nathanhaigh

#!/bin/bash
# Usage: interleave_fastq.sh f.fastq r.fastq > interleaved.fastq
# 
# Interleaves the reads of two FASTQ files specified on the
# command line and outputs a single FASTQ file of STDOUT.
# 
# Can interleave 100 million paired reads (200 million total
# reads; a 2 x 22Gbyte files), in memory (/dev/shm), in 6m54s (414s)
# 
# Latest code: https://gist.github.com/4544979

satoruhiga

#!/usr/bin/env python

'''
DEPENDENCIES:
$ brew install ffmpeg
$ brew install imagemagick

$ python ./mov2gif.py input.mov output.gif 15
'''

knmkr

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

import argparse
from wikitools import wiki  # https://github.com/alexz-enwp/wikitools
from wikitools import page

def search_snpedia(snp):
    """
    http://snpedia.com/index.php/Bulk

bradrydzewski

#!/bin/bash
#
# Generates client and server certificates used to enable HTTPS
# remote authentication to a Docker daemon.
#
#     See http://docs.docker.com/articles/https/
#
# To start the Docker Daemon:
#
#     sudo docker -d                 \

surjikal

#!/usr/bin/env bash

brew install openssl

git clone git://anongit.mindrot.org/openssh.git
cd openssh

# The './configure' script does not exist, so we have to build it
autoreconf

SamStudio8

"""
Provides functions for the purpose of parsing a Sun Grid Engine (SGE)
accounting file for job metadata.
"""

__author__ = "Sam Nicholls <msn@aber.ac.uk>"
__copyright__ = "Copyright (c) Sam Nicholls"
__version__ = "0.0.32"
__maintainer__ = "Sam Nicholls <msn@aber.ac.uk>"

Brainiarc7

Transient compute clustering with GNU Parallel and sshfs:

GNU Parallel is a multipurpose program for running shell commands in parallel, which can often be used to replace shell script loops,find -exec, and find | xargs. It provides the --sshlogin and --sshloginfile options to farm out jobs to multiple hosts, as well as options for sending and retrieving static resources and and per-job input and output files.

For any particular task, however, keeping track of which files need to pushed to and retrieved from the remote hosts is somewhat of a hassle. Furthermore, cancelled or failed runs can leave garbage on the remote hosts, and if input and output files are large, sending them to local disk on the remote hosts is somewhat inefficient.

In a traditional cluster, this problem would be solved by giving all nodes access to a shared filesystem, usually with NFS or something more exotic. However, NFS doesn't wo

fsteffenhagen

# Input: list of rows with format: "<filesize> filename", e.g.
# filesizes.txt
#######################
# 1000K  file1.txt
# 200M   file2.txt
# 2G     file3.txt
#

# Output:
cat filesizes.txt | numfmt --from=iec | awk 'BEGIN {sum=0} {sum=sum+$1} END {printf "%.0f\n", sum}'

adam-garcia

Viridis Color Palette Generator

A simple tool for extracting discrete color palette values from the viridis collection of color palettes.

tommarute

#!/bin/bash

set -ex

gcc_ver=$(gcc --version | head -n 1 | awk '{print $3}')

# Install gcc 4.9 devtoolset
if [[ ! "$gcc_ver" =~ 4\.9\.* ]]; then
    sudo yum install epel-release -y
    sudo yum install centos-release-scl -y