Dear Biostar people,
Is there a working and tested way of installing Bioperl on Mac OSX Mavericks v10.9.3. I tried latest version of xcode and installing command line but there is no command line option (under properties/downloads) in xcode.
When I test for gcc in the terminal window, it retrieve clang error.
Any idea will be appreciated.
Thanks in advance,
[SOLVED STEPS] - updated and written on 9 March 2015:
The following is tested and working (you need internet connection and whole steps took 30 minutes at fast connection):
1. First, my situation is that I have a new and clan install of Yosemite, then upgrade from App store whatever it takes. (this is not important but just to describe my situation.)
3. Detailed steps:
a. Follow STEPS ONE, TWO & FIVE listed in this website (http://www.sysarchitects.com/bioperl) as I mentioned by doing this (note that STEPS THREE AND FOUR does not work with me and seems not needed):
STEPS ONE & TWO
1. Open app store and search for xcode
2. download it, open applications folder and double click on Xcode, install
3. open terminal and type
xcode-select --install. Wait till it installed (again !!) (this step is mentioned here: http://guide.macports.org/#installing.xcode)
4. Now install macports by going to this website (https://www.macports.org/install.php) and under "QuickStart" title, click on Yosemite 10.10. Install the pkg file.
NOW STEP FIVE (in http://www.sysarchitects.com/bioperl)
5. Open Terminal, type (sudo cpan YAML) and accept default (simply press enter, do not write any letter)
6. type (q) without brackets while you are at can prompt to quit cpan.
7. Open terminal again and type (sudo cpan)
8. type (install Bundle::LWP)
9. quit cpan, and re-load it again by typing (sudo cpan) (if you are still in terminal window) or reload terminal.
10. type (cpan> o conf prerequisites_policy follow) of course without can> because you are already at it.
11. type o conf commit (this step is not mentioned on the website but the system tells you to do so.
12. Quit cpan (by typing q) and reload cpan (by typing cpan) (of course while you are at terminal).
13. Now go to the second website (http://www.bioperl.org/wiki/Installing_BioPerl_on_Unix) by doing the following:
14. While you are at cpan prompt, type (cpan>d /bioperl/), it will give you several response.
15. Now, type the latest edition you have (cpan>install CJFIELDS/BioPerl-1.6.924.tar.gz)
16. 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 (http://etutorials.org/Programming/perl+bioinformatics/Part+II+Perl+and+Bioinformatics/Chapter+9.+Introduction+to+Bioperl/9.3+Testing+Bioperl/):
use Bio::Perl; # this script will only work with an internet connection # on the computer it is run on $seq_object = get_sequence('swissprot',"ROA1_HUMAN"); write_sequence(">roa1.fasta",'fasta',$seq_object);
17. I save it on desktop. 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 filename.pl (and then hit enter), it will create a new file on desktop.