RAREMETAL DOWNLOAD & BUILD

Useful Wiki Pages

• The RAREMETALWORKER documentation
• The RAREMETAL documentation
• The FAQ
• The Change Log

Where to Download

From version 4.13.6, RAREMETALWORKER and RAREMETAL are distributed within the same package.

• University of Michigan CSG users can go to the following:

 /net/wonderland/home/saichen/Raremetal/

GIT HUB

You can clone or download from Raremetal git hub page: https://github.com/traxexx/Raremetal

SOURCE CODE (v4.13.9)

To download source code for each platform, please go to the following:

• for Linux

Note Mac and Windows versions are still at v4.13.6

• for MAC OS X

• for Windows/CygWin64

• for Windows/MinGW

EXECUTABLES (v4.13.9)

If you cannot compile Raremetal source code, please download these executables. They can be used directly.

Note: if you want to use --labelHits option, please put executables "raremetal" and "raremetalworker" under your source code directory "Raremetal/bin/".

• for Linux

SCRIPTS

Calculating Odds Ratio from RAREMETALWORKER output

• If you want to estimate Odds Ratios of variants analyzed by RAREMETALWORKER, the script calculateOddsRatio.pl can help you augment RAREMETALWORKER output with estimated odds ratio to the last column.
• The script can also be found in the RAREMETAL package 4.13.6 and later, under directory raremetal/script/calculateOddsRatio.pl.

How to Compile

• gfortran is necessary to build RAREMETAL. If your system does not have it yet, please go to GNU gfortran for download.

• If you choose to build from the source files, you could start from decompress the package using the following command:

 prompt> tar xvf Raremetal_linux.tgz
 prompt> cd Raremetal

• If you prefer to build from scratch, then do the following:

 prompt> make clean
 prompt> make
 #This builds RAREMETAL and RAREMETALWORKER under bin/ directory. 

• If you prefer to build individual tool:

 prompt> cd Raremetal/raremetalworker/
 prompt> make
 #This will build RAREMETALWORKER under raremetal/bin/ directory.

 prompt> cd Raremetal/raremetal/
 prompt> make
 #This will build RAREMETAL under raremetal/bin/ directory.

• If your compiler is adaptable to openmp (parallel computing), then use the following to build RAREMETALWORKER that allows parallel computing. For more about openmp, please refer to openMP.

 prompt> cd raremetalworker/src
 prompt> make openmp
 #This will build RAREMETALWORKER under raremetal/bin/ directory.

• If you prefer to use the binary file downloaded above, then no compiling is needed, but it is not guaranteed to work due to system and library requirements.

FAQ

For compiling questions, please go to FAQ for more information.