Template:SeqShopExtSetup
Setup when running on your own outside of the SeqShop Workshop
This section is specifically for running on your own outside of the SeqShop Workshop.
If you are running during the SeqShop Workshop, please skip this section.
Workshop Setup Steps
If this is your first SeqShop tutorial, you need to run some initial setup steps.
These setup steps only need to be run once.
If you have already run another SeqShop tutorial, you can skip these steps (select 'Collapse' to hide the steps that you can skip)
Download & Build GotCloud
- cd to where you want GotCloud installed (you can change this to any directory you want)
mkdir -p ~/seqshop cd ~/seqshop/
- download, decompress, and build the version of gotcloud that was tested with this tutorial:
wget https://github.com/statgen/gotcloud/archive/gotcloud.workshop.tar.gz tar xvf gotcloud.workshop.tar.gz mv gotcloud-gotcloud.workshop gotcloud cd gotcloud/src make cd ../..
Remember the path to gotcloud/ - you will need to set the GC variable to the path.
Download the Workshop Example Data
wget http://www.sph.umich.edu/csg/mktrost/seqshopExample.tar.gz
Setup your run environment
Environment variables will be used throughout the tutorial.
We recommend that you setup these variables so you won't have to modify every command in the tutorial.
I'm using bash (replace the paths below with the appropriate paths):
- Point to where you installed GotCloud
export GC=~/seqshop/gotcloud
- Point to where you installed the seqshop files
export SS=~/seqshop/example
- Point to where you want the output to go
export OUT=~/seqshop/output
I'm using tcsh (replace the paths below with the appropriate paths):
- Point to where you installed GotCloud
setenv GC ~/seqshop/gotcloud
- Point to where you installed the seqshop files
setenv SS ~/seqshop/example
- Point to where you want the output to go
setenv OUT ~/seqshop/output