This page was last updated on Thursday, 12-Oct-2017 09:28:28 CDT

Installation notes for LinkImpute version 1.1 and LinkImputeR version 1.1.1

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Prerequisites

Installation

1. $ cd /programinstallers/
2. $ wget -N http://www.cultivatingdiversity.org/uploads/5/8/2/9/58294859/linkimpute.tar.gz
3. $ wget -N http://www.cultivatingdiversity.org/uploads/5/8/2/9/58294859/20170901_linkimputer.tar.gz
4. $ wget -N http://data.cultivatingdiversity.org/software_files/pythonscript.zip && mv pythonscript.zip linkimpute-pythonscript.zip
5. $ mkdir /usr/local/bin/linkimpute
6. $ cd /usr/local/bin/linkimpute
7. $ tar -zxvf /programinstallers/nas/linkimpute.tar.gz

   UserGuide.pdf
   LinkImpute.jar
   lib/
   lib/commons-cli-1.3-20140716.123849-104.jar
   apple.raw

8. $ tar -zxvf /programinstallers/nas/20170901_linkimputer.tar.gz

   UserGuide.pdf
   LinkImputeR.jar
   lib/
   lib/commons-logging-1.2.jar
   lib/commons-configuration2-2.0-beta1.jar
   lib/commons-math3-3.5.jar
   lib/commons-lang3-3.4.jar
   lib/commons-beanutils-1.9.2.jar
   accuracy.ini
   apple.vcf

9. $ unzip /programinstallers/nas/linkimpute-pythonscript.zip

   Archive:  /programinstallers/nas/linkimpute-pythonscript.zip
     inflating: Barcode.py              
     inflating: barcode_splitter.py     
     inflating: Barcodes.py             
     inflating: Sequence.py             
     inflating: Tag.py

10. $ chmod +x *.py
11. $ chmod 666 accuracy.ini
12. Add to default PATH for all users
    $ sudo nano /etc/profile
    ...
    PATH="$PATH:/usr/local/bin/linkimpute"
    ...
13. Test (need to run in an X session)
    $ java -jar /usr/local/bin/linkimpute/LinkImpute.jar --version
    Version 1.1 (30 September 2015)
14. $ java -jar /usr/local/bin/linkimpute/LinkImputeR.jar -v
    LinkImputeR version 1.1.1
15. Local copy of documentation
    $ mkdir /programinstallers/web/linkimpute
16. $ cp -puv UserGuide.pdf /programinstallers/web/linkimpute/