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

This page was last updated on Thursday, 13-Mar-2014 08:20:25 CDT

Installation notes for iTAK version v1.2 Aug-26-2011

Home Page

Web server version

Prerequisites

System requirement and dependencies
 
Linux (required)
Perl version 5.10.0 or higher (required). Perl was installed by default on most Linux systems
BioPerl version 1.006 or higher (required). Please check http://www.bioperl.org and wiki/Installing_BioPerl for more details on installation of BioPerl.
HMMER3 (required). Provided in iTAK.
2.0 GB free disk space for installation.

Installation

  1. $ cd /programinstallers/
  2. $ wget -N ftp://bioinfo.bti.cornell.edu/pub/program/itak/iTAK-1.2.x64.tar.gz
  3. $ wget -N ftp://bioinfo.bti.cornell.edu/pub/program/itak/iTAK_domain_database.tar.gz
  4. $ cd /usr/local/bin
  5. $ tar -zxvf /programinstallers/iTAK-1.2.x64.tar.gz
  6. Make a version-independent symlink
    $ ln -s iTAK-1.2.x64 iTAK
  7. Add to the default PATH
    $ sudo nano /etc/profile
    ...
    PATH="$PATH:/usr/local/bin/iTAK"
    ...
  8. Install the database previously downloaded in step 3
    $ cd /usr/local/bin/iTAK/database
  9. $ tar -zxvf /programinstallers/iTAK_domain_database.tar.gz
    TFHMM_3.hmm
    TFHMM_3.hmm.h3f
    TFHMM_3.hmm.h3i
    TFHMM_3.hmm.h3m
    TFHMM_3.hmm.h3p
  10. Files in the database directory
    total 55880
    -rw-r--r--. 1        7334 Oct  7  2010 TF_Rule
    -rw-r--r--. 1      797009 Oct  7  2010 SBHMM_3
    -rw-r--r--. 1    13941209 Oct  7  2010 PlantsPHMM3_89.hmm.h3p
    -rw-r--r--. 1    11881025 Oct  7  2010 PlantsPHMM3_89.hmm.h3m
    -rw-r--r--. 1        5631 Oct  7  2010 PlantsPHMM3_89.hmm.h3i
    -rw-r--r--. 1     1822273 Oct  7  2010 PlantsPHMM3_89.hmm.h3f
    -rw-r--r--. 1    28544873 Oct  7  2010 PlantsPHMM3_89.hmm
    -rw-r--r--. 1        3692 Oct  7  2010 PK_class_desc
    drwxr-xr-x. 2        4096 Oct  7  2010 mak_hmm_domain
    -rw-r--r--. 1      192882 Oct  7  2010 GA_table
    drwxr-xr-x. 2        4096 Dec  6  2010 wnk1_hmm_domain
    -rw-r--r--. 1        2429 Dec 14  2010 TF_family
    
    -rw-r--r--. 1  1010189536 Oct 13  2010 TFHMM_3.hmm
    -rw-r--r--. 1      846852 Oct 13  2010 TFHMM_3.hmm.h3i
    -rw-r--r--. 1    67206106 Oct 13  2010 TFHMM_3.hmm.h3f
    -rw-r--r--. 1   419719922 Oct 13  2010 TFHMM_3.hmm.h3m
    -rw-r--r--. 1   494049291 Oct 13  2010 TFHMM_3.hmm.h3p