Joined: 02 Nov 2014
|Posted: Fri Nov 28, 2014 3:56 am Post subject: HOWTO: Installing Mauve
|There are 2 ways to install Mauve (http://asap.genetics.wisc.edu/software/mauve/overview.php).
- A tar.gz from the website containing everything you need including static binaries.
- A hardmasked package from portage.
The portage version has advantages being the latest version. This guide is how to install Mauve using portage.
Step 1: getting mauvealigner to compile.
Mauve aligner wants to compile a static binary so you have to make sure dev-libs/boost is compiled with the static-libs and threads USE flag.
The build references a few -mt (multi threaded) libraries. While the dynamic libraries are symlinked from the -mt filename to the one without, this is not the case with the static ones. Make sure you have the following symlinks on your system:
|/usr/lib/libboost_filesystem-mt.a -> libboost_filesystem.a
/usr/lib/libboost_iostreams-mt.a -> libboost_iostreams.a
/usr/lib/libboost_program_options-mt.a -> libboost_program_options.a
/usr/lib/libboost_system-mt.a -> libboost_system.a
Step 2: getting mauve to compile.
The ebuild needs to be modified to add more items to the Java CLASSPATH. I copied mauve-9999.ebuild to mauve-10000.ebuild and made changes there.
The following needed to be added in EANT_GENTOO_CLASSPATH: commons-cli-1,goose,ant-core. The result:
You can check what you have installed with:
|java-config --list-available-packages |
Unfortunately, the java goose library is not available in portage. A copy is available in the checked out source under the "ext" folder though.
You can copy goose.jar from the svn-src to /usr/share/goose/lib/goose.jar.
The final step is adding the package.env file to /usr/share/goose/package.env. I copied a template using /usr/share/biojava/package.env.
Make sure that package.env contains the correct CLASSPATH variable:
There won't be a hash for mauve-10000.ebuild so install it with the --digest emerge parameter.
Caution: You may run into issues running both versions at the same time. Running the older binary version first, then the new one and opening the console via menu which was first opened by the other version may cause a crash.