Install

Installation

Tuque depends on other open-source software. Before using any of the Tuque programs,
ensure that these programs are available on your system:

• A Unix operating system, with bash, sort, awk, and grep
• Python 2.7 or newer - Available from http://www.python.org/ Don't use Python 3
• Biopython - Available from http://biopython.org/wiki/Download
• bowtie and bowtie-build - Available from http://bowtie-bio.sourceforge.net/index.shtml Don't use Bowtie 2
• blat and pslCDnaFilter - Available from http://hgdownload.cse.ucsc.edu/admin/exe/
• samtools and tabix - Available from http://sourceforge.net/projects/samtools/files/
• genomeCoverageBed - Available from http://code.google.com/p/bedtools/

The programs can be installed anywhere; they do not need to be in a system directory or on the PATH.

To install Tuque, download and decompress http://sourceforge.net/projects/tuque/files/tuque.tar.gz in a convenient
location.
Leave the tuque scripts in their installation directory so that they can find their library files. For convenience you
can place symbolic links to tuqueSplice, tuqueSplice_ps, tuqueMap, tuqueIndex, and tuqueCount in a directory on your
PATH. e.g. ln -s $(pwd)/tuque/tuqueSplice ~/bin

Edit the file tuque.cfg in the tuque folder so that the program paths correspond to the locations on your
system. Customized copies of tuque.cfg can be saved under another name and invoked with the -c option to the tuque programs