Paolo Di Tommaso pditommaso

💭

Vita brevis, ars longa

Chief Architect & Co-founder of Seqera Labs. Distributed, parallel and reactive programming. Creator of http://nextflow.io.

pditommaso / reseqtut_lmw.py

Last active August 29, 2015 14:17 — forked from samuell/reseqtut_lmw.py

	import luigi
	from luigis_monkey_wrench import *

	REF='human_17_v37.fasta'
	INDIVIDUALS=['NA06984','NA07000']
	SAMPLES=['1','2']
	BASENAME='.ILLUMINA.low_coverage.17q_'
	PICARDDIR='/sw/apps/bioinfo/picard/1.69/kalkyl/'
	KNOWNSITES='/proj/g2014207/labs/gatk/ALL.chr17.phase1_integrated_calls.20101123.snps_indels_svs.genotypes.vcf'

pditommaso / bash.generate.random.alphanumeric.string.sh

Last active August 29, 2015 14:17 — forked from earthgecko/bash.generate.random.alphanumeric.string.sh

	#!/bin/bash
	# bash generate random alphanumeric string
	#
	dd bs=18 count=1 if=/dev/urandom 2>/dev/null \| base64 \| tr +/ 0A

pditommaso / Git notes

Last active February 14, 2017 17:52 — forked from richardcornish/git.md

pditommaso / request.sh

Last active August 29, 2015 14:08 — forked from nuxlli/unix_socket_request.sh

	#!/bin/bash

	# References
	# http://www.computerhope.com/unix/nc.htm#03
	# https://github.com/daniloegea/netcat
	# http://unix.stackexchange.com/questions/26715/how-can-i-communicate-with-a-unix-domain-socket-via-the-shell-on-debian-squeeze
	# http://unix.stackexchange.com/questions/33924/write-inside-a-socket-open-by-another-process-in-linux/33982#33982
	# http://www.linuxjournal.com/content/more-using-bashs-built-devtcp-file-tcpip
	# http://www.dest-unreach.org/socat/
	# http://stuff.mit.edu/afs/sipb/machine/penguin-lust/src/socat-1.7.1.2/EXAMPLES

pditommaso / github_dl_stats.py

Last active August 29, 2015 14:06 — forked from chapmanb/github_dl_stats.py

	#!/usr/bin/env python
	"""Get download stats for releases from GitHub.

	Needs development version of github3.
	pip install github3
	pip install git+https://github.com/sigmavirus24/github3.py.git
	"""
	import github3

	repo = github3.repository("chapmanb", "bcbio.variation")

pditommaso / memusg

Created August 27, 2014 15:08 — forked from netj/memusg

	#!/usr/bin/env bash
	# memusg -- Measure memory usage of processes
	# Usage: memusg COMMAND [ARGS]...
	#
	# Author: Jaeho Shin <[email protected]>
	# Created: 2010-08-16
	set -um

	# check input
	[ $# -gt 0 ] \|\| { sed -n '2,/^#$/ s/^# //p' <"$0"; exit 1; }

pditommaso / docker-clean

Created August 19, 2014 17:31 — forked from michaelneale/docker-clean

	#!/bin/sh

	remove_dangling() {
	echo "Removing dangling images ..."
	docker rmi $(docker images -f dangling=true -q)
	}

	remove_stopped_containers() {
	echo "Removing stopped containers ..."
	docker rm $(docker ps -qa)

pditommaso / tmux-cheatsheet.markdown

Created August 15, 2014 14:53 — forked from MohamedAlaa/tmux-cheatsheet.markdown

tmux shortcuts & cheatsheet

start new:

tmux

start new with session name:

tmux new -s myname

pditommaso / read_kmers.hs

Created August 5, 2014 09:51 — forked from michaelbarton/read_kmers.hs

	import System.Environment
	import Data.List.Split
	import Data.List
	import qualified Data.Map.Strict as Map

	main = do
	[f] <- getArgs
	contents <- readFile f
	putStr . unlines . map unwords . map (kmers 6) . getSequences $ contents

pditommaso / BuilderASTStrategies.groovy

Created May 1, 2014 12:52 — forked from dmahapatro/BuilderASTStrategies.groovy

	/* Sample use cases of @Builder AST which is added in Groovy 2.3 */

	import groovy.transform.builder.*
	import groovy.transform.ToString

	//DefaultStrategy
	@ToString(includeNames=true)
	@Builder(builderStrategy=DefaultStrategy)
	class Person {
	String name