Install command line tools on a Mac

[trasver]

Hi all

I've searched around a bit and found nothing which makes me think that it's just not possible.

I'd like to install the roche 454 command line data analysis tools for use on my Mac. I don't need or want the GUI.

Any suggestions?

Thanks!

[GenoMax]

You will need to install apple developer tools to get the compiler and such. http://developer.apple.com/xcode/

If you are willing to spend the time then it should be possible unless there are specific libraries that are not available on MacOS.

[lukas1848]

I'd rather recommend to install bio linux on a virtual machine and install any further command line tools in bio linux.

here's the link if you're interested: http://nebc.nerc.ac.uk/tools/bio-linux/bio-linux-6.0

[kmcarr]

The Roche/454 software can not be installed on Mac OS X. They are only distributed a precompiled binaries for Linux, and a Redhat variant of Linux. (Installs on other distros are possible but require work arounds.) If you want to install them "on your Mac" you will have to do as Lukas suggest and install VM software (e.g. Parallels or vmware), create a Linux virtual machine and then install the tools there.

Alternatively you could install Linux on some other computer, install the Roche tools and then just ssh to that box from your Mac, the experience will be the same from your POV.

[cliffbeall]

Mac 454 software

About a year ago, I installed the Roche software in a virtual machine on my mac. It was in Parallels and the linux I used was Fedora. It ran, including the GUI, but I never really used it for real work. You can also use virtualbox, which is free.

That being said, the thing I have run into with VMs is that the memory is too limited for NGS stuff. What I have done to get around that is to install a bootable Linux. Right now I have Ubuntu on a second internal drive in a MacPro. It is also possible to partition your main drive using rEFIt (refit.sourcforge.net).

Good luck!

[ajthomas]

I've been using VirtualBox and Fedora for quite some time now. It has worked flawlessly for me. As for the memory, you can assign as much as you want to the virtual machine. On one of our computers, which runs Red Hat, I have installed VirtualBox with Windows7 as the guest OS and assigned 6 CPUs and 16GB memory to it. It runs just fine like that. As long as you have the memory and can spare it for the virtual machine, you should be fine.

[cliffbeall]

I looked into this and it seems my problem is that I have a slightly older model MacPro that doesn't boot into the 64-bit kernel. Strangely enough I can run other applications as 64-bit, but not VirtualBox. More into here:

https://forums.virtualbox.org/viewtopic.php?f=8&t=34982

http://support.apple.com/kb/HT3770

http://macperformanceguide.com/SnowLeopard-64bit.html

[ajthomas]

That's important to know. The OP should keep that in mind when trying a VM.

[trasver]

Thanks all for the help and advice.

Virtual box did the job and after 1 hour installation of everything it's now running no problems.

Note I wasn't too concerned about RAM etc as I'm not using the GUI for analysis...just as a reference point for some command line analysis I'm doing.