tgirke

Nvim-R-Tmux: Neovim-based IDE for R

!!! This Gist tutorial is deprecated. Its new version is available here !!!

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• Author: Thomas Girke
• Last update: 18-Nov-2020

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dyndna

merge bams file and add @RG and @CO

Let's say you have two bam files from two different runs you need to merge.

1. bam1_batch1.bam
2. bam1_batch2.bam

Using samtools view -H <bamfile>, get @RG information for each of two bams. I usually get ID, DT and PL info. from bam header and then add SM (sample tag) tag using following script. You can run this script before samtools merge command in your PBS script.

jwinder

1 Welcome to Sonic Pi

Welcome friend :-)

Welcome to Sonic Pi. Hopefully you're as excited to get started making your own sounds as I am to show you. It's going to be a really fun ride where you'll learn all about music, synthesis, programming, composition, performance and more.

lestoni

via (https://www.linux.com/learn/tutorials/442438-vim-tips-folding-fun)

• zf#j creates a fold from the cursor down # lines.
• zf/string creates a fold from the cursor to string .
• zj moves the cursor to the next fold.
• zk moves the cursor to the previous fold.
• zo opens a fold at the cursor.
• zO opens all folds at the cursor.
• zm increases the foldlevel by one.
• zM closes all open folds.

digitaljhelms

Branching

Quick Legend

Description, Instructions, Notes

Instance	Branch

nathanhaigh

#!/bin/bash
# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]
# 
# Deinterleaves a FASTQ file of paired reads into two FASTQ
# files specified on the command line. Optionally GZip compresses the output
# FASTQ files using pigz if the 3rd command line argument is the word "compress"
# 
# Can deinterleave 100 million paired reads (200 million total
# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s)
# 

m14t

#/bin/bash
#-- Script to automate https://help.github.com/articles/why-is-git-always-asking-for-my-password

REPO_URL=`git remote -v | grep -m1 '^origin' | sed -Ene's#.*(https://[^[:space:]]*).*#\1#p'`
if [ -z "$REPO_URL" ]; then
  echo "-- ERROR:  Could not identify Repo url."
  echo "   It is possible this repo is already using SSH instead of HTTPS."
  exit
fi

MohamedAlaa

tmux shortcuts & cheatsheet

start new:

tmux

start new with session name:

tmux new -s myname

ngcrawford

import os
import sys
import glob
import pysam
import argparse
import multiprocessing

def get_args():
    '''Parse sys.argv'''
    parser = argparse.ArgumentParser()