Help with installing samtools on a Mac

[Ash]

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]

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

[rahul.m.dhodapkar]

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]

Success! Thanks for the tip folks.

A

[libiyagirl]

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]

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]

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

[nilshomer]

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.