This is a test version of Biostars. For the public version, visit https://www.biostars.org.
how to setup miRDeep2 on osx 10.10 (Yosemite)

Hello I want use miRDeep2 on my mac (Yoseimite).

So I downloaded miRDeep2 here

I open iterm and change dir to Download/mirdeep2

type ./install.pl

but there are error message like this :

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Use of uninitialized value $new in pattern match (m//) at ./install.pl line 20.
making backup of .bashrc,.bash_profile and .cshrc and removing all entries of mirdeep in those files
~/.bashrc backup is ~/.bashrc_1454562646
~/.bash_profile backup is ~/.bash_profile_1454562646
file /Users/XXXX/.cshrc.bak not found

Error:
    no gcc compiler installed. Please install a gcc compiler
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

but I already installed gcc

How can I solve this problem?

mirna mirdeep2
• 2,722 views • link
updated by Ram Ram • written by khblack • khblack

Have you got Xcode installed and have you opened it to configure?

• 0 views • link
updated by Ram Ram • written by andrew.j.skelton73 andrew.j.skelton73

1 answer

Hi khblack,

Assuming you installed gcc yourself, can you make sure that location of your gcc is in your PATH variable by typing echo $PATH in your terminal? If you see any problem you can add the location to your .bash_profile file and re-open a terminal window.

To avoid any complications, you can always download Xcode Developer Tools (a good how-to can be found here) as well.

• 0 views • link
updated by Ram Ram • written by jth jth

Log in to answer this question.

More posts like this