Carrot root and DNA VCRU Bioinformatics USDA ARS Vegetable Crops Research Unit

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Installation notes for PAGIT version 1 - Feb 14, 2012

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Prerequisites

"We assume that java and the tcsh-shell is installed"
Java instructions
$ sudo apt-get install tcsh

PAGIT relies on other freely available bioinformatics software developed by third parties. The list of this third-party software is as follows:

Installation

Note, separate instructions for installing RATT

  1. $ cd /programinstallers/
  2. $ wget -N ftp://ftp.sanger.ac.uk/pub4/resources/software/pagit/PAGIT.V1.64bit.tgz
  3. $ cd /usr/local/bin
  4. $ tar -zxvf /programinstallers/PAGIT.V1.64bit.tgz
  5. $ ./installme.sh
    Installation successfully!
    
    If you intend to use RATT to transfer annotation for species with different start / codons or splice sites, please adapt the file /usr/local/bin/PAGIT/RATT/RATT.config.
    
    Each time you run please type: source /usr/local/bin/PAGIT/sourceme.pagit
    Alternatively include the line in your ~/.bashrc file.
    
    We assume that java and the tcsh-shell is installed
  6. $ rm installme.sh
  7. To allow scripts to find Perl, did this
    $ ln -s /usr/bin/perl /usr/local/bin/perl
  8. Under "Bugs" saw this text: The script to join chromosomes for ABACAS was missing. Please download it and unzip the content in the PAGIT/ABACAS directory.
    $ cd /usr/local/bin/PAGIT/ABACAS/
  9. $ wget -N ftp://ftp.sanger.ac.uk/pub4/resources/software/pagit/PAGIT_MissingScripts.zip
  10. $ unzip PAGIT_MissingScripts.zip
    Archive:  PAGIT_MissingScripts.zip
    replace joinMultifasta.pl? [y]es, [n]o, [A]ll, [N]one, [r]ename:
    y
      inflating: joinMultifasta.pl
    replace split2Multifasta.pl? [y]es, [n]o, [A]ll, [N]one, [r]ename:
    y
      inflating: split2Multifasta.pl
      inflating: SeperateSequences.pl
      inflating: splitABACASunion.pl
  11. $ rm PAGIT_MissingScripts.zip
  12. Make an alias to the setup script
    $ sudo nano /etc/profile

    alias pagitinit='source /usr/local/bin/PAGIT/sourceme.pagit'