diff --git a/performance/compare.py b/performance/compare.py index 5d0ad0c..1ed1984 100644 --- a/performance/compare.py +++ b/performance/compare.py @@ -1,3 +1,12 @@ +# This script requires pv. + +# https://www.ivarch.com/programs/pv.shtml + +# There is a Homebrew formula to install pv on macOS. + +# This script also depends on the simulation data: +# make -C data + import subprocess import sys diff --git a/performance/data/.gitignore b/performance/data/.gitignore index c54835f..3ab62c7 100644 --- a/performance/data/.gitignore +++ b/performance/data/.gitignore @@ -1,2 +1,3 @@ * !Makefile +!requirements.txt diff --git a/performance/data/Makefile b/performance/data/Makefile index 9765638..cabfc63 100644 --- a/performance/data/Makefile +++ b/performance/data/Makefile @@ -1,3 +1,14 @@ +# The make recipes require bcftools and bgzip. + +# https://samtools.github.io/bcftools/howtos/install.html +# https://www.htslib.org/doc/bgzip.html + +# On macOS, there are Homebrew formulas for bcftools and htslib, +# which contains bgzip. + +# The Python requirements are listed in requirements.txt: +# pip install -r requirements.txt + .PHONY: all clean all: sim_10k.vcz diff --git a/performance/data/requirements.txt b/performance/data/requirements.txt new file mode 100644 index 0000000..e6b46df --- /dev/null +++ b/performance/data/requirements.txt @@ -0,0 +1,3 @@ +stdpopsim +tskit +bio2zarr