Software Requirements (NGS)

This program will make use of a large number of software packages, some of which will be installed on a High Performance server but many of which can also be installed on a personal computer running a version of linux.  (some packages will also install on Mac OSX and Windows, but linux is recommended). Students may want to install some of these packages themselves.  We will briefly go over the necessary steps for installing software on linux and compiling from source. Most software is command line, but two tools in particular make use of an graphic interface. 1. IGV (integrated genome viewer, Broad institute) 2. R studio and R, which was likely used in earlier parts of this course.  R itself can be run on command line, but both the native R GUI and R studio are helpful tools for the use of this package. A brief list of additional tools that are used for NGS

Installing compilers and make tools

> sudo zypper install gcc, gcc-c++
> sudo zypper install make

Installing Samtools.

The default samtools installation does not work well with the OpenSuse version of linux that is installed on the systems in the classroom.  We will need to download the package and build it on our systems, after first making some changes to the Makefile [ = instructions to the system on how to build/compile ]

1. download from this page samtools-0.1.9.tar.gz
2. open the archive.  this will create a directory with all the samtools source code
3. Within this directory is a Makefile, with instructions on how to compile.
4. download from this page Makefile.tar.gz
5. open this archive, it will give a single file, Makefile
6. copy this file into the samtools-0.1.9 directory
7. the command to compile samtools is simply
> Make
8. If this does not work, you need to install Make onto your system.  (> sudo zypper install gcc, sudo zypper install Make).  Please see the instructor
9. If this does work, you should see a long list of information printed to the screen as the program compiles.  Once finished, you should have a program call samtools.
10. test it out
> ./samtools
11. link to this file in your /home/bin directory so that it is available in your path

(may need sudo zypper install zlib-devel)





Leave a Reply