
The MAPRSeq pipeline uses modified versions of RSeQC and tophat.  The patched versions are included in this archive, but you can apply them yourself with the following steps:


RSeQC

This code has been modified primarily to generate PNG image files rather than PDF files. 


Download RSeQC 2.3.7 from:

http://downloads.sourceforge.net/project/rseqc/RSeQC-2.3.7.tar.gz

Unpack the archive with:

tar cvfz RSeQC-2.3.7.tar.gz

Patch the code with:

patch -p0 < RSeQC-2.3.7_pdf_to_png.patch  

Build per instructions in the RSeQC package.



TopHat

This code has been modified to permit execution in stages to limit memory usage.


Download TopHat 2.0.6 from:

http://tophat.cbcb.umd.edu/downloads/tophat-2.0.6.Linux_x86_64.tar.gz

TopHat_2.0.6.patch

patch -p0 < TopHat_2.0.6.patch

Place the tophat install into your path.



