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]