sjessa

# Usage: $ lmake <make options here> <optional make target>

function lmake ()
{
	echo "Appending make command output to make.log"
	echo "Running command..."

	echo "" >>make.log
	echo "------------------------------------------" >>make.log
	echo " MAKE LAUNCHED" >>make.log

sjessa

# Source a file in the same directory as the script regardless of the
# working directory from which the script is being called.
# Works in conjunction with argparser.
# Adapted from http://stackoverflow.com/a/1815743

command <- commandArgs(trailingOnly = FALSE)
script_name <- sub("--file=", "", command[grep("--file=", command)])
script_path <- dirname(script_name)
my_functions <- file.path(script_path, "functions.R")
source(my_functions, chdir = TRUE)

sjessa

PROMPT=" %{$fg[magenta]%}%n%{$reset_color%} @ %{$fg[yellow]%}%m%{$reset_color%} in %{$fg[green]%}%c%{$reset_color%} # %{$fg[blue]%}\${STY}%{$reset_color%} # %{$fg[blue]%}\$(git_prompt_info)%{$fg[blue]%} % %{$reset_color%}
%{$fg[blue]%}➜ %{$reset_color%} "

ZSH_THEME_GIT_PROMPT_PREFIX="%{$fg[cyan]%}"
ZSH_THEME_GIT_PROMPT_SUFFIX="%{$reset_color%}"
ZSH_THEME_GIT_PROMPT_DIRTY="%{$fg[blue]%} %{$fg[green]%}✗%{$reset_color%}"
ZSH_THEME_GIT_PROMPT_CLEAN="%{$fg[blue]%}"

sjessa

R -e 'library(knitr); knit("report.Rmd", "report.md")'; pandoc report.md --output snapshot.pdf --variable 'geometry:margin=1in'

sjessa

```{r setup, echo = FALSE, message = FALSE, warning = FALSE}

knitr::opts_chunk$set(dev = "pdf",            # Save figures as PDFs
                      fig.keep = "all",
                      fig.path = "figures/",  # Figures are saved to this directory
                      message = FALSE,        # Hide messages/warnings/errors from loading packages
                      warning = FALSE,
                      error = FALSE,
                      cache = TRUE)           # By default, cache results to avoid re-running
                                              # super long things every time you knit

sjessa

# Filters

library(tidyverse)

sample_filters <- quos(project %in% c("dev", species %in% c("mouse")))

sample_list <- data.frame(
  project = c("dev", "pbt"),
  species = c("mouse", "human"),
  dont_filter = c("a", "b"))

sjessa

# to add to ~/.bashrc
# e.g. selinjessa @ iMacPro @ ~ # 22846.test $
export PS1="\[\e[34m\]\u \[\e[m\]@ \[\e[31m\]\h \[\e[m\]@ \[\e[36m\]\W \[\e[m\]# ${STY} $ "

sjessa

# save in .bashrc
# usage: knit 01-analysis.Rmd

function knit() {
    R --no-save -e "rmarkdown::render('""$1""', 'html_document')"
}