Runtime Error

[cutykaka]

Hello.

I installed Cactus as follows.

git clone https://github.com/ComparativeGenomicsToolkit/cactus.git --recursive cd cactus virtualenv -p python3 cactus_env echo "export PATH=$(pwd)/bin:\$PATH" >> cactus_env/bin/activate echo "export PYTHONPATH=$(pwd)/lib:\$PYTHONPATH" >> cactus_env/bin/activate source cactus_env/bin/activate python3 -m pip install -U setuptools pip python3 -m pip install -U . python3 -m pip install -U -r ./toil-requirement.txt

However, when I try to perform a Cactus-Pangenome analysis, I get a runtime error. Why is that? Do I need to install Docker separately?

Traceback (most recent call last): File "/BiO/Program/cactus/cactus_env/lib/python3.7/site-packages/cactus/shared/common.py", line 378, in setupBinaries verify_local() File "/BiO/Program/cactus/cactus_env/lib/python3.7/site-packages/cactus/shared/common.py", line 370, in verify_local raise RuntimeError("Cactus isn't using Docker, but it can't find " RuntimeError: Cactus isn't using Docker, but it can't find the Cactus binaries. Please add Cactus's bin directory to your PATH (and run make in the Cactus directory if you haven't already).

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/BiO/Program/cactus/cactus_env/bin/cactus-pangenome", line 8, in sys.exit(main()) File "/BiO/Program/cactus/cactus_env/lib/python3.7/site-packages/cactus/refmap/cactus_pangenome.py", line 117, in main setupBinaries(options) File "/BiO/Program/cactus/cactus_env/lib/python3.7/site-packages/cactus/shared/common.py", line 381, in setupBinaries verify_docker() File "/BiO/Program/cactus/cactus_env/lib/python3.7/site-packages/cactus/shared/common.py", line 363, in verify_docker raise RuntimeError("The docker executable wasn't found on the " RuntimeError: The docker executable wasn't found on the system. Please install Docker if possible, or use --binariesMode local and add cactus's bin directory to your PATH.

This is my command line. cactus-pangenome ./ testPangenome.txt --reference Bae --outDir test-pg --outName test-pg

Thank you.

[glennhickey]

You did not install Cactus correctly. See https://github.com/ComparativeGenomicsToolkit/cactus/releases

Notably, you have to download the binaries and follow the instructions in BIN-INSTALL.md

[cutykaka]

solved! Thank you!!