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| − | | + | [[Category:RAREMETAL]] |
| − | | + | [[Category:RAREMETALWORKER]] |
| | == Useful Wiki Pages == | | == Useful Wiki Pages == |
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| − | There are several pages in this Wiki that may be useful to RAREMETALWORKER users. Here are links to key pages:
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| | * 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''']] |
| | + | * The [[RAREMETAL_Change_Log | '''Change Log''']] |
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| − | == Where to Download == | + | ===GitHub=== |
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| − | 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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| − | * The source package for Linux can be downloaded here: [[Media:LINUX_raremetal.0.4.9.tgz |'''for Linux''']]
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| − | * The source package for Linux can be downloaded here: [[Media:MAC_raremetal.0.4.9.tgz |'''for MAC OS X''']]
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| − | * The source package for Linux can be downloaded here: [[Media:CYGWIN64_raremetal.0.4.9.tgz |'''for Cygwin64 in Windows''']]
| + | All source code is available on GitHub: |
| | | | |
| − | * The source package for Linux can be downloaded here: [[Media:MINGW_raremetal.0.4.9.tgz |'''for MinGW in Windows''']]
| + | https://github.com/statgen/Raremetal |
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| − | 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.
| + | 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 binary of RAREMETALWORKER to run on Linux can also be downloaded here: [[Media:RMW.binary.0.4.9.tgz|'''RAREMETALWORKER BINARY for Linux''']]
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| − | * If you prefer to start from the source files, you can start from decompress the package using the following command:
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| − | tar xvf Raremetalworker.0.4.9.tgz
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| − | * For UM CSG cluster users, no installation is needed. It is available at /net/fantasia/home/sfengsph/code/Rare-Metal/RareMetalWorker/bin/raremetalworker
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| − | == How to Compile ==
| + | 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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| − | * Go to /RareMetalWorker_0.4.9/RareMetalWorker/src and use the following command:
| + | ===SCRIPTS=== |
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| − | make
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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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| − | For compiling questions, please go to [http://genome.sph.umich.edu/wiki/RAREMETAL_FAQ ''' FAQ'''] for more information.
| + | ====Calculating Odds Ratio from RAREMETALWORKER output==== |
| | + | *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'''. |
