mojaveazure

Useful Commands

Bash

Command	Meaning
echo -en "\rSomeText"	Return carriage to the beginning of the line (-e and \r), write "SomeText" at that point in time. Do not output a new line at the end of the statement (-n). Useful for dynamic terminal messages.
find . -exec touch -am {} \;	Update the access and modified times for all files in this current directory and all subdirectories. Useful for keeping files around when set to expire after a given amount of time.
find . -name 'foo-exclude-me' -prune -o -name 'foo*' -print	Find all files with foo*, ignoring foo-exlude-me

mojaveazure

#!/bin/bash

set -euo pipefail

MY_FILE="$1"
declare -ax ARRAY=($(<"${MYFILE}"))

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

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

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 python3

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

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

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 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

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

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)); \