Question: Problems installing samtools on linux (make command)
0
gravatar for axelwilhelm
5.3 years ago by
axelwilhelm100
Sweden
axelwilhelm100 wrote:

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)?

linux samtools • 19k views
ADD COMMENTlink modified 2.8 years ago by ruterpereira0 • written 5.3 years ago by axelwilhelm100

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.   

ADD REPLYlink modified 5.3 years ago • written 5.3 years ago by Ashutosh Pandey11k

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

ADD REPLYlink written 5.3 years ago by axelwilhelm100

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

ADD REPLYlink written 2.8 years ago by ruterpereira0

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.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by genomax75k
9
gravatar for dfornika
5.3 years ago by
dfornika1000
Vancouver, British Columbia, Canada
dfornika1000 wrote:

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
ADD COMMENTlink written 5.3 years ago by dfornika1000

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.

ADD REPLYlink modified 5.3 years ago • written 5.3 years ago by axelwilhelm100

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)

 

ADD REPLYlink written 5.3 years ago by David W4.7k
2
gravatar for Charles Plessy
5.3 years ago by
Charles Plessy2.7k
Japan
Charles Plessy2.7k wrote:

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.

ADD COMMENTlink written 5.3 years ago by Charles Plessy2.7k
1
gravatar for David W
5.3 years ago by
David W4.7k
New Zealand
David W4.7k wrote:

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.

ADD COMMENTlink written 5.3 years ago by David W4.7k

Samtools 1.0

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

ADD REPLYlink written 5.3 years ago by axelwilhelm100
1

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.
 

ADD REPLYlink written 5.3 years ago by Devon Ryan93k
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