Use explicit paths to all important program used in pipeline

[Nicklas Nordborg]

Eg. Tophat and bowtie. It is already possible to set a path in the reggie-ogs-hosts.xml file for most of the programs, but tophat also uses bowtie and will look it up in the PATH, which may or may not be the same as in our configuration.

The default configuration file should include complete paths to tophat and bowtie. The generate script for alignment should extend the PATH with the path to bowtie.

[Nicklas Nordborg]

(In [2762]) References #653: Use explicit paths to all important program used in pipeline

Added full paths to bowtie and tophat in the configuration file.

[Nicklas Nordborg]

(In [2769]) Fixes #653: Use explicit paths to all important program used in pipeline

Set PATH to bowtie before running tophat to make sure the expected version of bowtie is used.

[Nicklas Nordborg]

(In [2786]) References #653: Use explicit paths to all important program used in pipeline

Use samtools in $SAMTOOLS if it is already set.

[Nicklas Nordborg]

(In [2787]) References #653: Use explicit paths to all important program used in pipeline

Added full path to samtools in the configuration file. This is exported in SAMTOOLS variable so that 'alignment_statistics.sh' can use it.