Monday, July 27, 2015


It's that time of year again!! Just when you've finished ripping your hair out instailling BioPerl on Mavericks, Mac decides that it is not pissing off its users enough and decides to upgrade its operating system. And just when you can't take the notifications any longer, you are faced with that critical decision: jeapardize the security of your system for the sake of never having to reinstall bioperl, or update the OSX and know that the impending doom of reinstalling bioperl lingers--waiting to ruin your afternoon.

Well, it did just that! After hundreds of attempts to try to find the missing YAML library, I had to resort to installing perlbrew, which I did once, and it didn't work for me, but then I tried a different aspect of implementing the implementation in perlbrew several hours later, and it happened to work. If you are having serious trouble from the suggested cpan installation, give this a try:

curl -L http://install.perlbrew.pl | bash
source ~/perl5/perlbrew/etc/bashrc #and put this in your .bash_profile

#now we are going to pretend like we are in cpan, but we have to give ourselves permission first
#change your user name from mine (in pink)
sudo chown loloyohe /Users/loloyohe/.cpanm

#install cpanm
perlbrew install-cpanm

#install the builder from CPAN--oh, NOW it knows where YAML is!!!! >:|
sudo cpanm install Module::Build

#nothing really prints to screen, but it works!
sudo cpanm install CJFIELDS/BioPerl-1.6.923.tar.gz

#test to see if it works!
perl -MBio::Seq -e 0

Naturally, you will likely not have any of the same issues as me but a completely unique set of horrific issues specific to you! 

1 comment:

  1. you saved my day, no no... actually my week! Thanks a lot!

    ReplyDelete