When I install samtools, the linux cannot find -lcurses and cannot find -lz. How can I tangle these problems?

Question

[18137792217]

When I install samtools, the linux cannot find -lcurses and cannot find -lz. How can I tangle these problems?

[Alex Reynolds]

What version of Linux are you running? (This determines what packages to install.)

[finswimmer]

And beside this question, are you trying to install samtools via the package manager of your linux version or by compiling it?

fin swimmer

[18137792217]

My linux's version is ubuntu15.04, when i install the samtools-0.1.19, it reminders "cannot find -lcurses", then i download libncurses5-dev, but it is not suitable for the version of ubuntu15.04, it always reminders similar answer like "$ sudo apt-get install libncurses5-dev: Depends: libncurses5 (= 5.7+20090803-2ubuntu2) but 5.7+20090803-2ubuntu3 is to be installed", so i want to get a suitable version of libncurses. Thank you !

[h.mon]

You are using a release which reached its end of life. I suggest you upgrade to the latest LTS release (Ubuntu 16.04.2) or, if you don't mind having to upgrade often, to the latest version (currently, Ubuntu 17.04).

[18137792217]

It always upgraded unsuccessfully, I install the version 0f ubuntu12.04 on another computer, this is a frequently-used version, so i want to a suitable version of libncurses for ubuntu12.04. Thank you so much!

[WouterDeCoster]

I install the version 0f ubuntu12.04

It's also 5 years old.
Installing Ubuntu16.04 shouldn't be impossible on your computer, I have a laptop which was used by Aristotle, and it runs fine using Ubuntu16 LTS. But this forum is not the most appropriate place to help you with installation issues.

Answer 1

[h.mon]

You can untangle the problems by installing the package manager samtools. Correct me if I am wrong, but as you probably use Ubuntu :

sudo apt-get install samtools

I have excellent ways of tangling a system, but seriously, I only recommend them as a hobby.

[GenoMax]

As long as one accepts that there is a chance of not getting the latest version of a program, this is the least painful way.

[18137792217]

Thank you, i tried but failed.

[h.mon]

How it failed? You had o power outage during installation? A hard drive failure? You spilled coffee on your computer and it short-circuited?

Or maybe, just maybe, it threw an error message which can help identify what went wrong and how to solve it?

Answer 2

[Alex Reynolds]

There are third-party packages needed to compile and install the samtools suite from source. You could do the following to install these and other libraries on CentOS 7:

$ sudo yum install zlib-devel
$ sudo yum install bzip2-devel
$ sudo yum install xz-devel
$ sudo yum install ncurses-devel

Further, you may or may not need to edit the samtools makefile to change the linking statement for LIBCURSES from -lcurses to -lncurses. See: https://stackoverflow.com/a/33985976/19410

If you're on a Debian/Ubuntu Linux, the names of these packages and the package installer will be different. Feel free to follow up once you've found out what you're running.

If you install samtools from a package manager, instead of compiling from source, you'll likely avoid some or all of this work as the package manager will try to install any dependencies for you.