dfjenkins3

IGV Batch Screenshots

IGV provides functionality that allows a user to create a script to take screenshots of regions of interest.

Table of Contents

1. Requirements
2. Workflow
3. Create BED File

chenshuo

#pragma once

#include <stdint.h>
#include <stdlib.h>
#include <string.h>

#include <type_traits>

typedef uint32_t khint_t;
typedef khint_t khiter_t;

scottfrazer

"My First WDL" Template

task name {
  String in
  command {
    echo '${in}'
  }
  output {
 String out = read_string(stdout())

sofyan-ahmad

# Make sure you grab the latest version
curl -OL https://github.com/google/protobuf/releases/download/v3.2.0/protoc-3.2.0-linux-x86_64.zip

# Unzip
unzip protoc-3.2.0-linux-x86_64.zip -d protoc3

# Move protoc to /usr/local/bin/
sudo mv protoc3/bin/* /usr/local/bin/

# Move protoc3/include to /usr/local/include/

f0k

#!/usr/bin/env python
# -*- coding: utf-8 -*-

"""
Outputs some information on CUDA-enabled devices on your computer,
including current memory usage.

It's a port of https://gist.github.com/f0k/0d6431e3faa60bffc788f8b4daa029b1
from C to Python with ctypes, so it can run without compiling anything. Note
that this is a direct translation with no attempt to make the code Pythonic.

edawson

library(vcfR)

# Import VCF
my.vcf <- read.vcfR('my.vcf.gz')
# Combine CHROM thru FILTER cols + INFO cols
my.vcf.df <- cbind(as.data.frame(getFIX(my.vcf)), INFO2df(my.vcf))

cbergman

- Skelley et al 2013:
  - paper: http://genome.cshlp.org/content/23/9/1496.long
  - ena: http://www.ebi.ac.uk/ena/data/view/SRP018005 (includes RNA-seq)
  - 22 diverse Scer strains
  
- Bergstrom et al 2014
  - paper: https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msu037
  - SGRP2 
  - 19 Scer
  - 22 Spar

lindenb

REF="/path/to/human_g1k_v37.fasta"
java_exe="java"
gatk_jar="/path/to/GenomeAnalysisTK.jar"
params.test_flag="F"
params.prefix="20180515.NEXTFLOW"
params.callers=["samtools","freebayes","hapcaller"]
params.description="${params.prefix} : Pierre test Nextflow "

elowy01

#Example 1:

#!/usr/bin/env nextflow

params.str = 'Hello world!'

process AFcalc {

    """
    echo  '${params.str}'

lindenb

/**
Pierre Lindenbaum, 2019

gcc -o a.out -O3 -Wall -Isamtools/include discordant.c  -Lsamtools/lib -lhts

*/
#include <stdio.h>
#include <stdlib.h>
#include <errno.h>
#include <string.h>