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@dereneaton
dereneaton / install_clumpp_conda.sh
Created Feb 13, 2017
Install clumpp v1.1.2 binary into your conda dir
View 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 $CONDAPKG/
@dereneaton
dereneaton / install_structure_conda.sh
Last active Feb 13, 2017
installs structure 2.3.4. into your conda dir
View install_structure_conda.sh
## save our current directory so we can return to it
CURDIR=$(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 $CONDAPKG/
View install_ibpp_conda.sh
## save our current directory so we can return to it
CURDIR=$(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 $CONDAPKG/
@dereneaton
dereneaton / install_bpp_conda.sh
Last active Sep 12, 2018
Install bpp 3.3 into your conda dir
View install_bpp_conda.sh
## save our current directory so we can return to it
CURDIR=$(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 $CONDAPKG/
@dereneaton
dereneaton / install_ibpp.sh
Last active Dec 3, 2016
Download and install iBPP (v.2.1) into ~/local/src/iBPP/src
View install_ibpp.sh
## save our current directory so we can come back here when we're done
WORKDIR=$(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
@dereneaton
dereneaton / install_bpp.sh
Last active Dec 3, 2016
Download and install bpp (v.3.3) locally (into ~/local/src/bpp/src)
View 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
View 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
View toy_heatmap.ipynb
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View gist:3e50570074b49c0485e6
<style>
html {
font-size: 62.5% !important; }
body {
font-size: 1.5em !important; /* currently ems cause chrome bug misinterpreting rems on body element */
line-height: 1.6 !important;
font-weight: 400 !important;
font-family: "Raleway", "HelveticaNeue", "Helvetica Neue", Helvetica, Arial, sans-serif !important;
color: #222 !important; }