66
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
=== 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
# 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>.
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 ==
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"
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
----------------------------------------------------------------------------------
----------------------------------------------------------------------------------
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
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]
----------------------------------------------------------------------------------
----------------------------------------------------------------------------------
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.
###############################################################################
###############################################################################
== 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.
