Deploy

This document covers Step 5:

Table of Contents:

Luna

Please note that the current setup script supports only a single version of Prism be installed on Luna.

You can either use Fabric or do it manually.

Make sure to use your own private key and UNIX account.

$ fab -i ~/.ssh/id_rsa -u chunj -H u36.cbio.mskcc.org rsync_luna

Upload the installation package to Luna:

$ scp prism-v1.0.0.tgz chunj@u36.cbio.mskcc.org:/home/chunj

Log in to u36.cbio.mskcc.org.

Uncompress the installation package:

$ mkdir prism-setup-v1.0.0
$ tar xvzf prism-v1.0.0.tgz -C prism-setup-v1.0.0

Start installation:

$ cd prism-setup-v1.0.0/setup/scripts
$ ./install-production.sh -l
$ ./configure-reference-data.sh -l ifs

Log out and log back in.

The most up-to-date instructions can be found here.

Get genome assemblies files and place them under ./setup/data/assemblies.

Upload the installation package to the VM (this uses rsync):

$ sync-to-vm.sh -p 7777 -u chunj

Log in to the virtual machine.

Create a directory where Prism will be installed:

$ sudo mkdir -p /ifs && sudo chmod a+w /ifs

Install cmo wrapper:

$ cd /tmp/prism-setup/scripts
$ ./install-cmo.sh

Start installation:

$ ./install-production.sh -l
$ ./configure-reference-data.sh -l local

Log out and log back in.