Software requirements

In addition to the requirements listed in the ref:installation section, the BAM pipelien requires that a several other pieces of software be installed:

• AdapterRemoval v2.1+ [Lindgreen2012]
• SAMTools v0.1.18+ [Li2009b]
• Picard Tools v1.124+

The Picard Tools JAR-file (picard.jar) is expected to be located in ~/install/jar_root/ by default, but this behaviour may be changed using either the --jar-root command-line option, or via the global configuration file (see section Configuring the BAM pipeline).

Furthermore, one or both of the following sequence aligners must be installed:

• Bowtie2 v2.1.0+ [Langmead2012]
• BWA v0.5.9+ or v0.6.2+ or v0.7.9+ [Li2009a]

In addition, the following packages are used by default, but can be omitted if disabled during runtime:

• mapDamage 2.0.2+ [Jonsson2013]
• Genome Analysis ToolKit [McKenna2010]

If mapDamage is used to perform rescaling of post-mortem DNA damage, then the GNU Scientific Library (GSL) and the R packages listed in the mapDamage installation instructions are required; these include 'inline', 'gam', 'Rcpp', 'RcppGSL' and 'ggplot2' (>=0.9.2). Use the following commands to verify that these packages have been correctly installed:

$ gsl-config
Usage: gsl-config [OPTION]
...

$ mapDamage --check-R-packages
All R packages are present

The GATK JAR is only required if the user wishes to carry out local realignment near indels (recommended), and is expected to be placed in the same folder as the Picard Tools JAR (see above).

The example projects included in the PALEOMIX source distribution may be used to test that PALEOMIX and the BAM pipeline has been correctly installed. See the Example projects and data-sets section for more information.

In case of errors, please consult the Troubleshooting section.