Difference between revisions of "RAREMETAL DOWNLOAD & BUILD"

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(Useful Wiki Pages)
(SOURCE CODE (v4.13.8))
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   /net/wonderland/home/saichen/Raremetal/
 
   /net/wonderland/home/saichen/Raremetal/
  
===SOURCE CODE (v4.13.8)===
+
===SOURCE CODE (v4.13.9)===
  
 
To download source code for each platform, please go to the following:
 
To download source code for each platform, please go to the following:
  
* [[Media:LINUX_raremetal.4.13.8.tgz ‎|'''for Linux''']]  
+
* [[Media:Raremetal_linux.tgz ‎|'''for Linux''']]  
  
 
Note Mac and Windows versions are still at v4.13.6
 
Note Mac and Windows versions are still at v4.13.6

Revision as of 12:40, 14 July 2016

Useful Wiki Pages

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/

SOURCE CODE (v4.13.9)

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

Note Mac and Windows versions are still at v4.13.6

EXECUTABLES (v4.13.8)

Executables for RAREMETAL and RAREMETALWORKER can be downloaded in the following. If these don't work on your platform, you might have to build from source code which can be downloaded above.

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 LINUX_raremetal.4.13.8.tgz
 prompt> cd LINUX_raremetal.4.13.8
  • If you prefer to build two tools all at once, then do the following:
 prompt> make
 #This builds RAREMETAL and RAREMETALWORKER under bin/ directory. 
  • If you prefer to build individual tool:
 prompt> cd LINUX_raremetal.4.13.8/raremetalworker/src
 prompt> make
 #This will build RAREMETALWORKER under raremetal/bin/ directory.
 prompt> cd LINUX_raremetal.4.13.8/raremetal/src
 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.