Installation

Install using BiocManager

We are preparing to submit PhyloProfile to Bioconductor. Once the package is accepted, you can easily install it using BiocManager:

if (!requireNamespace("BiocManager"))
    install.packages("BiocManager")

BiocManager::install("PhyloProfile")

Until then please install the dev version of PhyloProfile from our github repository using devtools.

Install using devtools

To install the dev version from github:

if (!requireNamespace("devtools"))
    install.packages("devtools", repos = "http://cran.us.r-project.org")

devtools::install_github(
    "bionf/phyloprofile",
    INSTALL_opts = c('--no-lock'),
    build_opts = c('--no-resave-data')
)

For Windows Users:

Please run R as administrator in order to install the libraries into R library path.

In some cases, you need to install bindrcpp before installing PhyloProfile.

install.packages("bindrcpp", repos = "http://cran.us.r-project.org")

devtools::install_github(
    "bionf/phyloprofile",
    INSTALL_opts = c('--no-lock'),
    build_opts = c('--no-resave-data')
)

Start PhyloProfile GUI tool

library(phyloprofile)
run_phyloprofile()

Check your web browser, PhyloProfile will be displayed there ;-)

Troubleshooting

Independent packages cannot be installed

If for any reasons some packages cannot be installed automatically, please do the installation by yourself using the instruction:

# Get list of missing packages
packages <- c("ape", "bioDist", "BiocStyle", "Biostrings", "colourpicker", "data.table", "dendextend", "devtools", "dplyr", "DT", "energy", "GenomeInfoDbData", "ggplot2", "gplots", "GO.db", "grDevices", "gridExtra", "gtable", "knitr", "RColorBrewer", "RCurl", "reshape2", "rmarkdown", "scales", "shiny", "shinyBS", "shinycssloaders", "shinyjs", "stats", "stringr", "svMisc", "tidyr", "taxize", "utils", "OmaDB", "plyr", "zoo")
missingPkg <- packages[!packages %in% rownames(installed.packages())]
missingPkg

# Then install the missing packages
install.packages(missingPkg, dependencies = TRUE, repos="http://cran.us.r-project.org")

Vignettes cannot be installed (e.g. due to missing X11 fonts)

The installation of PhyloProfile can be terminated due to the unsuccessfully generated vignettes. In this case, you can turn off the option to create the vignettes while installing the tool.

devtools::install_github("bionf/phyloprofile", INSTALL_opts = c('--no-lock'))

The startup takes ages

For the first time running, the tool will download a pre-caculated taxonomy data. Please be patient until you see a message for uploading input files.

If it takes more than 10 minutes, or you just don't want to wait, you can manually download the taxonomy data, unzip it and copy those files into phyloprofile/phyloprofile/data folder.

# To find the library path, where PhyloProfile has been installed, use this command in R terminal
.libPaths()

Python dependencies for OMA parsing scripts

Converting OrthoXML files to an input that works with PhyloProfile or manually downloading OMA data is right now done with Python scripts (data/convert_oma_standalone_orthoxml.pl or data/get_oma_browser.py), which come with their own dependencies.

These can be installed with pip install bs4 and pip install lxml.

Additionally, if you want to use scripts/get_oma_browser.py to get OMA Orthologous Proteins from OMA Browser, you need to install the Core API Library with pip install coreapi.