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Introduction

OK. So you just read the latest issue of Bioinformatics (or did a Google search) and have discovered some new pieces of software that promise to slice and dice your data in new, interesting, and useful ways. Most often, these tools will be designed to run in a Linux environment. Unfortunately, the helpful support staff at TACC may not have had time to test these tools and make a proper module out of them (or maybe they didn't want to make 1,000+ modules for every piece of bioinformatics software out there). Perhaps there is a TACC module, but it was made a month or two back when the software was at version 1.01 and now it's at version 1.03, which has a bug fix or some nifty new bell and whistle.

...

$login cdw
$login wget ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_v2.5.5_x86_64.tgz
$login tar -xvzf ssaha2_v2.5.5_x86_64.tgz
$login cd ssaha2_v2.5.5_x86_64
$login mkdir -p $HOME/local/bin
$login mv ssaha* $HOME/local/bin

How the shell finds executables: $PATH

...

Instead of writing out the entire path to the executable to run it, like thisin one of these examples:

login1$ /home1/01502/jbarrick/local/bin/ssaha2
login1$ $HOME/local/bin/ssaha2

Assuming you are using the bash shell, you can do this by editing your $HOME/.profile or $HOME/.profile_user configuration file. This file is These files are basically just a bash script scripts that is are run whenever you log in. You want to add a line that looks like this to the top of $HOME/.profile:

export PATH="$HOME/local/bin:$PATH"

...

Important! In order to have this change take effect, you must log out or log in again to force the shell to re-read the $HOME/.profile_user file. (Alternately, you can use one of these commands to re-read it at any time:

login1$ . $HOME/.profile_user
login1$ source $HOME/.profile_user

...

Case 2: Install from the source code

Note on TACC compilers

There are multiple compilers available on TACC:

• intel or icc - the default compiler. Preferred for optimizing speed of compiled executables.
• gcc - the GNU compiler collection. Tends to be more compatible.

Be aware that if you compile libraries and programs that link to them, that generally you must compile all components with the same compiler.

If you run into an error during compilation, try the gcc compiler by loading its module. You may get a message like this:

login1$ module load gcc

Error: You can only have one compiler module loaded at time.
You already have intel loaded.
To correct the situation, please enter the following command:

  module swap intel gcc/4.4.5

Please submit a consulting ticket if you require additional assistance.

So, follow the directions:

login1$ module swap intel gcc/4.4.5

You will need to do this to get breseq to compile in the next example.

Example: Install breseq from a source code archive

breseq is a tool developed by the Barrick lab. You 're going to might use it in the next a later lesson. It is a good example of a tool that can be downloaded and compiled.

breseq web page
breseq download page

breseq uses the common GNU build system install sequence. If you install other GNU tools then the same ./configure; make; make install command sequence will often be used.

$login1 cdw
$login1 wget http://breseq.googlecode.com/files/breseq-0.17d19.tar.gz
$login1 tar -xvzf breseq-0.17d19.tar.gz
$login1 cd breseq-0.17d19
$login1 ./configure --prefix=$HOME/local
$login1 make
$login1 make install

The extra option --prefix to ./configure sets where the executable and any other files associated with the program will be installed. If you leave off this flag, then it will try to install them in a system-side location. You must have administrator privileges to do this and would generally have to substitute sudo make install for the last step to get this to work. That won't work on TACC! (sudo means "super-user do".)

For some other tools, the instructions may tell you to skip straight to make, or you might also have to install some other programs or libraries that the tool you want to use needs to run. Generally, you can find this information in the online documentation or an INSTALL file in the root of the downloaded code.

More Examples

Example: Install the latest version of Bowtie2

There is a newer version of Bowtie2 available than the one loaded into a module on TACC. You might want to use it because it includes some new bug fixes. You can download either a source code version to compile using the above instructions or a binary version of bowtie2. Try to get this running on your own.

Other Cases

In other lessons we'll cover various deviations and elaborations on these two procedures in order to install specific programs, R modules, Perl modules, Python modules, etc.