform de novo assembly with MEGAHIT: Assembling reads
                           that were cleaned with the 'clean' command is
                           recommended, but reads cleaned elsewhere are also allowed
                extract = Recover targeted markers with BLAT and Scipio: Extracting
                          markers from the assembly obtained with the 'assemble'
                          command is recommended, but any other assemblies in FASTA
                          format are also allowed.
                align = Align extracted markers across samples with MAFFT or MUSCLE:
                        Marker alignment depends on the directory structure created
                        by the 'extract' command. This step also performs paralog
                        filtering and alignment trimming using ClipKIT

Help:
  -h, --help  Show this help message and exit
  --version   Show Captus' version number

For help on a particular command: captus_assembly command -h

The manual way

You will have to install all the the dependencies separately yourself:

Captus was written for python >= v3.7, the only required library is tqdm but if you want to produce the HTML reports you will also need pandas and plotly

* Bundled with Captus

Once you have all the dependencies installed you can proceed to clone the repository and install Captus as described before:

git clone https://github.com/edgardomortiz/Captus.git
cd Captus
pip install .
Tip

If you don’t want to install Captus you can simply add the directory where you cloned the repository to your system $PATH and use captus_assembly-runner.py instead of captus_assembly

Created by Edgardo M. Ortiz (06.08.2021)
Last modified by Edgardo M. Ortiz (21.11.2023)