85 lines
1.8 KiB
TOML
85 lines
1.8 KiB
TOML
[workspace]
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authors = ["IvisTang <me@ivistang.com>"]
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channels = [
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"https://prefix.dev/julia-forge",
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"conda-forge",
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"bioconda"
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]
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name = "biyelunwen"
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platforms = ["linux-64"]
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version = "0.1.0"
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[pypi-options]
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index-url = "https://mirrors.bfsu.edu.cn/pypi/web/simple"
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[tasks]
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[feature.base.dependencies]
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sra-tools = "*"
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fastp = "*"
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trinity = "*"
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hisat2 = ">=2.2.1,<3"
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samtools = ">=1.22.1,<2"
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busco = ">=6.0.0,<7"
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transdecoder = ">=5.7.1,<6"
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cd-hit = ">=4.8.1,<5"
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orthofinder = ">=3.1.0,<4"
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pip = ">=25.2,<26"
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seqkit = ">=2.10.1,<3"
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r-rstan = ">=2.32.7,<3"
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biopython = ">=1.85,<2"
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trimal = ">=1.5.0,<2"
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treeshrink = ">=1.3.9,<2"
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r-ape = ">=5.8_1,<6"
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raxml-ng = ">=1.2.2,<2"
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modeltest-ng = ">=0.1.7,<0.2"
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aster = ">=1.23,<2"
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julia = "1.12.*"
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conda = ">=25.9.1,<26"
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r-phangorn = ">=2.12.1,<3"
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r-languageserver = ">=0.3.16,<0.4"
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seqmagick = ">=0.8.6,<0.9"
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maven = ">=3.9.11,<4"
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matplotlib = ">=3.10.8,<4"
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ete3 = ">=3.1.3,<4"
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xvfbwrapper = ">=0.2.15,<0.3"
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r-ggplot2 = ">=4.0.1,<5"
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macse = ">=2.7,<3"
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td2 = ">=1.0.6,<2"
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mmseqs2 = ">=18.8cc5c,<19"
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paml = ">=4.10.9,<5"
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beagle-lib = "==3.1.2"
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mrbayes = ">=3.2.7,<4"
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cairosvg = ">=2.8.2,<3"
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r-devtools = ">=2.4.6,<3"
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r-phytools = ">=2.5_2,<3"
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r-argparser = ">=0.7.2,<0.8"
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r-processx = ">=3.8.6,<4"
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[feature.genome.dependencies]
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gffread = ">=0.12.9,<0.13"
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orthofinder = ">=3.1.5,<4"
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seqkit = ">=2.13.0,<3"
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tmux = ">=3.7b_,<4"
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numpy = "<2.5"
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python = "3.12.*"
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biopython = ">=1.87,<2"
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macse = ">=2.7,<3"
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trimal = ">=1.5.1,<2"
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treeshrink = ">=1.4.0,<2"
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raxml-ng = ">=2.0.2,<3"
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modeltest-ng = ">=0.1.7,<0.2"
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mrbayes = ">=3.2.7,<4"
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seqmagick = ">=0.8.6,<0.9"
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aster = ">=1.25,<2"
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julia = ">=1.12.6,<1.13"
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r-ape = ">=5.8_1,<6"
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r-languageserver = ">=0.3.18,<0.4"
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conda = ">=26.7.0,<27"
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minimap2 = ">=2.31,<3"
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[environments]
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# base = ["base"]
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default = ["genome"]
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