Difference between revisions of "RAREMETAL DOWNLOAD & BUILD"

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(Created page with " == Where to Download == We have tested our source code package on several platforms, including Linux/Ubuntu, Linux/Debian, Linux/RedHat, Linux/CentOS, Mac OS X 10.8, CygWIN6...")
 
(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]]
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== Useful Wiki Pages ==
  
== Where to Download ==
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* The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]
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* The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']]
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* The [[RAREMETAL FAQ | '''FAQ''']]
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* The [[RAREMETAL_Change_Log | '''Change Log''']]
  
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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===GitHub===
  
* The source package for Linux can be downloaded here: [[Media:LINUX_raremetal.0.4.9.tgz ‎|'''for Linux''']]
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All source code is available on GitHub:
  
* The source package for Linux can be downloaded here: [[Media:MAC_raremetal.0.4.9.tgz ‎|'''for MAC OS X''']]
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https://github.com/statgen/Raremetal
  
* The source package for Linux can be downloaded here: [[Media:CYGWIN64_raremetal.0.4.9.tgz ‎|'''for Cygwin64 in Windows''']]
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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:MINGW_raremetal.0.4.9.tgz ‎|'''for MinGW in 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].
  
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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===SCRIPTS===
* The binary of RAREMETALWORKER to run on Linux can also be downloaded here: [[Media:RMW.binary.0.4.9.tgz|'''RAREMETALWORKER BINARY for Linux''']]
 
* If you prefer to start from the source files, you can start from decompress the package using the following command:
 
  tar xvf Raremetalworker.0.4.9.tgz
 
* For UM CSG cluster users, no installation is needed. It is available at /net/fantasia/home/sfengsph/code/Rare-Metal/RareMetalWorker/bin/raremetalworker
 
  
== How to Compile ==
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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.  
* Go to /RareMetalWorker_0.4.9/RareMetalWorker/src and use the following command:
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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'''.
 
  make
 
* 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.