Thursday, June 12, 2014

Going to install the Olfactory Receptor family Assigner (

Downloaded the .gz.tar

Install Bioperl.

#need to find out version of perl
perl -v
# it is v.5.16.2

#woops of course you have to install fink

#of course there is no fink installation for macs OS > 10.8
#following general installation on unix

#first install CPAN
perl -MCPAN -e shell #answer a bunch of questions--try to select automate
#CPAN interface will install
cpan>install Bundle::CPAN #a bunch of installing lines happen
#takes several minutes and you have to answer questions in between

cpan>q #quits the CPAN interface

To get the most updated version of BioPerl (which I'm sure I'll regret down the line), install it via cpan (assuming you got cpan working as well).
>perl -MCPAN -e shell
cpan>d /bioperl/
Reading '/home/francisco/.cpan/Metadata'
  Database was generated on Wed, 19 Mar 2014 13:17:02 GMT
Distribution    BOZO/Fry-Lib-BioPerl-0.15.tar.gz
Distribution    CJFIELDS/BioPerl-1.6.923.tar.gz
Distribution    CJFIELDS/BioPerl-DB-1.006900.tar.gz
Distribution    CJFIELDS/BioPerl-Network-1.006902.tar.gz
Distribution    CJFIELDS/BioPerl-Run-1.006900.tar.gz
cpan>install CJFIELDS/BioPerl-1.6.923.tar.gz 
#now a million things will happen and you should run the tests to make
#sure that it worked

Now you have to set up a local module. For some reason this cpan thing seems to work better and they are begging you to use it. What I have highlighted in pink is what you should change for your home directory.

>perl -e shell -MCPAN
cpan>o conf makepl_arg PREFIX=/Users/loloyohe/My_Local_Perl_Modules
cpan>o conf mbuildpl_arg "--prefix /Users/loloyohe/My_Local_Perl_Modules"
cpan>o conf commit

Should be done now!
Test to see if it worked:

Quit cpan and type in your terminal:
>perl -MBio::Seq -e 0

If there are no errors, you have installed it correctly :)

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