Clockwork Python code

This is all intended to be run inside the clockwork singularity container.

If you want to develop the code and/or run the tests, please look in the vagrant/ directory for how to make a VM to do this.

I really want to install everything by hand anyway

You will need these dependencies:

• BWA
• bcftools
• cortex. Set the environment variable CLOCKWORK_CORTEX_DIR to the absolute path to the root cortex directory.
• enaBrowserTools (so the scripts enaDataGet and enaGroupGet work)
• fastqc
• fqtools
• picard. Set the environment variable CLOCKWORK_PICARD_JAR to the absolute path to the picard .jar file.
• samtools
• stampy. Set the environment variable CLOCKWORK_STAMPY_SCRIPT to the absoulate path to the stampy.py script.
• trimmomatic. Set the environment variable CLOCKWORK_TRIMMO_DIR to the absolute path to the root Trimmomatic directory.
• vcftools. Set the environment variable CLOCKWORK_VCFTOOLS_DIR to the absolute path to the root vcftools directory.

The code will check first for each of those environment variables, Whenever one is not defined, the code then looks for /bioinf-tools/ for executables/directories/jar files. The vagrant VM and the container install everything in /bioinf-tools. The script scripts/install_dependencies.sh may help - it is used to install dependencies in the Vagrant VM and in the Singularity container.

Run the tests:

NXF_VER=22.10.0 python3 setup.py test

If the tests pass, install:

python3 setup.py install