Installing Samtools on MacOS

kriskris · 05-30-2012, 04:00 PM

Hi,

I'm trying to install samtools on my Mac (OS X 10.6.8). I downloaded samtols-0.2.1.18tar.bz2 and unzipped it on my desktop. Then in terminal, I entered that directory and typed "make". It says "command not found".

I saw that zlib is required, so I also downloaded that and put the samtools into that directory and tried typing "make", which gave the same "command not found" message.

I'm new to unix but have successfully installed and used other programs (Bowtie, etc.), so I'm not sure why I'm having such problems with Samtools.

Any help would be greatly appreciated!

maubp · 05-30-2012, 04:23 PM

Have you installed Apple's Xcode? That provides gcc, make, etc. Get it free from the Apple App Store (big download).

kriskris · 05-30-2012, 05:43 PM

I have not installed Xcode, as I was told it wasn't was required for samtools. Is it necessary? I did a quick search at the Apple App store and it seems that only Xcode 4, which isn't compatible with my OS X 10.6.8, is freely available. Do you know where I could find the appropriate version of Xcode if I need it?

Thanks!

Wallysb01 · 05-30-2012, 05:53 PM

Xcode for OSX 10.6 is $5, I think. Its free if you have OSX 10.7. You can still download Xcode 4 for 10.6, and you will need it for samtools or any program that requires a "make" command.

maubp · 05-31-2012, 12:58 AM

Quote:

Originally Posted by kriskris

I have not installed Xcode, as I was told it wasn't was required for samtools. Is it necessary? I did a quick search at the Apple App store and it seems that only Xcode 4, which isn't compatible with my OS X 10.6.8, is freely available. Do you know where I could find the appropriate version of Xcode if I need it?

Thanks!

It used to be on the DVD that came with your Mac.

mbblack · 05-31-2012, 04:50 AM

Quote:

Originally Posted by kriskris

I have not installed Xcode, as I was told it wasn't was required for samtools. Is it necessary? I did a quick search at the Apple App store and it seems that only Xcode 4, which isn't compatible with my OS X 10.6.8, is freely available. Do you know where I could find the appropriate version of Xcode if I need it?

Thanks!

Strictly speaking, XCode is not necessary, but you need a gcc compiler and tools in order to compile Samtools. There are open source tools available for OS X, but by far the simplest to set up would be to spring for XCode and install it.

XCode is only available from Apple, either through the App store or by paying to register as a developer.

ChrisBird · 11-07-2012, 07:55 AM

If you have OSX Lion, then Xcode does not automatically install the command line tools.

When trying to install SAM Tools using Make, you will get the error message that make isn't found.

You have to open Xcode, goto Preferences/Downloads, and then install the command line tools.

HESmith · 11-07-2012, 09:50 AM

FYI, the latest version of Xcode doesn't include some standard GNU compiling components (e.g., automake, autoconf, libtools), even after installing the Command Line Tools as suggested.

-Harold

HESmith · 11-07-2012, 10:14 AM

Follow up: apparently, Autotools was dropped by Apple due to GPLv3 licensing issues. Also, gcc in current Xcode is actually a symlink to llvm-gcc (which doesn't have the licensing issue).

-Harold

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05-30-2012, 04:00 PM	#1
kriskris Junior Member Location: California, USA Join Date: May 2012 Posts: 4	Installing Samtools on MacOS Hi, I'm trying to install samtools on my Mac (OS X 10.6.8). I downloaded samtols-0.2.1.18tar.bz2 and unzipped it on my desktop. Then in terminal, I entered that directory and typed "make". It says "command not found". I saw that zlib is required, so I also downloaded that and put the samtools into that directory and tried typing "make", which gave the same "command not found" message. I'm new to unix but have successfully installed and used other programs (Bowtie, etc.), so I'm not sure why I'm having such problems with Samtools. Any help would be greatly appreciated!

11-07-2012, 07:55 AM	#7
ChrisBird Junior Member Location: Texas Join Date: Nov 2012 Posts: 2	Solution to make: command not found If you have OSX Lion, then Xcode does not automatically install the command line tools. When trying to install SAM Tools using Make, you will get the error message that make isn't found. You have to open Xcode, goto Preferences/Downloads, and then install the command line tools.

05-30-2012, 04:23 PM	#2
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	Have you installed Apple's Xcode? That provides gcc, make, etc. Get it free from the Apple App Store (big download).

05-30-2012, 05:43 PM	#3
kriskris Junior Member Location: California, USA Join Date: May 2012 Posts: 4	I have not installed Xcode, as I was told it wasn't was required for samtools. Is it necessary? I did a quick search at the Apple App store and it seems that only Xcode 4, which isn't compatible with my OS X 10.6.8, is freely available. Do you know where I could find the appropriate version of Xcode if I need it? Thanks!

05-30-2012, 05:53 PM	#4
Wallysb01 Senior Member Location: San Francisco, CA Join Date: Feb 2011 Posts: 286	Xcode for OSX 10.6 is $5, I think. Its free if you have OSX 10.7. You can still download Xcode 4 for 10.6, and you will need it for samtools or any program that requires a "make" command.

11-07-2012, 09:50 AM	#8
HESmith Senior Member Location: Bethesda MD Join Date: Oct 2009 Posts: 509	FYI, the latest version of Xcode doesn't include some standard GNU compiling components (e.g., automake, autoconf, libtools), even after installing the Command Line Tools as suggested. -Harold

11-07-2012, 10:14 AM	#9
HESmith Senior Member Location: Bethesda MD Join Date: Oct 2009 Posts: 509	Follow up: apparently, Autotools was dropped by Apple due to GPLv3 licensing issues. Also, gcc in current Xcode is actually a symlink to llvm-gcc (which doesn't have the licensing issue). -Harold