pixi.toml

[project]
name = "try_pixi"
channels = ["conda-forge", "bioconda"]
platforms = ["linux-64", "osx-64"]

[tasks]
bootstrap_init = "bash tools/bin/bootstrap_init"

[dependencies]
astpretty = "*"
attrs = ">=23.2.0"
awscli = "*"
bash = ">=5.2.21"  # MacOS default is 3.2.5
bcftools = "1.15"
bedtools = "2.30.0"
boto3 = "*"
bwa = "0.7.17"
cattrs = ">=23.2.3"
conda-env-builder = "*"
dvc = "3.*"
dvc-s3 = "*"
flake8 = "*"
flake8-use-fstring = "*"
google-api-python-client = "*"
google-auth = "*"
ipython = "*"
jq = "1.6"
jupyter = "*"
jupytext = "*"
matplotlib = "*"
pandas = "*"
pre-commit = "*"
pyarrow = "15.0.0"
pyright = "1.1.365"
pysam = "*"
pytest = ">=8.2.2,<8.3"
python = "3.10.14"
python-lsp-server = "*"
pyyaml = "*"
retry = "*"
samtools = ">=1.20"
scipy = "~=1.11"
seaborn = "0.11.2"
structlog = "*"
tomli = "*"
tomli-w = "*"
types-pyyaml = "*"
validators = "*"
xmltodict = "*"
arriba = "2.3.0"
cutadapt = "*"
dfam = "3.7"
ensembl-vep = "109.3"
fastqc = "0.12.1"
fgbio-minimal = "2.0.2"
fgsv = "0.0.1"
gatk4 = "4.4.0.0"
hmmer = "3.4"
kallisto = "0.48.0"
mantis-msi2 = "~=2"
minimap2 = "2.24"
multiqc = "1.15"
perl-db-file = "1.855"
picard = "3.1.0"
pizzly = "0.37.3"
rsem = "1.3.3"
ruff = "0.4.7"
samblaster = "0.1.26"
seqtk = "1.3"
snpeff = "5.1"
tabix = "1.11"
varscan = "2.4.6"
vcftools = "0.1.16"
miniwdl = "*"
yarl = ">=1.9.4,<1.10"
toolz = ">=0.12.1,<0.13"
rich = ">=13.7.1,<13.8"
pybedtools = "*"
pybedlite = "*"
"backports.strenum" = "*"
vcfpy = ">=0.13"
paraphase = "*"
RSeQC = "*"

[pypi-dependencies]
# We STRONGLY prefer conda packages over PyPI packages

[target.linux-64.dependencies]
lima = "2.9.0"
pbmarkdup = "1.0.3"
pbtk = "3.1.0"
ucsc-genepredtobed = "447"
ucsc-gtftogenepred = "447"
whatshap = ">=2.3"

[environments]

[system-requirements]
linux = "4.15.0"