Difference between revisions of "RAREMETAL DOWNLOAD & BUILD"

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(Where to Download)
(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 ==
  
There are several pages in this Wiki that may be useful to RAREMETALWORKER users. Here are links to key pages:
 
 
* The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]
 
* The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]
 
* The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]
 
* The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]
 
* The [[RAREMETAL FAQ | '''FAQ''']]
 
* The [[RAREMETAL FAQ | '''FAQ''']]
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* The [[RAREMETAL_Change_Log | '''Change Log''']]
  
== Where to Download ==
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===GitHub===
  
We have tested our source code package on several platforms, including Linux/Ubuntu, Linux/Debian, Linux/RedHat, Linux/CentOS, Mac OS X 10.8, and MinGW for Windows.
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All source code is available on GitHub:
From version 4.9, RAREMETALWORKER and RAREMETAL source code are distributed within the same package. For source code for each platform, please go to the following:
 
  
* [[Media:LINUX_raremetal.0.4.9.tgz ‎|'''for Linux''']]
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https://github.com/statgen/Raremetal
  
* [[Media:MAC_raremetal.0.4.9.tgz ‎|'''for MAC OS X''']]
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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.
  
* [[Media:MINGW_raremetal.0.4.9.tgz ‎|'''for MinGW for Windows''']]
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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].
  
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===SCRIPTS===
  
 
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====Calculating Odds Ratio from RAREMETALWORKER output====
The 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.
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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.  
*[[Media:linux_executables.0.4.9.tgz|'''for Linux''']]
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*The script can also be found in the RAREMETAL package 4.13.6 and later, under directory '''raremetal/script/calculateOddsRatio.pl'''.
*[[Media:cygwin64_executables.0.4.9.tgz|'''CygWin64 for Windows''']]
 
*[[Media:mingw_exe.0.4.9.tgz|''' MinGW for Windows''']]
 
 
 
== 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 choose to build from the source files, you could start from decompress the package using the following command:
 
  prompt> tar xvf LINUX_raremetal.0.4.9.tgz
 
  prompt> cd raremetal_0.4.9
 
 
 
* If you prefer to build two tools all at once, then do the following:
 
  prompt> cd raremetal
 
  prompt> make
 
  #This builds RAREMETAL and RAREMETALWORKER under bin/ directory.
 
 
 
* If you prefer to build individual tool:
 
  prompt> cd raremetal/raremetalworker/src
 
  prompt> make
 
  #This will build RAREMETALWORKER under raremetal/bin/ directory.
 
 
 
  prompt> cd raremetal/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 [http://openmp.org/wp/openmp-compilers/ openMP].
 
  prompt> cd raremetal/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.