mojaveazure

FROM rocker/r-ver:latest

RUN apt-get update && \
    apt-get install -y cmake git wget pandoc

# RUN Rscript -e "repos <- paste0('https://', c('mojaveazure', 'tiledb-inc'), '.r-universe.dev')" \
#     -e "repos <- unlist(lapply(repos, \(x) paste0(x, c('/bin/linux/jammy/4.3/', ''))))" \
#     -e "repos <- paste(shQuote(repos), collapse = ', ')" \
#     -e "cat('options(repos = c(', repos, ', getOption(\"repos\")))\n', sep = '')" | \
#     tee -a ~/.Rprofile

mojaveazure

#!/usr/bin/env Rscript

suppressPackageStartupMessages(library(tiledbsoma))
suppressPackageStartupMessages(library(argparser))

parser <- argparser::arg_parser("", hide.opts = TRUE)
parser <- argparser::add_argument(
  parser = parser,
  arg = '--input',
  help = "Input Seurat, SingleCellExperiment, or SummarizedExperiment object as Rds",

mojaveazure

FROM rocker/r-base:latest

RUN apt-get update && \
    apt-get install -y ca-certificates lsb-release curl cmake git
RUN curl -O https://apache.jfrog.io/artifactory/arrow/$(lsb_release --id --short | tr 'A-Z' 'a-z')/apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb
RUN apt-get install -yV ./apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb
RUN apt-get update && apt-get install -y libarrow-dev

RUN Rscript -e "\
    ncores <- as.integer(system2('grep', c('-c', 'processor', '/proc/cpuinfo'), stdout = TRUE)); \

mojaveazure

FROM rocker/r-ver:4.2.2

RUN apt-get update && apt-get upgrade -y

RUN Rscript -e "\
    install.packages('remotes'); \
    remotes::install_version('Matrix', '1.5.1'); \
    install.packages('SeuratObject', repos = 'https://cloud.r-project.org')"

RUN Rscript -e "print(packageVersion('Matrix'))"

mojaveazure

#!/usr/bin/env Rscript

#' Minimal R version
#'
#' Find the lowest accepted R version for a package and all of its dependencies
#'
#' @param package Name of CRAN package
#'
#' @return A \code{\link[base]{numeric_version}} with the lowest possible R
#' version to install \code{package} and all of its dependencies

mojaveazure

Installing RStudio Server on the Windows Subsystem for Linux

Setting up RStudio Server on the Windows Subsystem for Linux (WSL) is an excellent way for R developers to use and interact with R on Linux while running Windows. While not perfect, it provides a nearly seamless way for Windows users to consume Linux-only packages, and for developers to test on both Windows and Linux at the same time. Moreover, the same benefits of running RStudio server, such as leaving jobs running in the background, apply to RStudio Server on WSL. These are my notes for successfully setting up and using RStudio Server on WSL

Setting up WSL

The first thing that needs to happen in enabling the WSL and installing a Linux distro. To install the WSL, open PowerShell as an administrator and run

dism.exe /online /enable-feature /featurename:Microsoft-Windows-Subsystem-Linux /all /norestart

mojaveazure

#!/usr/bin/env python3

"""Generate an H5AD file from the PBMC3k dataset"""

import os
import sys
import time
import shutil
import urllib
import logging

mojaveazure

Keybase proof

I hereby claim:

• I am mojaveazure on github.
• I am mojaveazure (https://keybase.io/mojaveazure) on keybase.
• I have a public key ASB4Z0EBpYA3cVTGJWx8Ndx3OSvgxPqondPxy1_0TbMOwgo

To claim this, I am signing this object:

mojaveazure

#!/usr/bin/env Rscript

args <- commandArgs(trailingOnly = TRUE)

msg <- "Please pass 'bitbucket' or 'github' to choose where we install Seurat from"

if (length(x = args) != 1) {
    stop(msg)
}

mojaveazure

#!/usr/bin/env python3

"""Translate Ensembl codes into gene names"""

import sys
if sys.version_info.major is not 3 and sys.version_info.minor < 5:
    sys.exit("Please use Python 3.5 or higher for this program")


import argparse