Template:SeqShopExtSetup

From Genome Analysis Wiki
Jump to: navigation, search

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://csg.sph.umich.edu//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