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| | + | [[Category:RAREMETAL]] |
| | + | [[Category:RAREMETALWORKER]] |
| | == Useful Wiki Pages == | | == Useful Wiki Pages == |
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| | * The [[RAREMETAL_Change_Log | '''Change Log''']] | | * The [[RAREMETAL_Change_Log | '''Change Log''']] |
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| − | == Where to Download == | + | ===GitHub=== |
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| − | From version 4.13.6, RAREMETALWORKER and RAREMETAL are distributed within the same package.
| + | All source code is available on GitHub: |
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| − | * University of Michigan CSG users can go to the following:
| + | https://github.com/statgen/Raremetal |
| − | /net/wonderland/home/saichen/Raremetal/
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| | | | |
| − | ===SOURCE CODE (v4.13.9)===
| + | 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. |
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| − | To download source code for each platform, please go to the following:
| + | 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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| − | * [[Media:Raremetal_linux.tgz |'''for Linux''']]
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| − | | |
| − | Note Mac and Windows versions are still at v4.13.6
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| − | * [[Media:MAC_raremetal.4.13.6.tgz |'''for MAC OS X''']]
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| − | * [[Media:CYGWIN64_raremetal.4.13.6.tgz |'''for Windows/CygWin64''']]
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| − | * [[Media:MINGW_raremetal.4.13.6.tgz |'''for Windows/MinGW''']]
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| − | ===EXECUTABLES (v4.13.9)===
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| − | If you cannot compile Raremetal source code, please download these executables, then put "raremetal" and "raremetalworker" under "Raremetal_linux/bin/".
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| − | *[[Media: Raremetal_linux_executables.tgz |'''for Linux''']]
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| | ===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'''. |
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| − | == How to Compile ==
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| − | * 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.
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| − | * If you choose to build from the source files, you could start from decompress the package using the following command:
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| − | prompt> tar xvf Raremetal_linux.tgz
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| − | prompt> cd Raremetal
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| − | * If you prefer to build from scratch, then do the following:
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| − | prompt> make clean
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| − | prompt> make
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| − | #This builds RAREMETAL and RAREMETALWORKER under bin/ directory.
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| − | * If you prefer to build individual tool:
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| − | prompt> cd Raremetal/raremetalworker/
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| − | prompt> make
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| − | #This will build RAREMETALWORKER under raremetal/bin/ directory.
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| − |
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| − | prompt> cd Raremetal/raremetal/
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| − | prompt> make
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| − | #This will build RAREMETAL under raremetal/bin/ directory.
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| − | * 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].
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| − | prompt> cd raremetalworker/src
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| − | prompt> make openmp
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| − | #This will build RAREMETALWORKER under raremetal/bin/ directory.
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| − | * 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.
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| − | ==FAQ==
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| − | For compiling questions, please go to [http://genome.sph.umich.edu/wiki/RAREMETAL_FAQ ''' FAQ'''] for more information.
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