Problems installing samtools on linux (make command)

Question

[axelwilhelm]

I am having troubles installing Samtools 1.0 on my Ubuntu laptop. I have downloaded and unziped so I have a folder called */home/awe/samtools*.

Nothing happens when I type samtools and press enter (command not found) so I try to type make but I get make: *** No targets specified and no makefile found. Stop.. I try find -name onfi but there is no ./config file available.

Edit:

The last lines in my .bashrc are

export SAMTOOLS_HOME=/home/awe/samtools/samtools-1.0
export PATH=$SAMTOOLS_HOME:$PATH
export PATH=$SAMTOOLS_HOME/bcftools/:$PATH
export PATH=$SAMTOOLS_HOME/misc/:$PATH

Whats my problem (please skip general derogatory answers about me)?

[Ashutosh Pandey]

1. You need to go in the samtools directory and then type 'make' and 'make install' to create and install executables. Sth like 'cd /home/awe/samtools'
2. The add the executables to your path by modifying .bash_profile.

Second step is only needed if you want to call samtools from anywhere otherwise you can directly use the absolute path to the executable created in the samtools directory.

Also stop being a sissy boy. Trolling is the birth right of every internet user. Fun intended.

[axelwilhelm]

1) I am. 2) I have (see edit). 3) whats my problem?

[ruterpereira]

I am a beginner in linux and also in bioinformatics.. so I really need help.. I tried to install sam tools but it fails and the command line showed this "curses development files not found". What does it mean? Thank you

[GenoMax]

It means you are missing ncurses/ncurses-devel libraries on your system. If you search for "install ncurses your_OS_name" you should get links for how to install that library.

BTW: Please don't use old threads to ask new questions in the area reserved for answers for the original question. Start a new thread instead.

Answer 1

[dfornika]

Do you have root or sudo rights on the machine? If so, you should be able to install samtools system-wide by typing:

sudo apt-get install samtools

If you'd still like to install from source, you first need to run the 'configure' script in the samtools source directory. If you don't have permissions to write to system directories like /usr/local then you should pass a prefix value to the configure script.

./configure --prefix=/home/awe
make
​make install

This will install samtools to /home/awe/bin. If you'd like to be able to run samtools by simply typing 'samtools' instead of /home/awe/bin/samtools then you need to add /home/awe/bin to your PATH environment variable if it hasn't already been added.

You can always check the current value of your PATH by typing:

echo $PATH

[axelwilhelm]

Installing from command line did it. Command line is best. I do not know why I tried a browser download. I betrayed the command line, let it down and cheated on it. It punished me like the righteous all knowing, all powerfull higher being it is. That was my problem. Thank you for turning my straying soul to the right path.

[David W]

This is almost certainly not samtools 1.0. dpkg -s samtools | grep Version will show you the installed version (0.1.19 for the latest ubuntu)

Answer 2

[Charles Plessy]

If you specifically need SAMtools version 1.0 you can try to install the Debian packages currently in our Experimental section. You will also need to install libhts1. Usually, mixing Debian and Ubuntu packages is not recommended, but if just for these two packages, it will be fine.

Answer 3

[David W]

Which package did you download?

Samtools1.0xxx has the source code and a Makefile in the root directory. If you type make your system will attempt to build the execultable

samtools-bcftools-htslibxxx has the compiled exectuables for the whole suite. They are in the bin directory.

[axelwilhelm]

Samtools 1.0

make: *** No targets specified and no makefile found. Stop.

[Devon Ryan]

You probably downloaded the binary, not the source code. Next time, just look at what's actually in the directory. It should then be obvious what you have.