How to install samtools on MAC OS X?

[Mickey Lee]

Dear all,

I am trying to run the samtools on MAC OS X 10.8.2.
When I type in "make" it showed "-bash: make: command not found"
How to run it ?

thanks!!

[chadn737]

You probably don't have make installed and need to install Xcode.

Download Xcode and install it, should solve your issue.

[Mickey Lee]

Yes, I am working on the Xcode....
Thanks!!

[maubp]

Once you've got XCode there's a menu option to also download the command line tools - you'll need to do that too. I can check the exact wording later if you're stuck.

[jorhodes]

It's worth pointing out that you'll need Xcode Developer. Then go onto XCode preferences, and under the 'Downloads' tab there will be an option to install command line tools.

[Mickey Lee]

Thanks!
I have tried that, but failed to find the "source" group.
How can I do it?

[Mickey Lee]

Once you've got XCode there's a menu option to also download the command line tools - you'll need to do that too. I can check the exact wording later if you're stuck.

Yes, I got the command line tools in Xcode. would you please send me a script to show me how to do it?

appreciate!!

[GenoMax]

Have you tried the compilation after installing "xcode" tools? Post the errors if you are getting any.

[id0]

You can also install samtools and many other packages on a Mac using Homebrew. Easier than make and installation is optimized for the Mac.

[Irshad]

Error while installing samtools on my Mac

Hi all,

I get an error message when I extract samtools-0.1.19.tar.bz2.

comand line "tar jxvf samtools-0.1.19.tar.bz2"

gives me "failed to open samtools-0.1.19.tar.bz2"

can anyone help in this regard??

Thank you very much!

Irshad

[mastal]

How to install samtools on MAC OS X?

What happens if you just type 'tar' or 'tar jtvf ./samtools-0.1.19.tar.bz2'.

[rhinoceros]

Hi all,

I get an error message when I extract samtools-0.1.19.tar.bz2.

comand line "tar jxvf samtools-0.1.19.tar.bz2"

gives me "failed to open samtools-0.1.19.tar.bz2"

can anyone help in this regard??

Thank you very much!

Irshad

You're probably issuing the command in the wrong folder..

[Irshad]

Hi Mastal,
thank you for your answer.

Giving the command line you mentioned results in the following

tar: Option f requires an argument
Usage:
List: tar -tf <archive-filename>
Extract: tar -xf <archive-filename>
Create: tar -cf <archive-filename> [filenames...]
Help: tar --help

[Irshad]

How can I address this problem or how do I know that the folder is not right one??

[Irshad]

Hi Mastal,
thank you for your answer.

Giving the command line you mentioned results in the following

tar: Option f requires an argument
Usage:
List: tar -tf <archive-filename>
Extract: tar -xf <archive-filename>
Create: tar -cf <archive-filename> [filenames...]
Help: tar --help