test: PhyloProfile

#' Startup script for PhyloProfile
#' 1) install and load packages
#' 2) start the PhyloProfile app

source("R/functions.R")

# List of dependent packages --------------------------------------------------
packages <- c("shiny", "shinyBS", "shinyjs", "colourpicker", "DT",
              "devtools", "ggplot2", "reshape2",
              "plyr", "dplyr", "tidyr", "scales", "grid",
              "gridExtra", "ape", "stringr", "gtable",
              "dendextend", "ggdendro", "gplots", "data.table",
              "taxize", "zoo", "RCurl", "energy",
              "RColorBrewer")

# Set path for install packages while deploy into shiny server ----------------
# (from https://gist.github.com/wch/c3653fb39a00c63b33cf)

#' By default, the directories in .libPaths() aren't writable on shinyapps.io
#' so create a subdir where we'll install our package.
# if (!file.exists("R-lib")) {
#   dir.create("R-lib")
# }

#' Unfortunately, there's no way to get deployapp() to ignore this directory,
#' so make sure to remove it locally before you call deployapp().
#' This can be done with:
# unlink("R-lib", recursive = TRUE)

#' You may also need to restart R before calling deployapp(), because calling
#' runApp() will modify your libpath (below), which can confuse deployapp().

#' Add ./R-lib/ to the libPaths
# .libPaths( c(normalizePath("R-lib/"), .libPaths()) )

# Find & install missing packages ---------------------------------------------
install_packages(packages)

# Load packages
lapply(packages, library, character.only = TRUE)

# Check version and install ggplot2 (require v >= 2.2.0) ----------------------
version_above <- function(pkg, than) {
    compareVersion(as.character(packageVersion(pkg)), than)
}

if ("ggplot2" %in% rownames(installed.packages())) {
    install_packages("ggplot2")
    library(ggplot2)
}

# Install packages from bioconductor ------------------------------------------
bioconductor_pkgs <- c("Biostrings", "bioDist")
install_packages_bioconductor(bioconductor_pkgs)
lapply(bioconductor_pkgs, library, character.only = TRUE)

# Install OmaDB and its dependencies
oma_pkgs <- c("GO.db", "GenomeInfoDbData")
install_packages_bioconductor(oma_pkgs)
lapply(oma_pkgs, library, character.only = TRUE)

if (!("OmaDB" %in% rownames(installed.packages()))) {
    devtools::install_github("trvinh/OmaDB", force = TRUE)
}
library(OmaDB)

# Install shinycssloaders from github -----------------------------------------
if (!("shinycssloaders" %in% rownames(installed.packages()))) {
    devtools::install_github('andrewsali/shinycssloaders', force = TRUE)
    library(shinycssloaders)
}