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Vivek Krishnakumar vivekkrish

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@diosmosis
diosmosis / example.py
Created August 15, 2011 22:41
Python decorator that catches exceptions and logs a traceback that includes every local variable of each frame.
import os
from log_exceptions import log_exceptions
def throw_something(a1, a2):
raise Exception('Whoops!')
@log_exceptions(log_if = os.getenv('MYAPP_DEBUG') is not None)
def my_function(arg1, arg2):
throw_something(arg1 + 24, arg2 - 24)
@nathanhaigh
nathanhaigh / deinterleave_fastq.sh
Last active May 6, 2024 06:38
deinterleave FASTQ files
#!/bin/bash
# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]
#
# Deinterleaves a FASTQ file of paired reads into two FASTQ
# files specified on the command line. Optionally GZip compresses the output
# FASTQ files using pigz if the 3rd command line argument is the word "compress"
#
# Can deinterleave 100 million paired reads (200 million total
# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s)
#
@rgreenjr
rgreenjr / postgres_queries_and_commands.sql
Last active July 18, 2024 22:25
Useful PostgreSQL Queries and Commands
-- show running queries (pre 9.2)
SELECT procpid, age(clock_timestamp(), query_start), usename, current_query
FROM pg_stat_activity
WHERE current_query != '<IDLE>' AND current_query NOT ILIKE '%pg_stat_activity%'
ORDER BY query_start desc;
-- show running queries (9.2)
SELECT pid, age(clock_timestamp(), query_start), usename, query
FROM pg_stat_activity
WHERE query != '<IDLE>' AND query NOT ILIKE '%pg_stat_activity%'
@nathanhaigh
nathanhaigh / interleave_fastq.sh
Last active March 28, 2022 09:11
Interleave reads from 2 FASTQ files and output to STDOUT.
#!/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
@perival
perival / cg-meta-graph.adoc
Last active August 4, 2023 07:03
A Simple Meta-Data Model for a Graph Database - neo4j

A Simple Meta-Data Model for a Graph Database

Setting up a Meta-Data Framework

This GraphGist is a quick exploration of a simple meta-data administration which can be used to store the structure of the nodes and relationships in a graph database like neo4j.

The data that is set up here could be used in an application layer to provide tailored

@korya
korya / Subfolder to git repo.md
Last active July 18, 2024 18:47
Convert subfolder into Git submodule
@cmdcolin
cmdcolin / jbrowse-render
Last active November 7, 2017 00:04
JBrowse feature rendering outside browser
<html>
<head>
<title>JBrowse feature rendering outside of browser</title>
<link rel="stylesheet" type="text/css" href="css/genome.css">
<script type="text/javascript" src="src/dojo/dojo.js" data-dojo-config="async: 1, baseUrl: './src'"></script>
<script type="text/javascript" src="src/JBrowse/init.js"></script>
<script>
@mandiwise
mandiwise / Update remote repo
Last active July 11, 2024 17:32
Transfer repo from Bitbucket to Github
// Reference: http://www.blackdogfoundry.com/blog/moving-repository-from-bitbucket-to-github/
// See also: http://www.paulund.co.uk/change-url-of-git-repository
$ cd $HOME/Code/repo-directory
$ git remote rename origin bitbucket
$ git remote add origin https://github.com/mandiwise/awesome-new-repo.git
$ git push origin master
$ git remote rm bitbucket
@jasongilman
jasongilman / atom_clojure_setup.md
Last active May 11, 2024 02:25
This describes how I setup Atom for Clojure Development.

Atom Clojure Setup

This describes how I setup Atom for an ideal Clojure development workflow. This fixes indentation on newlines, handles parentheses, etc. The keybinding settings for enter (in keymap.cson) are important to get proper newlines with indentation at the right level. There are other helpers in init.coffee and keymap.cson that are useful for cutting, copying, pasting, deleting, and indenting Lisp expressions.

Install Atom

Download Atom

The Atom documentation is excellent. It's highly worth reading the flight manual.

@cmdcolin
cmdcolin / jbrowse-store-access
Last active November 7, 2017 00:38
<!DOCTYPE html>
<html>
<head>
<title>JBrowse - Retrieve data outside of browser</title>
<meta content="text/html;charset=utf-8" http-equiv="Content-Type">
<link rel="stylesheet" type="text/css" href="css/genome.css">
<script type="text/javascript" src="src/dojo/dojo.js" data-dojo-config="async: 1, baseUrl: './src'"></script>
<script type="text/javascript" src="src/JBrowse/init.js"></script>
<style>
pre {