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@lindenb
lindenb / BamServer.java
Last active December 3, 2015 00:07
Setting up a jetty server for https://www.biostars.org/p/168197/
import org.eclipse.jetty.server.*;
import org.eclipse.jetty.servlet.*;
public class BamServer {
public static void main(String[] args) throws Exception {
Server jettyServer = new Server(8080);
ServletContextHandler context = new ServletContextHandler();
context.setContextPath("/");
DefaultServlet servlet= new DefaultServlet();
@iMilnb
iMilnb / boto3_hands_on.md
Last active October 19, 2022 09:15
Programmatically manipulate AWS resources with boto3 - a quick hands on

boto3 quick hands-on

This documentation aims at being a quick-straight-to-the-point-hands-on AWS resources manipulation with [boto3][0].

First of all, you'll need to install [boto3][0]. Installing it along with [awscli][1] is probably a good idea as

  • [awscli][1] is boto-based
  • [awscli][1] usage is really close to boto's
@mtmorgan
mtmorgan / readKallisto.R
Last active December 4, 2017 11:51
read kallisto RNA-seq quantification into R / Bioconductor data structures
.require <-
function(pkg)
{
withCallingHandlers({
suppressPackageStartupMessages({
require(pkg, character.only=TRUE, quietly=TRUE)
})
}, warning=function(w) {
invokeRestart("muffleWarning")
}) || {
Install s3fs on Mac OS X
1 - Install Homebrew - http://brew.sh/
ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"
2 - Use Homebrew to install s3fs + dependencies
brew install s3fs
3 - Do some custom stuff. I only used the first step from here -> https://gist.github.com/fukayatsu/3910097
sudo /bin/cp -rfX /usr/local/Cellar/fuse4x-kext/0.9.2/Library/Extensions/fuse4x.kext /Library/Extensions
@rmflight
rmflight / post-commit
Last active March 29, 2024 19:43
useful commit hooks for R package dev
#!/path/2/Rscript
# License: CC0 (just be nice and point others to where you got this)
# Author: Robert M Flight <rflight79@gmail.com>, github.com/rmflight
#
# This is a post-commit hook that after a successful commit subsequently increments the package version in DESCRIPTION
# and commits that. Analogous to the pre-commit at https://gist.github.com/rmflight/8863882, but useful if you only have
# good reasons for not doing it on the pre-commit.
#
# To install it, simply copy this into the ".git/hooks/post-commit" file of your git repo, change /path/2/Rscript, and make
@sloria
sloria / bobp-python.md
Last active August 25, 2026 23:59
A "Best of the Best Practices" (BOBP) guide to developing in Python.

The Best of the Best Practices (BOBP) Guide for Python

A "Best of the Best Practices" (BOBP) guide to developing in Python.

In General

Values

  • "Build tools for others that you want to be built for you." - Kenneth Reitz
  • "Simplicity is alway better than functionality." - Pieter Hintjens
@hadley
hadley / curriculum.md
Created September 27, 2013 20:24
My first stab at a basic R programming curriculum. I think teaching just these topics without overall motivating examples would be extremely boring, but if you're a self-taught R user, this might be useful to help spot your gaps.

Notes:

  • I've tried to break up in to separate pieces, but it's not always possible: e.g. knowledge of data structures and subsetting are tidy intertwined.

  • Level of Bloom's taxonomy listed in square brackets, e.g. http://bit.ly/15gqPEx. Few categories currently assess components higher in the taxonomy.

Programming R curriculum

Data structures

@ogrrd
ogrrd / dnsmasq OS X.md
Last active September 27, 2026 11:01
Setup dnsmasq on OS X

Never touch your local /etc/hosts file in OS X again

To setup your computer to work with *.test domains, e.g. project.test, awesome.test and so on, without having to add to your hosts file each time.

Requirements

Install

@bkreider
bkreider / s3nbmanager.py
Last active May 26, 2021 02:39
Ipython notebook backed by S3
"""A notebook manager that uses S3 storage. (based on the Azure manager)
http://ipython.org/ipython-doc/dev/interactive/htmlnotebook.html#using-a-different-notebook-store
Drop this file in IPython/frontend/html/notebook
1. Create a new notebook profile - ipython profile create nbserver
2. edit ~/.ipython/profile_nbserver/ipython_notebook_config.py
3. Add these lines:
c.NotebookApp.notebook_manager_class = 'IPython.frontend.html.notebook.s3nbmanager.S3NotebookManager'
@obeattie
obeattie / s3signurl.py
Created July 19, 2011 10:27
Quick, dirty Python script that spits out a signed url for Amazon S3
#!/usr/bin/env python
import optparse
import sys
from boto.s3.connection import S3Connection
def sign(bucket, path, access_key, secret_key, https, expiry):
c = S3Connection(access_key, secret_key)
return c.generate_url(
expires_in=long(expiry),