[workspace]
authors = ["IvisTang <me@ivistang.com>"]
channels = [
    "https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/",
    "https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/",
    "conda-forge", 
    "bioconda"
]
name = "biyelunwen"
platforms = ["linux-64"]
version = "0.1.0"

[pypi-options]
index-url = "https://mirrors.bfsu.edu.cn/pypi/web/simple"

[tasks]

[feature.base.dependencies]
sra-tools = "*"
fastp = "*"
trinity = "*"
hisat2 = ">=2.2.1,<3"
samtools = ">=1.22.1,<2"
busco = ">=6.0.0,<7"
transdecoder = ">=5.7.1,<6"
cd-hit = ">=4.8.1,<5"
orthofinder = ">=3.1.0,<4"
pip = ">=25.2,<26"
seqkit = ">=2.10.1,<3"
r-rstan = ">=2.32.7,<3"
biopython = ">=1.85,<2"
trimal = ">=1.5.0,<2"
treeshrink = ">=1.3.9,<2"
r-ape = ">=5.8_1,<6"
raxml-ng = ">=1.2.2,<2"
modeltest-ng = ">=0.1.7,<0.2"
aster = ">=1.23,<2"
julia = "1.12.*"
conda = ">=25.9.1,<26"
r-phangorn = ">=2.12.1,<3"
r-languageserver = ">=0.3.16,<0.4"
seqmagick = ">=0.8.6,<0.9"
maven = ">=3.9.11,<4"
matplotlib = ">=3.10.8,<4"
ete3 = ">=3.1.3,<4"
xvfbwrapper = ">=0.2.15,<0.3"
r-ggplot2 = ">=4.0.1,<5"
macse = ">=2.7,<3"
td2 = ">=1.0.6,<2"
mmseqs2 = ">=18.8cc5c,<19"
paml = ">=4.10.9,<5"
beagle-lib = "==3.1.2"
mrbayes = ">=3.2.7,<4"
cairosvg = ">=2.8.2,<3"

[feature.beast.dependencies]
beagle-lib = ">=4.0.1,<5"
beast = ">=10.5.0,<11"

[environments]
default = ["base"]
beast = ["beast"]