![]() Installing BioPerl often works only with using force or even fforce sudo cpan Then use the cpan method to install bioperl (use CPAN shell, do not attempt to install from tar ball unless you know exactly what you are doing. Instead, follow the unix instructions using subsection "CPAN install". Do not follow the MacOS instructions to install BioPerl unless you want to use Fink. perlbrew to install a clean and independent perl and add-on packages as complex as bio perl. I strongly advise against using the system perl under MacOS, it might break at any time. Rule of thumb, if there is an error message ("Error"), then there was an error ) You need to report that error. You really need to get the basics right, possibly you did not install BioPerl correctly. Open terminal, and go to desktop (by typing cd Desktop (no worries about capital or small letter, both works), when you are at desktop, type perl (and then hit enter), it will create a new file on desktop. Write_sequence(">roa1.fasta",'fasta',$seq_object) $seq_object = get_sequence('swissprot',"ROA1_HUMAN") # this script will only work with an internet connection If you wish to test it, try install textwrangler or whatever suitable text editor and type the following and save as perl file (taken from here: use Bio::Perl Now, type the latest edition you have cpan>install CJFIELDS/BioPerl-1.6.While you are at cpan prompt, type cpan>d /bioperl/, it will give you several response.Now go to the second website by doing the following.Quit cpan (by typing q) and reload cpan (by typing cpan) (of course while you are at terminal).type o conf commit (this step is not mentioned on the website but the system tells you to do so.type cpan> o conf prerequisites_policy follow of course without cpan> because you are already at it. ![]() quit cpan, and re-load it again by typing sudo cpan (if you are still in terminal window) or reload terminal.type q while you are at can prompt to quit cpan.Open Terminal, type sudo cpan YAML and accept default (simply press enter, do not write any letter) Now install macports by going to this website ( ) and under "QuickStart" title, click on Yosemite 10.10. Wait till it installed (again !!) (this step is mentioned here. open terminal and type xcode-select -install.download it, open applications folder and double click on Xcode, install.Follow STEPS ONE, TWO & FIVE listed in this website as I mentioned by doing this (note that STEPS THREE AND FOUR does not work with me and seems not needed): Overall, I followed two protocols listed here and here (under installing using CPAN).Ī.(this is not important but just to describe my situation.) ![]()
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