Getting SAMtools to work on Ubuntu

[KnowNothing2]

So I have my .sam file aligned from Bowtie2 and have dowloaded SAMtools and BCFtools. I added SAMtools to PATH using:

export PATH:$PATH:#path/#to/SAMtools (I renamed whatever the samtools name was to just "SAMtools"

Now, the instructions say that to convert from .sam to .bam, you simply type:

samtools view -bS filename.SAM > filename.BAM

However, no matter what I try I keep getting "samtools: command not found"

What am I doing wrong?

[ECO]

Can you run samtools from the full path?

Did you download a compiled version?

[KnowNothing2]

Can you run samtools from the full path?

Did you download a compiled version?

So I'm very new at bioinformatics and linux. From what I'm reading, I need to "make" SAMtools. I'm doing to exact same thing it says under "Installing SAMtools"

http://biobits.org/samtools_primer.html

However, I get an error that says

make[1]: Entering directory `/home/adam/SAMtools'
make[2]: Entering directory `/home/adam/SAMtools'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
In file included from bgzf.c:32:0:
bgzf.h:33:18: fatal error: zlib.h: No such file or directory
compilation terminated.
make[2]: *** [bgzf.o] Error 1
make[2]: Leaving directory `/home/adam/SAMtools'
make[1]: *** [lib-recur] Error 1
make[1]: Leaving directory `/home/adam/SAMtools'
make: *** [all-recur] Error 1
adam@ubuntu:~/SAMtools$ make samtools
make[1]: Entering directory `/home/adam/SAMtools'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o
In file included from bgzf.c:32:0:
bgzf.h:33:18: fatal error: zlib.h: No such file or directory
compilation terminated.
make[1]: *** [bgzf.o] Error 1
make[1]: Leaving directory `/home/adam/SAMtools'
make: *** [lib-recur] Error 1

[GenoMax]

You need to install zlib (which is missing) via apt-get. Then try the "make" again.

$sudo apt-get install zlib1g-dev

or you can use "Ubuntu software center". Search for "zlib1g-dev" and then install.

PS: Taking a chance and assuming that you are using Ubuntu (since many "new to unix" people do).

[KnowNothing2]

You need to install zlib (which is missing) via apt-get. Then try the "make" again.



or you can use "Ubuntu software center". Search for "zlib1g-dev" and then install.

PS: Taking a chance and assuming that you are using Ubuntu (since many "new to unix" people do).

I did sudo apt-get install build-essential, which supposedly has the make function in it. Do i still need zlib1g-dev?

yes, ubuntu 12.04 LTS

[eco32i]

Better yet, just do:
$ sudo apt-get install samtools

this should take care of the required dependencies.

[GenoMax]

I did sudo apt-get install build-essential, which supposedly has the make function in it. Do i still need zlib1g-dev?

yes, ubuntu 12.04 LTS

You do. "zlib1g-dev" provides "libraries" (e.g. zlib.h) which are needed by the "make" to compile samtools. This is basically code that can be used by multiple applications. WikiPedia link for explanation of "libraries": http://en.wikipedia.org/wiki/Library_%28computing%29

[GenoMax]

Better yet, just do:
$ sudo apt-get install samtools

this should take care of the required dependencies.

Indeed. Samtools appears to be available from ubuntu software center. I am not sure what version though. Is it the latest?

[eco32i]

Version: 0.1.18 (r982:295)

But I am on 13.04. It's probably behind on LTS.

[KnowNothing2]

You do. "zlib1g-dev" provides "libraries" (e.g. zlib.h) which are needed by the "make" to compile samtools. This is basically code that can be used by multiple applications. WikiPedia link for explanation of "libraries": http://en.wikipedia.org/wiki/Library_%28computing%29

Cool, so I installed that and reran "make" in my SAMtools directory. It made a bunch of 'object' files. Now I tried rerunning my code:

samtools view -bS filename.sam > filename.bam

And it still stays:

samtools: command not found

Theres mention of moving the samtools binary into PATH. Which file is the binary?

I added #path/to/SAMtools to my PATH, but it still doesnt work.

[GenoMax]

Cool, so I installed that and reran "make" in my SAMtools directory. It made a bunch of 'object' files. Now I tried rerunning my code:

samtools view -bS filename.sam > filename.bam

And it still stays:

samtools: command not found

Theres mention of moving the samtools binary into PATH. Which file is the binary?

In your SAMtools directory there should be a file called "samtools". Name should be "green" in color if you are using the default terminal in ubuntu, which indicates that it is an "executable" file.

You can run the command this way:

$/home/adam/SAMtools/samtools view -bS filename.sam > filename.bam

[eco32i]

Cool, so I installed that and reran "make" in my SAMtools directory. It made a bunch of 'object' files. Now I tried rerunning my code:

samtools view -bS filename.sam > filename.bam

And it still stays:

samtools: command not found

Theres mention of moving the samtools binary into PATH. Which file is the binary?

I added #path/to/SAMtools to my PATH, but it still doesnt work.

Run $ sudo make install after you run make. This will put the binaries where they are expected to be on the system.

[KnowNothing2]

Thanks everyone. I just made it easy on myself and ran apt-get install samtools. Worked right away.

[sophiespo]

export PATH:$PATH:#path/#to/SAMtools (I renamed whatever the samtools name was to just "SAMtools"

is wrong.

It should be:

export PATH=$PATH:/path/to/SAMtools

[KnowNothing2]

is wrong.

It should be:

Yeah, I did it the correct way, sorry just sloppy notation. When I performed

echo $PATH

I saw my directory.