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| | | |
| === Download from webpage === | | === Download from webpage === |
− | Through this link [http://www.sph.umich.edu/csg/jich/FallInBed/ FallInBed Download], you can download a copy of FallInBed. | + | Through this link [http://www.sph.umich.edu/csg/jich/FallInBed/ FallInBed Download], you can download a copy of GREGOR. |
| | | |
| === Download from GitHub with Git === | | === Download from GitHub with Git === |
| You can create your own git clone(copy) using: | | You can create your own git clone(copy) using: |
| | | |
− | git clone https://github.com/jinchen-umich/FallInBed.git | + | git clone https://github.com/jinchen-umich/GREGOR.git |
| or | | or |
− | git clone git://github.com/jinchen-umich/FallInBed.git | + | git clone git://github.com/jinchen-umich/GREGOR.git |
| | | |
− | Either of these two commands creates a directory called FallInBed in the current directory. | + | Either of these two commands creates a directory called GREGOR in the current directory. |
| | | |
| === Update your copy === | | === Update your copy === |
| If you have already downloaded your copy, use the following commands to update: | | If you have already downloaded your copy, use the following commands to update: |
− | 1. cd pathToYourCopy/FallInBed | + | 1. cd pathToYourCopy/GREGOR |
| 2. git pull | | 2. git pull |
| | | |
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| # Latest Code (master branch) | | # Latest Code (master branch) |
| #: via Website | | #: via Website |
− | #:# Go to : https://github.com/jinchen-umich/FallInBed | + | #:# Go to : https://github.com/jinchen-umich/GREGOR |
| #:# Click on the <code>Download ZIP</code> button on the right side panel. | | #:# Click on the <code>Download ZIP</code> button on the right side panel. |
| #: via Command Line | | #: via Command Line |
− | #:: <code>wget https://github.com/jinchen-umich/FallInBed/archive/master.zip</code> | + | #:: <code>wget https://github.com/jinchen-umich/GREGOR/archive/master.zip</code> |
| | | |
| After downloading the file, uncompress (unzip/untar) it. The directory created will be named <code>FallInBed</code>. | | After downloading the file, uncompress (unzip/untar) it. The directory created will be named <code>FallInBed</code>. |
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| To build GREGOR, copy the GREGOR package to the directory you want, and then run the following command: | | To build GREGOR, copy the GREGOR package to the directory you want, and then run the following command: |
| | | |
− | tar xzvf FallInBed.tar.gz | + | tar xzvf GREGOR.tar.gz |
| | | |
− | After you unzip, you can find 3 directories in "FallInBed" (./example ./lib ./script). | + | After you unzip, you can find 3 directories in "GREGOR" (./example ./lib ./script). |
| | | |
| == Download reference files == | | == Download reference files == |
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| Download the reference files from this link [http://www.sph.umich.edu/csg/jich/FallInBed/ FallInBed Download], then un-package the file | | Download the reference files from this link [http://www.sph.umich.edu/csg/jich/FallInBed/ FallInBed Download], then un-package the file |
| | | |
− | tar xzvf FallInBed.ref.tar.gz | + | tar xzvf GREGOR.ref.tar.gz |
| | | |
| After unzip, you will get 47 reference files in the directory "~/ref" | | After unzip, you will get 47 reference files in the directory "~/ref" |
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| When you run | | When you run |
| | | |
− | perl FallInBed.pl | + | perl GREGOR.pl |
| | | |
− | you will get some information about FallInBed | + | you will get some information about GREGOR |
| | | |
| ---------------------------------------------------------------------------------- | | ---------------------------------------------------------------------------------- |
− | FallInBeds.pl : Functional annotation of trait-associated variants
| + | GREGOR.pl : Functional annotation of trait-associated variants |
| ---------------------------------------------------------------------------------- | | ---------------------------------------------------------------------------------- |
| This program tests for enrichment of an input list of trait-associated index | | This program tests for enrichment of an input list of trait-associated index |
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| Report Bug(s) : jich[at]umich[dot]edu | | Report Bug(s) : jich[at]umich[dot]edu |
| ---------------------------------------------------------------------------------- | | ---------------------------------------------------------------------------------- |
− | Usage : perl FallInBeds.pl --conf [conf.file] | + | Usage : perl GREGOR.pl --conf [conf.file] |
| ---------------------------------------------------------------------------------- | | ---------------------------------------------------------------------------------- |
| | | |
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| The following command is a typical command line: | | The following command is a typical command line: |
| | | |
− | perl FallInBed.pl --conf [conf.file] | + | perl GREGOR.pl --conf [conf.file] |
| | | |
| Example configuration file can be found in example directory. Users have to modify the configurations before running. | | Example configuration file can be found in example directory. Users have to modify the configurations before running. |
| | | |
| == Configuration File == | | == Configuration File == |
− | The example configuration file below illustrate how to configure the FallInBed configuration file. | + | The example configuration file below illustrate how to configure the GREGOR configuration file. |
| | | |
| ############################################################################### | | ############################################################################### |
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| | | |
| == Testing GREGOR == | | == Testing GREGOR == |
− | There is an example directory in ~/FallInBed. You can find index SNP file, 3 bed files, bed file index and example config file. | + | There is an example directory in ~/GREGOR. You can find index SNP file, 3 bed files, bed file index and example config file. |
| After change your config file, you can run a test. | | After change your config file, you can run a test. |
| | | |
− | perl ~/FallInBed/script/FallInBed.pl --conf ~/FallInBed/example/example.conf | + | perl ~/GREGOR/script/GREGOR.pl --conf ~/GREGOR/example/example.conf |
| | | |
| After running 2 minutes +/- 1 minutes. You will get result file "StatisticSummaryFile.txt" in your defined output directory. | | After running 2 minutes +/- 1 minutes. You will get result file "StatisticSummaryFile.txt" in your defined output directory. |