In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

knitr::opts_chunk$set(echo = FALSE, warning = FALSE, message = FALSE)

Required libraries for Linux systems

Below you can find commands to install the required libraries for different Linux distributions and their releases. If you are not sure which release are you using, check contents of the /etc/os-release file.

Don't forget to update the package database of your package manager. E.g. for Ubuntu: sudo apt update

suppressPackageStartupMessages(library(magrittr))
dists <- remotes:::supported_os_versions()
## -- See https://github.com/rstudio/r-system-requirements#operating-systems
unsupported_releases <- list(ubuntu = c("14.04"), centos = c("6"), redhat = c("6"), opensuse = c("15.0"), sle = c("15.0"))
res <- purrr::map_dfr(names(dists), function(dist) {
  res_dist_release <- purrr::map_dfr(dists[[dist]], function(release) {
    if (!release %in% unsupported_releases[[dist]]) {
      tibble::tibble(
        distribution = dist,
        release = release,
        install_cmd = remotes::system_requirements(os = dist, os_release = release)
      )
    }
  }) %>%
    dplyr::bind_rows() %>%
    dplyr::mutate(install_cmd = paste("sudo", install_cmd))
})

res_grp <- res %>%
  dplyr::group_by(distribution, release) %>%
  dplyr::summarise(install_cmd = paste(install_cmd, collapse = "\n")) %>%
  dplyr::ungroup() %>%
  dplyr::arrange(dplyr::desc(distribution), dplyr::desc(release))

x <- apply(res_grp, 1, function(row) {
  row <- as.list(row)
  cat(glue::glue("- [{row$distribution} {row$release}](#{row$distribution}-{row$release})\n", .trim = FALSE))
})

---

x <- apply(res_grp, 1, function(row) {
  row <- as.list(row)
  cat(glue::glue("\n\n## {row$distribution} {row$release}\n\n", .trim = FALSE))
  cat("```bash\n")
  cat(row$install_cmd)
  cat("\n```")
})

bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.