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Ray

Ray is a de novo assembler which uses MPI for parallel processing.[1]

Locally Installed Version

Proteus provides Ray 2.3.1 with the following module file:

ray/gcc/2.3.1

It requires the following modulefiles to run:

gcc proteus-openmpi/gcc/64/1.8.1-mlnx-ofed

Instructions for compiling it yourself follow.

Download

Download the latest version from the download page.[2] We suggest using the SourceForge download site since it clearly tags the release version.

Scan the installation instructions in the files INSTALL.txt and README.md.

Configure

Load an appropriate MPI modulefile:

module load proteus-openmpi/gcc/64/1.8.1-mlnx-ofed

Edit Compilation Flags

Edit the provided Makefile to change CXXFLAGS:[3] (not strictly necessary)

CXXFLAGS = -O3 -march=corei7-avx -std=c++98 -Wall

Edit Install Location Prefix

PREFIX = /mnt/HA/groups/myrsrchGrp/apps/Ray-2.3.1

Compile

[juser@proteusa01 Ray-2.3.1]$ make -j 12 | tee Make.out

You will see a lot of output. This output is also written to the file named Make.out. Once it is done, you should find the executable "Ray" in that directory. You may optionally strip symbols to make a smaller executable file:

[juser@proteusa01 Ray-2.3.1]$ strip Ray

Optionally, build the documentation for the code:

[juser@proteusa01 Ray-2.3.1]$ cd code [juser@proteusa01 code]$  doxygen DoxygenConfigurationFile

Install

[juser@proteusa01 Ray-2.3.1]$ make install | tee Make.install.out Installing Ray to /mnt/HA/groups/myrsrchGrp/apps/Ray-2.3.1

Set Up Environment

Either write an environment module, or modify your PATH environment variable.

Example Job Script

See the example in /mnt/HA/examples/Ray/: documented at Job Script Example 04 Ray assembler

References

[1] Ray -- parallel genome assembler using MPI

[2]

[3] Compiling with GCC