[workspace]
authors = ["Seth Stadick <sstadick@gmail.com>"]
channels = ["conda-forge", "bioconda"]
name = "perbase"
platforms = ["osx-arm64", "linux-64"]
version = "0.1.0"
[tasks]
plot-benchmarks = "python plot_benchmarks_comprehensive.py"
generate-plots = "python plot_benchmarks_comprehensive.py"
plot-simple = "python plot_benchmarks_simple.py"
[dependencies]
hyperfine = ">=1.19.0,<2"
aspera-cli = ">=4.20.0,<5"
lftp = ">=4.9.3,<5"
python = ">=3.11,<4"
pandas = ">=2.2,<3"
matplotlib = ">=3.8,<4"
seaborn = ">=0.13,<0.14"
numpy = ">=1.26,<2"
[environments]
bench = ["bench"]
[feature.bench.dependencies]
bam-readcount = ">=1.0.1,<2"
samtools = ">=1.22,<2"
sambamba = ">=1.0.1,<2"
mosdepth = ">=0.3.11,<0.4"
[feature.bench.tasks]
subsample = "samtools view -b -s 12.75 -o ./data/ERR1395576_30X.bam ./data/ERR1395576.bam && samtools ./data/index ERR1395576_30X.bam"
bench = "bash bench.sh"
fetch-data = "bash ./fetch_data.sh"