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Old 06-28-2010, 08:06 AM   #1
Ash
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Default 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
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Old 06-28-2010, 08:33 AM   #2
maubp
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Try ./samtools rather than just samtools (meaning look in the current directory).
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Old 06-28-2010, 09:13 AM   #3
rahul.m.dhodapkar
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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.
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Old 06-29-2010, 01:56 AM   #4
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Success! Thanks for the tip folks.

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Old 01-27-2011, 04:58 PM   #5
libiyagirl
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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!
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Old 01-27-2011, 05:22 PM   #6
nilshomer
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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"?
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Old 01-27-2011, 05:36 PM   #7
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it said make: command not found. I also typed ./samtools it said no such directory!
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Old 01-27-2011, 05:55 PM   #8
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Quote:
Originally Posted by libiyagirl View Post
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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