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HaploSync installation

We suggest installing the tool within a dedicated virtual environment (even when possessing sudo credentials) to avoid conflicts with the existing global environment.

conda create --name haplosync python=2.7

Download HaploSync

From GitHub repo

Install HaploSync by running the following in your preferred working directory:

  • Move to the desired directory:
 cd /path/to/installation/directory
  • Download the executables:
 git clone https://github.com/andreaminio/HaploSync

From release tarball

Download and unpack the desired release version from the releases reporsitory.

Install dependencies

Using conda

  1. Activate the virtual environment:
conda activate haplosync
  1. Install R and R packages
# install r
conda install -c conda-forge r-base

# install r packages
conda install -c conda-forge r-curl r-tidyverse r-optparse r-plotly r-plyr r-flexdashboard r-gridextra r-devtools r-knitr r-svglite r-gridsvg r-svgpanzoom r-ggrepel
  1. Install python libraries:
# get pip
wget https://bootstrap.pypa.io/pip/2.7/get-pip.py
python get-pip.py

# install
pip install Cython networkx==2.1 pandas scipy numpy toml datetime multiprocessing pyyaml matplotlib biopython==1.76
  1. Install a local version of the 3rd party tools
conda install libgit2
conda install -c conda-forge parallel
conda install -c bioconda minimap2 samtools bedtools blat gmap=2019.09.12
  1. Install Mummer v4 Download Mummer version 4.0.0.beta5 or later from GitHub and install the tool in the Conda environment
wget https://github.com/mummer4/mummer/releases/download/v4.0.0.beta5/mummer-4.0.0beta5.tar.gz
tar -xzf mummer-4.0.0beta5.tar.gz
cd mummer-4.0.0beta5/
./configure --prefix=$CONDA_PREFIX
make install
  1. Copy the conf.toml, fields can be left empty since tools are already in the path
cd /path/to/installation/directory/HaploSync
cp HaploSync.conf.toml_empty HaploSync.conf.toml

Manually

To use HaploSync, be sure to have installed the follwing tools, libraries and packages

Python libraries

Make sure to install the following python libraries:

  • Python ver >2.7
  • networkx ver >2.1 (previous versions are incompatible because of different function implementation)
  • Biopython
  • numpy
  • yaml
  • scipy
  • toml
  • datetime
  • pandas
  • multiprocessing

Tools

The tools below run the pipeline. It is not necessary for these to be in your $PATH; see Setup to set custom paths for these tools.

  • Mandatory
    • Minimap2
    • Gmap
      • Note: we suggest installing version 2019.09.12, which is the last version not affected by a bug (@2020.07.16). In version 2020.06.01 and 2020.04.08, separators between some attributes are missing in the gff3 output. While HaploSync can handle this known issue, the result may be parsed incorrectly if you use the tool independently.
    • Mummer v.4 , Mummer version 4.0.0.beta5 download
      • Note 1: Mummer v3 is not compatible because it does not permit multi-threading.
      • Note 2: Some releases of Mummer v.4 < beta 5 (4.0.0.beta5) should be avoided; a bug allows the tool to report hits between large regions of Ns in the sequences. This does not affect the assembly performance of HaploSync, but dotplots will report unexpected gap-to-gap hits. Installation of the tool through Conda should be avoided. The Bioconda repository only hosts a beta2 version of the tool (@2020.07.16), which is affected by the bug.
    • Samtools
    • Bedtools
    • R v4.0 or higher, with the following libraries:
      • plotly
      • optparse
      • plyr
      • svgPanZoom
      • knitr
        • Note: version 1.29 required
      • ggplot2
        • Note: version 3.3.2 required
  • Optional

R Packages

  • In R, install the package using the following command lines: 
    install.packages("tidyverse")
install.packages("optparse")
install.packages("plotly")
install.packages("plyr")
install.packages("flexdashboard")
install.packages("gridExtra")
install.packages("devtools")
require(devtools)
install_version("knitr", version = "1.29", repos = "http://cran.us.r-project.org")
install_version("ggplot2", version = "3.3.2", repos = "http://cran.us.r-project.org")
install.packages("svglite")
install.packages("gridSVG")
install.packages("svgPanZoom")
install.packages("ggrepel")

Setup custom paths with custom manual installation of tools

If you want to use compatible tool installations that are not accessible directly in your $PATH you can configure the tool for use in custom paths.

If you set up a virtual environment using conda and installed a local version of the tools, you don’t need to customise:

Generate the file HaploSync.conf.toml and then edit the content with desired custom paths:

cd /path/to/installation/directory/HaploSync
cp HaploSync.conf.toml_empty HaploSync.conf.toml
vim HaploSync.conf.toml

The original file looks like:

title = "HaploBuild configuration file"

[paths]
minimap2 = ""
samtools = ""
bedtools = ""
nucmer = ""
show-coords = ""
gmap = ""
blat = ""

To set custom paths to the tools, add the absolute path to the folder containing each tool between the quotation marks above. Leave the space between the quotation marks empty if the tools are in your $PATH.

References

  • Minimap2: Li H. (2018). Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34:3094-3100.
  • Gmap: Wu T. D. and Watanabe C. K. (2005). GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics, 21:1859-1875
  • Samtools: Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009). The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25:2078-9
  • Bedtools: Quinlan A. R., Hall I. M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, 26:841–842,
  • Plotly: Sievert C (2020). Interactive Web-Based Data Visualization with R, plotly, and shiny. Chapman and Hall/CRC. ISBN 9781138331457
  • Blat: Kent, W.J. (2002). BLAT -- The BLAST-Like Alignment Tool. Genome Research 4: 656-664.
  • Mummer v.4: Marçais G., Delcher A.L., Phillippy A.M., Coston R.,Salzberg S.L., Zimin A., (2018). MUMmer4: A fast and versatile genome alignment system. PLoS computational biology, 14(1): e1005944.