Deren Eaton dereneaton

## R-amova.ipynb

      
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                dereneaton
                / R-amova.ipynb
            
            
              Created
              September 5, 2017 15:17
            
              
                R-amova-tutorial
              
          
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## install_bpp_conda.sh
## save our current directory so we can return to it
CURDIR=$(pwd)

## find the path to our conda bin dir (this _should_ be in our PATH)
CONDADIR=$(which conda)
CONDABIN=$(dirname $CONDADIR)
CONDAPKG=$(dirname $CONDABIN)/pkgs

## download bpp source into the conda pkgs dir
cd $CONDAPKG/

## PE-GBS_empirical.ipynb

      
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                dereneaton
                / PE-GBS_empirical.ipynb
            
            
              Last active
              April 16, 2018 21:04
            
              
                ** PERMALINKED **
              
          
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## install_clumpp_conda.sh
## save our current directory so we can return to it
CURDIR=$(pwd)

## find the path to our conda bin dir (this _should_ be in our PATH)
CONDADIR=$(which conda)
CONDABIN=$(dirname $CONDADIR)
CONDAPKG=$(dirname $CONDABIN)/pkgs

## download linux CLUMPP into the conda pkgs dir
cd $CONDAPKG/

## install_structure_conda.sh
## save our current directory so we can return to it
CURDIR=$(pwd)

## find the path to our conda bin dir (this _should_ be in our PATH)
CONDADIR=$(which conda)
CONDABIN=$(dirname $CONDADIR)
CONDAPKG=$(dirname $CONDABIN)/pkgs

## download linux no-console version into the conda pkgs dir
cd $CONDAPKG/

## install_ibpp_conda.sh
## save our current directory so we can return to it
CURDIR=$(pwd)

## find the path to our conda bin dir (this _should_ be in our PATH)
CONDADIR=$(which conda)
CONDABIN=$(dirname $CONDADIR)
CONDAPKG=$(dirname $CONDABIN)/pkgs

## download bpp source into the conda pkgs dir
cd $CONDAPKG/

## install_ibpp.sh

## save our current directory so we can come back here when we're done
WORKDIR=$(pwd)

## To install local software I keep a directory in my home dir called 'local/'
## the command below will make this dir if it does not already exist.
mkdir -p ~/local/src/

## move into your local/src directory
cd ~/local/src

## install_bpp.sh

## save our current directory so we can come back here when we're done
WORKDIR=$(pwd)

## To install local software I keep a directory in my home dir called 'local/'
## the command below will make this dir if it does not already exist.
mkdir -p ~/local/src/

## move into your local/src directory
cd ~/local/src

## example_condor.sh

#!/bin/bash

## reload .bashrc b/c I'm not sure it's reloaded on UW's Condor
source /mnt/gluster/jlmcdaniel/.bashrc

## change into the directory with your params file
cd  /mnt/gluster/jlmcdaniel/ipyrad/porroglossum

## call ipyrad to run some step, by default it will use all available cores

## gist:7031947
{
 "metadata": {
  "name": "PyRAD_STACKS"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
	## save our current directory so we can return to it
	CURDIR=$(pwd)

	## find the path to our conda bin dir (this _should_ be in our PATH)
	CONDADIR=$(which conda)
	CONDABIN=$(dirname $CONDADIR)
	CONDAPKG=$(dirname $CONDABIN)/pkgs

	## download bpp source into the conda pkgs dir
	cd $CONDAPKG/

	## save our current directory so we can come back here when we're done
	WORKDIR=$(pwd)

	## To install local software I keep a directory in my home dir called 'local/'
	## the command below will make this dir if it does not already exist.
	mkdir -p ~/local/src/

	## move into your local/src directory
	cd ~/local/src

	#!/bin/bash

	## reload .bashrc b/c I'm not sure it's reloaded on UW's Condor
	source /mnt/gluster/jlmcdaniel/.bashrc

	## change into the directory with your params file
	cd /mnt/gluster/jlmcdaniel/ipyrad/porroglossum

	## call ipyrad to run some step, by default it will use all available cores
	{
	"metadata": {
	"name": "PyRAD_STACKS"
	},
	"nbformat": 3,
	"nbformat_minor": 0,
	"worksheets": [
	{
	"cells": [
	{