mikelove

RUNS, = glob_wildcards("fastq/{run}_1.fastq.gz")

SALMON = "/proj/milovelab/bin/salmon-1.4.0_linux_x86_64/bin/salmon"

ANNO = "/proj/milovelab/anno"

rule all:
    input: expand("quants/{run}/quant.sf", run=RUNS)

rule salmon_index:

mikelove

get_deps <- function(what="Suggests") {
  deps <- desc::desc_get_deps()
  suggests <- deps$package[deps$type==what]
  setdiff(suggests, sub(".*/","",find.package(suggests, quiet=TRUE)))
}

mikelove

• xcode
• iterm2
• source code pro / fire mono
• homebrew
• zsh
• git
• emacs & ESS
• R & Rstudio
• mactex
• ispell

mikelove

svn co https://svn.r-project.org/R/trunk R
cd R
tools/rsync-recommended
./configure
make

lots of info from here: http://pj.freefaculty.org/blog/?p=315

mikelove

alias ls='ls -G'
alias ll='ls -lh'
alias rm='rm -i'
alias mv='mv -i'
alias cp='cp -i'

alias R='R --quiet'
alias Rdevel='/home/love/bin/R/bin/R --quiet'

alias emacs='emacs -nw'

mikelove

options(repos=c("https://cran.rstudio.com/"),showWarnCalls=TRUE,showErrorCalls=TRUE,
        max.print=1000,width=100,menu.graphics=FALSE)
options(defaultPackages = c(getOption("defaultPackages"),"devtools","rmarkdown"))
# Sys.setenv(TZDIR = "/usr/share/zoneinfo") # this is for a peculiar Mac OS X setup
library(utils)
rc.settings(ipck=TRUE)
if (interactive()) message(R.version$version.string)

mikelove

; mike love's .emacs

; general stuff
(menu-bar-mode -1)
(tool-bar-mode -1)
(global-set-key "\C-x\C-b" 'electric-buffer-list)
(global-unset-key (kbd "\C-x DEL") )
(global-unset-key (kbd "\C-t") )
(setq inhibit-startup-screen t)
(setq backup-directory-alist '(("" . "~/emacs-backup")))