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Installing RUM
This page describes how to obtain and install the RUM pipeline.
RUM should work anywhere you have most of the standard Unix command-line tools, Perl, and can get the blat, bowtie and mdust binaries to execute, however we haven't tested it on every platform. Unless you have a relatively small genome, you'll probably need a 64 bit machine. For the human or mouse genome this will definitely be necessary. For a lane of 20 million 100 base-pair reads, paired-end, expect to use about 100-200 GB disk space.
You will now need the autodie Perl module. If you are using Perl >=
5.10, this should already be installed. If not, you may need to
install it. You should be able to install it very quickly by running:
cpan -i autodieLog::Log4perl is recommended, but not required. You should be able to install it by running:
cpan -i Log::Log4perlIf you are able to install Log::Log4perl, you will be able to
fine-tune the logging output by modifying the conf/rum_logging.conf
file in the RUM distribution. This is very useful when developing RUM,
but is not necessary for normal usage. If Log::Log4perl is not
installed, RUM will use its own logging system, which will print the
most important log messages to the log files as described in the
Logging section above. So if you aren't able to install
Log::Log4perl, don't worry, you will most likely still get all the
logging output you need for normal (non-development) usage.
See http://mschilli.github.com/log4perl/ for more information about the module.
We recommend that you download the latest release from https://github.com/PGFI/rum/tags. If you need the latest development version, you can fork the repository from https://github.com/PGFI/rum.
The new recommended way to install RUM is to use the standard Perl module installation process:
# Assuming that you are in the root directory of RUM
Perl Makefile.PL
make
make test # (optional, takes a couple minutes)If you wish to install RUM system wide:
make install # (may need sudo)You can also install RUM system wide in a non-standard location by
passing a INSTALL_BASE=/some/path option to the perl Makefile.PL.
RUM should automatically find all of its Perl modules if you
install it in this manner.
perl Makefile.PL INSTALL_BASE=/some/path
Some versions of Perl (e.g 5.8.8) do not recognize the INSTALL_BASE option.
In this case, it is better to put the source distribution in the
desired installation directory, followed by perl Makefile.PL && make.
This will set the proper include paths for RUM libraries and scripts. For example, if you wanted to install RUM to /opt/rum and be able to run /opt/rum/bin/rum_runner, then you would do the following:
cd /opt
wget https://github.com/downloads/PGFI/rum/RUM-Pipeline-v2.0.1.tar.gz
tar -xvzf RUM-Pipeline-v2.0.1.tar.gz
mv RUM-Pipeline-v2.0.1 rum
cd rum
perl Makefile.PL
make
make test # optional
Next: Installing indexes