Vivek Krishnakumar vivekkrish

## bedtools_cheatsheet.md

      
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                ilevantis
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                Bedtools cheatsheet
              
          
    Bedtools Cheatsheet

General:


Tools
Description


flank
Create new intervals from the flanks of existing intervals.


slop
Adjust the size of intervals.


shift
Adjust the position of intervals.


subtract
Remove intervals based on overlaps b/w two files.


## gist:ebaca117ac9e44231421f04e7796d5ca
After automatically updating Postgres to 10.0 via Homebrew, the pg_ctl start command didn't work.
The error was "The data directory was initialized by PostgreSQL version 9.6, which is not compatible with this version 10.0."

Database files have to be updated before starting the server, here are the steps that had to be followed:

# need to have both 9.6.x and latest 10.0 installed, and keep 10.0 as default
brew unlink postgresql
brew install postgresql@9.6
brew unlink postgresql@9.6
brew link postgresql

## NOTES.md

      
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                cybersiddhu
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                notes
              
          
    Aim

The idea was to have a intermine prototype for dictybase, dictymine
running with a basic Genes -> GO -> GO annotation with all the basic features
up and running. And then try out a deploy to google
cloud using my stack of docker and
kuberntes
Progress


On the first day saw the new intermine UI
redgenes which i set it up with a simple


## jbrowse-store-access
<!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 {

## atom_clojure_setup.md

      
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                jasongilman
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                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.

  
## Update remote repo
// 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

## jbrowse-render
<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>


## Subfolder to git repo.md

      
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                korya
                / Subfolder to git repo.md
            
            
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                Convert subfolder into Git submodule
              
          
    Source: http://willandorla.com/will/2011/01/convert-folder-into-git-submodule/
1. Clone new repository

$ git clone --no-hardlinks original-repo copied-repo
2. Filter out the files you want to keep and remove the others


## cg-meta-graph.adoc

      
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                perival
                / cg-meta-graph.adoc
            
            
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                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


## interleave_fastq.sh
#!/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
Tools	Description
flank	Create new intervals from the flanks of existing intervals.
slop	Adjust the size of intervals.
shift	Adjust the position of intervals.
subtract	Remove intervals based on overlaps b/w two files.
	After automatically updating Postgres to 10.0 via Homebrew, the pg_ctl start command didn't work.
	The error was "The data directory was initialized by PostgreSQL version 9.6, which is not compatible with this version 10.0."

	Database files have to be updated before starting the server, here are the steps that had to be followed:

	# need to have both 9.6.x and latest 10.0 installed, and keep 10.0 as default
	brew unlink postgresql
	brew install postgresql@9.6
	brew unlink postgresql@9.6
	brew link postgresql
	<!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 {
	// 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
	<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>
	#!/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