Installation of the Cactus binary distribution

This describes the steps require to install the Cactus pre-compile binary, static linked distribution.

Extracting

If you have not already extract the distribution and cd into the cactus directory:

tar -xzf cactus-bin-v3.2.1.tar.gz
cd cactus-bin-v3.2.1

Setup

To build a python virtualenv and activate, do the following steps. This requires Python version >= 3.9 (so Ubuntu 18.04 users should use -p python3.9 below):

virtualenv -p python3 venv-cactus-v3.2.1
printf "export PATH=$(pwd)/bin:\$PATH\nexport PYTHONPATH=$(pwd)/lib:\$PYTHONPATH\nexport LD_LIBRARY_PATH=$(pwd)/lib:\$LD_LIBRARY_PATH\n" >> venv-cactus-v3.2.1/bin/activate
source venv-cactus-v3.2.1/bin/activate
python3 -m pip install -U setuptools pip wheel
python3 -m pip install -U .
python3 -m pip install -U -r ./toil-requirement.txt

Some tools required for hal2assemblyHub.py, cactus-hal2chains, cactus-maf2bigmaf, and cactus-phast are not included and must be downloaded separately. They are wigToBigWig faToTwoBit bedToBigBed bigBedToBed axtChain pslPosTarget bedSort hgGcPercent mafToBigMaf hgLoadMafSummary hgLoadChain genePredSingleCover gff3ToGenePred gtfToGenePred. More information can be found here. Note that some may require a license for commercial use. Static binaries are not available, but the following command should set them up successfully on many 64 bit Linux systems:

cd bin && for i in wigToBigWig faToTwoBit bedToBigBed bigBedToBed axtChain pslPosTarget bedSort hgGcPercent mafToBigMaf hgLoadMafSummary hgLoadChain genePredSingleCover gff3ToGenePred gtfToGenePred; do wget -q http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/${i}; chmod +x ${i}; done

vcfwave isn't included in the release binaries (but is in the docker image). You can can try building it and adding it to bin/ with the following command

build-tools/downloadVCFWave

Testing

To test Cactus, the following will run a tiny sumulated alignment.

cactus ./jobstore ./examples/evolverMammals.txt ./evolverMammals.hal
``