pixi.toml

[project]
name = "happ"
version = "0.1.0"
description = "Pixi project file for HAPP workflow"
authors = ["johnne <john.sundh@scilifelab.se>"]
channels = ["conda-forge", "bioconda", "main", "r", "msys2", "cduvallet"]
platforms = ["linux-64", "osx-64", "linux-aarch64", "osx-arm64"]

[feature.happ]
dependencies = {python = "*", snakemake = "8.21.0", scikit-learn = "*", biopython = "*", tqdm = "*", polars = "*", pandas = "*", seqkit = "*", conda = "*", r-ape = "*", 'r-data.table' = "*", snakemake-executor-plugin-slurm = "*", pigz = "*"}

[feature.blastn]
dependencies = {blast = "*"}
platforms = ["linux-64", "osx-64"]

[feature.datatable]
dependencies = {'r-data.table' = "*"}

[feature.dbotu3]
dependencies = {dbotu = "*"}
channels = ["conda-forge", "bioconda", "cduvallet"]

[feature.epang]
dependencies = {epa-ng = "*"}
platforms = ["linux-64", "osx-64"]

[feature.gappa]
dependencies = {gappa = "*"}

[feature.hmmer]
dependencies = {hmmer = "*"}

[feature.mafft]
dependencies = {mafft = "*"}

[feature.opticlust]
dependencies = {mothur = "*"}
platforms = ["linux-64", "osx-64"]

[feature.pal2nal]
dependencies = {pal2nal = "*"}

[feature.qiime2]
dependencies = {q2-vsearch = "*", q2-feature-classifier = "*", q2-feature-table = "*", qiime2 = "*", q2cli = "*"}
platforms = ["linux-64", "osx-64"]
channels = ["qiime2", "conda-forge", "bioconda"]

[feature.raxml]
dependencies = {raxml-ng = "*"}
platforms = ["linux-64", "osx-64", "linux-aarch64"]

[feature.seqinr]
dependencies = {r-seqinr = "*"}
platforms = ["linux-64", "osx-64", "linux-aarch64"]

[feature.swarm]
dependencies = {swarm = "*"}
platforms = ["linux-64", "osx-64", "linux-aarch64"]

[feature.vsearch]
dependencies = {vsearch = "*"}

[environments]
default = ["happ"]
blastn = ["blastn"]
datatable = ["datatable"]
dbotu3 = ["dbotu3"]
epang = ["epang"]
gappa = ["gappa"]
hmmer = ["hmmer"]
mafft = ["mafft"]
opticlust = ["opticlust"]
pal2nal = ["pal2nal"]
qiime2 = ["qiime2"]
raxml = ["raxml"]
seqinr = ["seqinr"]
swarm = ["swarm"]
vsearch = ["vsearch"]