CASAVA 1.8.2 Installation

CASAVA requires quite good memory and disk space requirements. More details about details about data processing solution or suitable server configuration can be referred from CASAVA user guide at illumina. Installation on 64-bit Linux Operating system (CentOs 5) is supported by illumina but you should be able to install and run it on other 64-bit Linux distributions such as RedHat, Fedora and Ubuntu (I use the last one).

There are several software per-requisites/dependencies to run CASAVA and it will be worth to check installation status of followings:

GNU make (3.81 recommended)
Perl (>= 5.8)
Python (>=2.3 and <=2.6)
PyXML
gnuplot (>= 3.7, 4.0 recommended)
ImageMagick (>= 5.4.7)
ghostscript
libxslt
libxslt-devel
libxml2
libxml2-devel
libxml2-python
ncurses
ncurses-devel
gcc (4.0.0 or newer up to and including version gcc 4.4.x, except 4.0.2), with c++
libtiff
libtiff-devel
bzip2
bzip2-devel
zlib
zlib-devel
Perl modules
perl-XML-Dumper
perl-XML-Grove
perl-XML-LibXML
perl-XML-LibXML-Common
perl-XML-NamespaceSupport
perl-XML-Parser
perl-XML-SAX
perl-XML-Simple
perl-XML-Twig
perldoc

It is worth and time saving to check all these requirements seriously to avoid installation troubles.

The CASAVA tar ball can be downloaded from illumina. You need to have MyIllumina (previously icom) account to access and download. In case you don`t have access, contacting the techsupport can be other option. Once tar ball (CASAVA_v1.8.2.tar.bz2) has been downloaded and saved to specific directory, we need to extract it.

$ cd /path to directory containing CASAVA-v1.8.2.tar.bz2

Once inside the directory, type the following command

$ tar xvjf CASAVA_v11.8.2.tar.bz2

This will create the extracted directory CASAVA_v1.8.2 in the same parent directory (containing the tar ball). We need to now create a new directory to build CASAVA and install it from here to location of your choice.

$ mkdir CASAVA-1.8.2-build

$ cd /CASAVA-1.8.2-build

Configure the CASAVA to build and install it at you your preferred location. (I would suggest to give all the commands as super/root user from this point onwards till final installation.)

$ sudo ../CASAVA_v1.8.2/src/configure –prefix=/selected installation location

Ideally, the CASAVA build up should have completed successfully.However, like some others, I too faced the compression utility error “CMake Error at cmake/cxxConfigure.cmake:71 (message): No support for gzip compression” resulting in process termination.

I was clueless about the error as zlibs (zlibs, zlibs-devel) were already installed. I would have not been able to resolve this error if not for this thread on SEQanswers. As suggested, copied the libz.so and libpthread* to /usr/lib folder

$ sudo cp /usr/lib/x86_64-linux-gnu/libz.so /usr/lib

$ sudo cp /usr/lib/x86_64-linux-gnu/libpthread* /usr/lib

Configuration was successful this time. Build CASAVA by following command

$ sudo make

Final installation

$ sudo make install