sdsc / abyss-roll

SDSC abyss roll

SDSC "abyss" roll

Overview

This Rocks roll bundles the ABySS sequence assembler package.

ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.

For more information about ABySS please visit the official web page.

Requirements

To build/install this roll you must have root access to a Rocks development machine (e.g., a frontend or development appliance).

If your Rocks development machine does not have Internet access you must download the appropriate abyss source file(s) using a machine that does have Internet access and copy them into the src/abyss directory on your Rocks development machine.

Dependencies

The sdsc-roll must be installed on the build machine, since the build process depends on make include files provided by that roll.

The roll sources assume that modulefiles provided by SDSC compiler and mpi rolls are available, but it will build without them as long as the environment variables they provide are otherwise defined.

The build process requires the boost libraries and assumes that the boost modulefile provided by the SDSC boost-roll is available. It will build without the modulefile as long as the environment variables it provides are otherwise defined.

Building

To build the abyss-roll, execute this on a Rocks development machine (e.g., a frontend or development appliance):

% make 2>&1 | tee build.log

A successful build will create the file abyss-*.disk1.iso. If you built the roll on a Rocks frontend, proceed to the installation step. If you built the roll on a Rocks development appliance, you need to copy the roll to your Rocks frontend before continuing with installation.

This roll source supports building with different compilers and for different MPI flavors. The ROLLCOMPILER and ROLLMPI make variables can be used to specify the names of compiler and MPI modulefiles to use for building the software, e.g.,

make ROLLCOMPILER=intel ROLLMPI=mvapich2_ib 2>&1 | tee build.log

The build process recognizes "gnu", "intel" or "pgi" as the value for the ROLLCOMPILER variable; any MPI modulefile name may be used as the value of the ROLLMPI variable. The default values are "gnu" and "rocks-openmpi".

Installation

To install, execute these instructions on a Rocks frontend:

% rocks add roll *.iso
% rocks enable roll abyss
% cd /export/rocks/install
% rocks create distro

Subsequent installs of compute and login nodes will then include the contents of the abyss-roll. To avoid cluttering the cluster frontend with unused software, the abyss-roll is configured to install only on compute and login nodes. To force installation on your frontend, run this command after adding the abyss-roll to your distro

% rocks run roll abyss host=NAME | bash

where NAME is the DNS name of a compute or login node in your cluster.

In addition to the software itself, the roll installs ABYSS environment module files in:

/opt/modulefiles/applications/abyss

Testing

The abyss-roll includes a test script which can be run to verify proper installation of the roll documentation, binaries and module files. To run the test scripts execute the following command(s):

% /root/rolltests/abyss.t