Aspen Resistance Study Project

This repository will be used to conduct analyses on our Holstrom aspen resistance study project. There are 2 primary experiments in this project that will have their own subdirectories choice-assay and wisasp_common-garden

The instructions herein are for the Lindroth Lab Linux computer Maximus:

## results of `lsb_release -a` (distro info):

LSB Version:	core-9.20160110ubuntu0.2-amd64:core-9.20160110ubuntu0.2-noarch:printing-9.20160110ubuntu0.2-amd64:printing-9.20160110ubuntu0.2-noarch:security-9.20160110ubuntu0.2-amd64:security-9.20160110ubuntu0.2-noarch
Distributor ID:	Zorin
Description:	Zorin OS 12.4
Release:	12
Codename:	xenial

Setup

Cloning and updating the project

This project is located on my github page: https://github.com/morrowcj/aspen-resistance-study/ To make a copy execute the following code in a git-enabled terminal:

git clone [email protected]:morrowcj/aspen-resistance-study.git [destination path]

To update the project, execute a git pull command from within the project folder. For more information on git: https://guides.github.com/introduction/git-handbook/

Other setup

All code in this document should be run from the project root directory unless otherwise specified. To ensure that your terminal starts in the proper working directory, locate the directory and move into it:

# Check starting directory
pwd

/home/morrowcj

# move to project directory
## relative to current directory
cd Documents/holstrom-resistance-study
## OR, absolute path (works from anywhere)
cd /home/morrowcj/Documents/holstrom-resistance-study/

Copying data into the projects

labstorage (L drive)

Phenotypic, plot layout, and identification data for WisAsp will be useful to our analyses. These data are located on the L drive ("/labstorage/Lindroth_Lab/WisAsp Study/Phenotype data summary table").

Find the most recent verision of the phenotype table and copy it to our project's data directory: Note most data will be updated and stored on github

cp "/labstorage/Lindroth_Lab/WisAsp Study/Phenotype data summary table/WisAsp Summary Table DRAFT 6 Dec 2018.xlsx" ~/Documents/holstrom-resistance-study/data/

Box.com data

Our data is housed on Box.com, so in order to use the data in this project, it has to be copied to our project folder. This will need to be done each time the data files are updated.

The Box.com foulder is mounted in the /home/morrowcj/mnt/ folder. Each time the computer is restarted, it needs to be remounted: mount /home/morrowcj/mount/Box.com [morrowcj's Box.com external password].

When the folder is mounted, the data folder can be updated with this code chunk:

rsync -urv /home/morrowcj/mnt/Box.com/lab-resources/projects/Hilldale/Data/ data/

To transfer individual files use cp [target file] [destination directory/]

Cleaned data

Cleaned data will be in .csv formats in the appropriate subdirectories of data/. These will be the files on which we will conduct our analyses. The raw data will be stored in raw-data in the appropriate subdirectories.