View trace2json.py
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#!/usr/bin/env python | |
# Convert Nextflow text file to JSON format | |
import json | |
headers = [] | |
data = {'trace': []} | |
with open ('NGI-RNAseq_trace.txt') as fh: | |
for l in fh: | |
s = l.split("\t") |
View NF_logo.png
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Save NextFlow logo as this file. |
View bioconda_badges.html
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<!DOCTYPE html> | |
<html lang="en"> | |
<head> | |
<!-- | |
BIOCONDA POSTER BADGE GENERATOR | |
Author: Phil Ewels <phil.ewels@scilifelab.se> (@ewels) | |
Date: August 2016 | |
To add more templates, create in Adobe Illustrator. |
View check_bismark_analysis.sh
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#!/bin/bash | |
# Check bisulfite analysis results for any modes of failure that I can think of. | |
# Assumes data is processed by Cluster Flow / bismark and is in subdirectories. | |
# For a basic quick summary, just run: | |
# bash check_bismark_analysis.sh | |
# To filter which subdirectories are checked, pass a glob expression. For example: | |
# bash check_bismark_analysis.sh run2_* |
View rcolorbrewer_example.html
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<!DOCTYPE html> | |
<html xmlns="http://www.w3.org/1999/xhtml"> | |
<head> | |
<meta charset="utf-8"> | |
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> | |
<meta name="generator" content="pandoc" /> |
View sra_illumina_stats.r
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#' --- | |
#' title: "SRA Sequencing Platform Analysis" | |
#' author: "Phil Ewels" | |
#' date: September 2014 | |
#' --- | |
#' The Sequence Read Archive [(SRA)](http://www.ncbi.nlm.nih.gov/sra) | |
#' contains the raw DNA-sequencing data for many published datasets. | |
#' We were interested in which sequencing platforms were prevalent, | |
#' or rather, how prevalent Illumina Sequencing is. We were specifically |
View cytobands.pl
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#!/usr/bin/perl | |
use CGI::Carp qw(fatalsToBrowser); # pipe errors to the browser instead of the terminal for debugging | |
use warnings; | |
use strict; | |
use Data::Dumper; | |
#print Dumper(\%args); | |
print "Content-type: text/plain\n\n"; | |
############################################################# | |
# Name: Cytobands - Coordinates: Online Version # |
View front-page.php
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<?php | |
if ( get_option( 'show_on_front' ) == 'posts' ) { | |
get_template_part( 'index' ); | |
} elseif ( 'page' == get_option( 'show_on_front' ) ) { | |
get_header(); | |
while ( have_posts() ) : the_post(); | |
View .bashrc
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# One command to extract them all | |
extract () { | |
if [ $# -ne 1 ] | |
then | |
echo "Error: No file specified." | |
return 1 | |
fi | |
if [ -f $1 ] ; then | |
case $1 in | |
*.tar.bz2) tar xvjf $1 ;; |
View front-page.php
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<?php | |
// Outputting the widget area on your homepage | |
// Accomodates one to four active widget areas, fits bootstrap columns accordingly | |
// front-page.php | |
$widget_count = 0; | |
for ($i = 1; $i <= 4; $i++){ | |
if ( is_active_sidebar('homepage-widget-area-'.$i) ) $widget_count++; | |
} | |
if ( $widget_count > 0) { |
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