Difference between revisions of "RAREMETAL DOWNLOAD & BUILD"

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(How to Compile)
(Release 4.15.0; simplify release notes to point to self-contained repository.)
 
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[[Category:RAREMETAL]]
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[[Category:RAREMETALWORKER]]
 
== Useful Wiki Pages ==
 
== Useful Wiki Pages ==
  
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* The [[RAREMETAL_Change_Log | '''Change Log''']]
 
* The [[RAREMETAL_Change_Log | '''Change Log''']]
  
== Where to Download ==
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===GitHub===
  
* University of Michigan CSG users can go to the following:
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All source code is available on GitHub:
  /net/wonderland/home/saichen/Raremetal/
 
  
===GIT HUB===
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https://github.com/statgen/Raremetal
  
Please clone or download from GitHub:
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See README.md for instructions on how to compile RAREMETAL for your environment. It should be possible to compile in Mac OS and Linux environments. You will need '''Cmake''' and '''Cget''' available.
  
https://github.com/traxexx/Raremetal
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Since version 4.13.6, RAREMETALWORKER and RAREMETAL are distributed within the same package in this repository. More information on changes may be found at our [https://github.com/statgen/raremetal/releases releases page].
 
 
Since v4.13.6, MAC and WINDOWS version are no longer updated. Please download old versions from here:
 
 
 
* [[Media:MAC_raremetal.4.13.6.tgz ‎|'''for MAC OS X''']]
 
 
 
* [[Media:CYGWIN64_raremetal.4.13.6.tgz ‎|'''for Windows/CygWin64''']]
 
 
 
* [[Media:MINGW_raremetal.4.13.6.tgz ‎|'''for Windows/MinGW''']]
 
 
 
From version 4.13.6, RAREMETALWORKER and RAREMETAL are distributed within the same package.
 
  
 
===SCRIPTS===
 
===SCRIPTS===
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*If you want to estimate '''Odds Ratios''' of variants analyzed by RAREMETALWORKER, the script [[Media:CalculateOddsRatio.tgz|'''calculateOddsRatio.pl''']] can help you augment RAREMETALWORKER output with estimated odds ratio to the last column.  
 
*If you want to estimate '''Odds Ratios''' of variants analyzed by RAREMETALWORKER, the script [[Media:CalculateOddsRatio.tgz|'''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'''.
 
*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 [http://gcc.gnu.org/wiki/GFortranBinaries '''GNU gfortran'''] for download.
 
 
* If you prefer to build from scratch, then do the following in your Raremetal directory:
 
  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 [http://openmp.org/wp/openmp-compilers/ 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 [http://genome.sph.umich.edu/wiki/RAREMETAL_FAQ ''' FAQ'''] for more information.
 

Latest revision as of 12:44, 14 March 2019

Useful Wiki Pages

GitHub

All source code is available on GitHub:

https://github.com/statgen/Raremetal

See README.md for instructions on how to compile RAREMETAL for your environment. It should be possible to compile in Mac OS and Linux environments. You will need Cmake and Cget available.

Since version 4.13.6, RAREMETALWORKER and RAREMETAL are distributed within the same package in this repository. More information on changes may be found at our releases page.

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.