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 ==
  
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, CygWIN64 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, which can be downloaded in the following:
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https://github.com/statgen/Raremetal
  
* The source package for Linux can be downloaded here: [[Media:LINUX_raremetal.0.4.9.tgz ‎|'''for Linux''']]
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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.
  
* The source package for Linux can be downloaded here: [[Media:MAC_raremetal.0.4.9.tgz ‎|'''for MAC OS X''']]
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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].
  
* The source package for Linux can be downloaded here: [[Media:CYGWIN64_raremetal.0.4.9.tgz ‎|'''for Cygwin64 in Windows''']]
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===SCRIPTS===
  
* The source package for Linux can be downloaded here: [[Media:MINGW_raremetal.0.4.9.tgz ‎|'''for MinGW in Windows''']]
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====Calculating Odds Ratio from RAREMETALWORKER output====
 
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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.  
For binary executables, we only distribute the one for Linux. For the other platforms, we recommend you build from source code that can be downloaded from above.
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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'''.
* The binary of RAREMETALWORKER to run on Linux can also be downloaded here: [[Media:RMW.binary.0.4.9.tgz|'''RAREMETALWORKER BINARY for Linux''']]
 
 
 
== 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.
 
 
 
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.