REAPR version 1.0.18 README file


_____________________________ INSTALLATION ___________________________________

Prerequisites:
 - R installed and in your path (http://www.r-project.org/)
 - The following Perl modules need to be installed:
    File::Basename
    File::Copy
    File::Spec
    File::Spec::Link
    Getopt::Long
    List::Util


To install REAPR, run

  ./install.sh

Note that (depending on your system) this could take quite a long time
because there are several third-party tools that need to be compiled.
Once it has finished, add ./reapr to your $PATH, or call it explicitly with
/path/to/your/installation/directory/reapr

Optionally, you might want to have Artemis installed
(http://www.sanger.ac.uk/resources/software/artemis/) to view the output.
It must be at least Artemis version 15.0.0.


______________________________ RUN THE TEST __________________________________

If you want to check the installation is ok, you can run a test of the
whole REAPR pipeline.

IMPORTANT: the test assumes that 'reapr' has been added to your $PATH.

The test data are available as a separate download. These are solely to check
that the installation runs, using a cut-down dataset. As such, the results
are not the same as those that would be obtained when running on the full
dataset. The data contains reads from the ENA (accession number SRR022865).
The remainder of the test data is from the GAGE paper
(Salzberg et al. 2011), using the Velvet assembly of S. aureus
(see http://gage.cbcb.umd.edu/data/index.html).

Download the test data tarball, unpack it and run the
test script from inside the test directory:

./test.sh


____________________________ MAPPING READS ___________________________________

SMALT (http://www.sanger.ac.uk/resources/software/smalt/) is recommended to
map the reads. REAPR has been tested using versions 0.6.4 and 0.7.0.1 of
SMALT, but we have noticed issues with writing a BAM file directly
(with the SMALT option -f bam). Please use -f samsoft when running SMALT, then
import to BAM with samtools or Picard.

REAPR can map reads for you using SMALT - you can run 'reapr smaltmap' with
the -x option to print a list of the mapping commands that REAPR would
run to produce a BAM for input to the REAPR pipeline.


________________________________ GET HELP ____________________________________

Please read the manual: manual.pdf


_______________________________ BRIEF USAGE __________________________________

All REAPR tasks are run via a call to

  reapr

Call with no arguments for a list of tasks.  Call any task with no arguments
to get the usage for that task.  To run the entire pipeline, run

  reapr pipeline

Full instructions can be found in the manual: manual.pdf.


__________________________ BUG REPORTS/QUESTIONS/COMMENTS ____________________

Please email Martin Hunt, mh12@sanger.ac.uk.
