Help with installing samtools on a Mac

Ash · 06-28-2010, 09:06 AM

Hi,

I'm fairly new to Unix (and bioinformatics generally!). I'm trying to open .bam files, and thought samtools might be the way forward. However, I'm struggling to get it working.

I downloaded samtools-0-1.1.7a.tar.bz2, and extracted it. In the terminal I then typed

$ make samtools

which appeared to compile it and put something called samtools in the folder which the terminal reckons is an application. However, when I try to open a .bam file with:

$ samtools view all-hg18.bam

I get

-bash: samtools: command not found

What am I doing wrong? All help gratefully received!

A

maubp · 06-28-2010, 09:33 AM

Try ./samtools rather than just samtools (meaning look in the current directory).

rahul.m.dhodapkar · 06-28-2010, 10:13 AM

and what maubp said is applicable to most other tools that you're going to need to install in the future. usually, using "./command" will work where "command" alone fails.

Ash · 06-29-2010, 02:56 AM

Success! Thanks for the tip folks.

A

libiyagirl · 01-27-2011, 05:58 PM

hello when I extracted samtools, I typed cd samtools-0.1.12a, then it went to the directory. Then I typed $ make samtools, it didn't work. How to install samtools anyway?

Thank you!

nilshomer · 01-27-2011, 06:22 PM

More information is required. What did it say when you typed "make samtools"? How do you know it didn't work. In the "samtool-0.1.12a" did you try running "./samtools"?

libiyagirl · 01-27-2011, 06:36 PM

it said make: command not found. I also typed ./samtools it said no such directory!

nilshomer · 01-27-2011, 06:55 PM

Quote:

Originally Posted by libiyagirl

it said make: command not found. I also typed ./samtools it said no such directory!

Make sure you have the developer tools and Xcode installed on your mac. They can be found on the Mac install disc.

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06-28-2010, 09:06 AM	#1
Ash Member Location: UK Join Date: Jun 2010 Posts: 15	Help with installing samtools on a Mac Hi, I'm fairly new to Unix (and bioinformatics generally!). I'm trying to open .bam files, and thought samtools might be the way forward. However, I'm struggling to get it working. I downloaded samtools-0-1.1.7a.tar.bz2, and extracted it. In the terminal I then typed $ make samtools which appeared to compile it and put something called samtools in the folder which the terminal reckons is an application. However, when I try to open a .bam file with: $ samtools view all-hg18.bam I get -bash: samtools: command not found What am I doing wrong? All help gratefully received! A

06-28-2010, 09:33 AM	#2
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	Try ./samtools rather than just samtools (meaning look in the current directory).

06-28-2010, 10:13 AM	#3
rahul.m.dhodapkar Member Location: New Haven Join Date: Jun 2010 Posts: 28	and what maubp said is applicable to most other tools that you're going to need to install in the future. usually, using "./command" will work where "command" alone fails.

06-29-2010, 02:56 AM	#4
Ash Member Location: UK Join Date: Jun 2010 Posts: 15	Success! Thanks for the tip folks. A

01-27-2011, 05:58 PM	#5
libiyagirl Member Location: canada Join Date: Jan 2011 Posts: 27	hello when I extracted samtools, I typed cd samtools-0.1.12a, then it went to the directory. Then I typed $ make samtools, it didn't work. How to install samtools anyway? Thank you!

01-27-2011, 06:22 PM	#6
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	More information is required. What did it say when you typed "make samtools"? How do you know it didn't work. In the "samtool-0.1.12a" did you try running "./samtools"?

01-27-2011, 06:36 PM	#7
libiyagirl Member Location: canada Join Date: Jan 2011 Posts: 27	it said make: command not found. I also typed ./samtools it said no such directory!