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

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Installation notes for OrthoMCL version 1.2 [2005-03-14]

Install notes for newer version 2.x

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Prerequisites

Installation

  1. $ cd /programinstallers/
  2. $ wget -N http://downloads.sourceforge.net/project/orthomcl/orthomcl/v1.2/orthomcl_v1.2.tar
  3. $ mkdir /usr/local/bin/orthomcl_1.2
  4. $ cd /usr/local/bin/orthomcl_1.2
  5. $ tar -xvf /programinstallers/orthomcl_v1.2.tar
    BLOSUM62
ORTHOMCL_INSTALL
orthomcl.pl
orthomcl_module.pm
sample_data/
sample_data/Ath.fa
sample_data/AtHsSc.bpo
sample_data/AtHsSc.gg
sample_data/Hsa.fa
sample_data/Sce.fa
  6. $ cd ..
  7. Create a launcher script in the default PATH called orthomcl
    $ nano orthomcl
    #!/bin/sh

PERL5LIB="$PERL5LIB:/usr/local/bin/orthomcl_1.2"
/usr/local/bin/orthomcl_1.2/orthomcl.pl $@
  8. $ chmod +x orthomcl
  9. As described in the ORTHOMCL_INSTALL file, configure the file orthomcl_module.pm
    $ nano /usr/local/bin/orthomcl_1.2/orthomcl_module.pm
    ...
    our $BLASTALL                            = "blastall";
our $FORMATDB                            = "formatdb";
our $MCL                                 = "/usr/local/bin/mcl/bin/mcl";

    ...
    our $PATH_TO_ORTHOMCL                    = "/usr/local/bin/orthomcl_1.2/";   # must end with "/"

    ... 
    our $MAX_WEIGHT_DEFAULT                  = 100;     # You need to see what's the second minimum p-value
                                                    # of your blast software. For example, if 9e-99 is
                                                    # the case you should use -log(9e-99)=100.

    ...
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