Installation

The installation workflow is simple and mostly automatic, and relies entirely on Mamba and Conda

Table of contents

  1. Requirements and setup
  2. Dependencies
    1. 1. Nanofilt
    2. 2. Pigz
    3. 3. Samtools
    4. 4. Minimap
    5. 5. BCFtools
    6. 6. Python Dependencies
    7. 7. MAFFT
    8. 8. IQtree
    9. 9. R
    10. 10. Astral
    11. 11. ASAP
    12. 12. GNU Parallel
    13. 13. BLAST

Requirements and setup

To install the pipeline, you must meet the following requirements:

  • Be on a POSIX or POSIX-like operating system (Ubuntu, Fedora, Debian, CentOS, macOS, etc.)
  • Have mamba and conda installed on your local machine.

If you do not meet these two basic requirements, please adjust to them before installing and running the pipeline.

After verifying these requirements, complete the setup by running:

git clone https://github.com/nhmvienna/AmpliPiper.git
cd AmpliPiper

Now that you are in the pipeline’s directory, run the following command to install it:

bash shell/setup.sh

This will create several conda environments in a subdirectory named envs. The process may take a while (sometimes it can even last hours, depending on your machine setup) and there might be problems. Please check out troubleshooting and, if you cannot find a solution or the problem persists, feel free to flag an issue on GitHub.

Dependencies

These are the conda environments that will be created:

envs/
├── R
├── asap
├── astral
├── bcftools
├── blast
├── iqtree
├── mafft
├── minimap
├── nanofilt
├── parallel
├── pigz
├── python_dependencies
└── samtools

Here is the breakdown of the dependencies that are contained within these environemnts:

1. Nanofilt

  • Dependencies: nanofilt, pigz

2. Pigz

  • Dependencies: pigz

3. Samtools

  • Dependencies: samtools=1.17

4. Minimap

  • Dependencies: minimap2=2.26, samtools=1.17

5. BCFtools

  • Dependencies: bcftools

6. Python Dependencies

  • Dependencies: python=3.10, pandas, matplotlib, biopython, edlib, cairosvg, pymsaviz, ete3, pandas=2.1.1, beautifulsoup4, scipy

7. MAFFT

  • Dependencies: mafft=7.520

8. IQtree

  • Dependencies: iqtree=2.2.5

9. R

  • Dependencies: r-base=4.1.3, bioconductor-ggtree, r-tidyverse, bioconductor-treeio, r-phytools, r-ape, r-treedist, r-reshape2

10. Astral

  • Dependencies: astral-tree=5.7.8

11. ASAP

  • Dependencies: asap-v0.1.2-h14c3975_0

12. GNU Parallel

  • Dependencies: parallel

13. BLAST

  • Dependencies: blast