oxlb

killall Xcode
xcrun -k
xcodebuild -alltargets clean
rm -rf "$(getconf DARWIN_USER_CACHE_DIR)/org.llvm.clang/ModuleCache"
rm -rf "$(getconf DARWIN_USER_CACHE_DIR)/org.llvm.clang.$(whoami)/ModuleCache"
rm -rf /Applications/Xcode.app
rm -rf ~/Library/Caches/com.apple.dt.Xcode
rm -rf ~/Library/Developer
rm -rf ~/Library/MobileDevice
rm -rf ~/Library/Preferences/com.apple.dt.Xcode.plist

lwaldron

metaphlanToPhyloseq <- function(
  metaphlandir,
  metadat=NULL,
  simplify=TRUE){
  ## tax is a matrix or data.frame with the table of taxonomic abundances, rows are taxa, columns are samples
  ## metadat is an optional data.frame of specimen metadata, rows are samples, columns are variables
  ## if simplify=TRUE, use only the most detailed level of taxa names in the final object
  ## metaphlanToPhyloseq("~/Downloads/metaphlan_bugs_list")
  .getMetaphlanTree <- function(removeGCF=TRUE, simplify=TRUE){
    if (!requireNamespace("ape")) {

benmarwick

# Adapted from https://stackoverflow.com/a/7267364/1036500 by Andrie de Vries

# This is it: theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5))

library(ggplot2)

td <- expand.grid(
  hjust=c(0, 0.5, 1),
  vjust=c(0, 0.5, 1),
  angle=c(0, 45, 90),

Theldus

cue_file = 'file.cue'

d = open(cue_file).read().splitlines()

general = {}

tracks = []

current_file = None

trinker

if (!require("pacman")) install.packages("pacman")
pacman::p_load(dplyr, venneuler)
pacman::p_load_current_gh('trinker/textshape', 'thomasp85/ggforce')


x <- matrix(sample(0:4, 80, TRUE, c(.6, .1, .1, .1, .1)), ncol=4)

colnames(x) <- LETTERS[1:4]

GDKO

Preface

This is my recommended pipeline for assembly and annotation of small eukaryotic genomes (50 - 500 Mb).

All small scripts are available at CGP-scripts. For the programs a link is provided.

Please cite if you found the pipeline useful!

dlebauer

library(data.table)
species <- fread('species.csv')
## identify and remove records that were present when we imported the table
usdaplants <- species[!is.na(NativeStatus) ] 

## data table method of renaming columns
setnames(usdaplants, 
     old = c('id', 'genus', 'species', 'scientificname', 'commonname'), 
     new = c('betydb.species.id', 'Genus', 'Species', 'ScientificName', 'CommonName'))

mw55309

x <- data.frame(d=runif(12), g=rep(1:4, each =3)) 

my.col <- c("deepskyblue3","darkorange2","darkgray","gold")

spacer <- c(1, 0.1, 0.1, 1, 0.1, 0.1, 1, 0.1, 0.1, 1, 0.1, 0.1)

bw <- 0.8

xmax <- (sum(spacer) * bw) + (nrow(x) * bw)

nickloman

tar -cf - $dir | tee >(ncftpput -v -F -u USER -p PASS -c HOST ${dir}.tar) | md5sum > ${dir}.md5

macmanes

interleave-reads.py file.1.fq.gz file.2.fq.gz \
| skewer -Q 2 -t 2 -x $HOME/Trimmomatic-0.33/adapters/TruSeq3-PE.fa - -1 \
| normalize-by-median.py --max-memory-usage 2e9 -C 30 -o -  - \
| trim-low-abund.py -V -M 2e9 -o - --cutoff 2 - \
| split-paired-reads.py --output-orphaned orph.fq -1 stream.1.fq -2 stream.2.fq -