The PeakSegPipeline requires the following UCSC tools, which can be installed either as pre-compiled binaries or by compiling the source code.

• bigWigInfo
• bigWigToBedGraph
• bedToBigBed
• bedGraphToBigWig

Check this page to see if UCSC has already compiled a binary for your system. For example I use Ubuntu on a machine with a 64-bit CPU, so that is the linux.x86_64 set of binaries. In the code below we download the binaries to ~/bin, so make sure that directory is on your PATH.

cd ~/bin
curl -OL http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigInfo
curl -OL http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToBedGraph
curl -OL http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed
curl -OL http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig
chmod a+x *

Install by downloading and compiling the source code. Note the first line installs some development libraries, which are required.

sudo aptitude install libmysqlclient-dev uuid-dev
cd
if [ ! -e jksrc.zip ]; then curl -OL http://hgdownload.soe.ucsc.edu/admin/jksrc.zip;fi
rm -rf kent
unzip jksrc.zip
export MACHTYPE=$(uname -m)
mkdir -p ~/bin/$MACHTYPE
cd kent/src
make libs
cd utils
for util in bigWigToBedGraph bedToBigBed bigWigInfo bedGraphToBigWig; do
    cd $util
    make
    cd ..
done

Note that the binaries are installed to ~/bin/$MACHTYPE, so you will either have to add that directory to your PATH, or move the binaries to another directory on your PATH.

BerkeleyDB STL is no longer required by PeakSegDisk, as of 2019.

The following is incorrect because there are positive labels with no sample groups.

chr2L:72,965-73,182 peakStart
chr2L:74,242-74,305 peakEnd
chr2L:75,000-76,000 noPeaks

For example the following is OK, because each positive label has two sample groups labeled as up (no sample groups should be present for negative/noPeaks labels).

chr2L:72,965-73,182 peakStart monocyte bcell
chr2L:74,242-74,305 peakEnd monocyte bcell
chr2L:75,000-76,000 noPeaks

See test-pipeline-input.