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.
References♯
[1] Ray -- parallel genome assembler using MPI
[2]