feat: add base_prokka tool and CRISPR-Cas analysis source code
- Add base_prokka genome annotation tool with pixi config - Add CRISPR-Cas analysis src (CRISPRCasFinder.pl, environment config) - Add test data and documentation Co-Authored-By: Claude <noreply@anthropic.com>
This commit is contained in:
zly
2
tools/base_prokka/0_genomeAnnotation/.gitattributes
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tools/base_prokka/0_genomeAnnotation/.gitattributes
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# SCM syntax highlighting & preventing 3-way merges
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pixi.lock merge=binary linguist-language=YAML linguist-generated=true
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3
tools/base_prokka/0_genomeAnnotation/.gitignore
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tools/base_prokka/0_genomeAnnotation/.gitignore
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# pixi environments
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.pixi/*
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!.pixi/config.toml
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70
tools/base_prokka/0_genomeAnnotation/00_genome_annoation.md
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tools/base_prokka/0_genomeAnnotation/00_genome_annoation.md
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# 模块 1：基因组注释
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> 目标：通过prokka对进行原核生物基因基因组注释 ，为后续分析提供输入文件。
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---
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## 1) Conda 环境
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- 环境名：`prokka`
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- 说明：运行prokka进行基因组注释
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- 激活：
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```bash
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conda env create -f prokka.yml
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conda activate prokka
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```
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> 已安装环境：✅（yml配置文件： `prokka.yml`）
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---
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## 2) 启动命令
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### 2.1 单基因组运行（推荐模板）
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```bash
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prokka \
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--outdir <OUTDIR> \
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--prefix <genome> \
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--cpus 8 \
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--genus Bacillus \
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--species Bacillus thuringiensis \
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genome.fna
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```
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---
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## 3) 参数说明（阈值含义 + 默认值）
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| 参数 | 含义 | 阈值/影响 | 默认值 |
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|---|---|---|---|
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| `--outdir` | 输出目录 | N/A | N/A |
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| `--prefix` | 输出结果文件前缀 | N/A | N/A |
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| `--cpus` | 线程数 | 影响速度 | N/A |
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| `--genus` | 物种所属“属” | N/A | N/A |
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| `--cpus` | 物种所属“种” | N/A | 8 |
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| `genome.fna` | 输入基因组 | N/A | NA |
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---
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## 4) 输出结果文件（结构与解析）
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### 4.1 输出目录结构（建议）
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```
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OUTDIR/
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<genome>.faa # 基因注释蛋白质文件
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<genome>.ffn # 基因注释核酸文件
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<genome>.fna # 基因组文件
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<genome>.gbk # genbank格式注释文件
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<genome>.gff # gff格式注释文件
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<genome>.log
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<genome>.fsa
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<genome>.sqn
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<genome>.tbl
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<genome>.tsv
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<genome>.txt
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<genome>.err
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```
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> prokka注释文件夹中的gbk、faa格式的文件用于杀虫素预测；faa、gff用于CRISPRCasFinder.pl的输入文件。
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---
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4795
tools/base_prokka/0_genomeAnnotation/pixi.lock
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4795
tools/base_prokka/0_genomeAnnotation/pixi.lock
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File diff suppressed because it is too large
Load Diff
368
tools/base_prokka/0_genomeAnnotation/pixi.toml
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tools/base_prokka/0_genomeAnnotation/pixi.toml
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[workspace]
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authors = ["zly <644706215@qq.com>"]
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channels = ["https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge", "bioconda", "conda-forge", "https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main", "ursky", "https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2", "https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main", "https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free", "main", "r", "msys2"]
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name = "prokka"
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platforms = ["linux-64"]
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version = "0.1.0"
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[tasks]
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[dependencies]
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_libgcc_mutex = { version = "==0.1", build = "conda_forge" }
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_openmp_mutex = { version = "==4.5", build = "2_gnu" }
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alsa-lib = { version = "==1.2.11", build = "hd590300_1" }
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aragorn = { version = "==1.2.41", build = "h7b50bb2_5" }
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argcomplete = { version = "==3.6.2", build = "pyhd8ed1ab_0" }
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argh = { version = "==0.31.3", build = "pyhd8ed1ab_1" }
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argtable2 = { version = "==2.13", build = "hd590300_1004" }
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aria2 = { version = "==1.23.0", build = "0" }
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arpack = { version = "==3.7.0", build = "hdefa2d7_2" }
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barrnap = { version = "==0.9", build = "hdfd78af_4" }
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bedtools = { version = "==2.31.1", build = "hf5e1c6e_2" }
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biocode = { version = "==0.12.1", build = "pyhdfd78af_0" }
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biopython = { version = "==1.85", build = "py311h49ec1c0_2" }
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blast = { version = "==2.16.0", build = "hc155240_3" }
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blast-legacy = { version = "==2.2.26", build = "hf7ff83a_5" }
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boost-cpp = { version = "==1.74.0", build = "h75c5d50_8" }
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brotli = { version = "==1.1.0", build = "hb03c661_4" }
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brotli-bin = { version = "==1.1.0", build = "hb03c661_4" }
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brotli-python = { version = "==1.1.0", build = "py311h1ddb823_4" }
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bzip2 = { version = "==1.0.8", build = "hda65f42_8" }
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c-ares = { version = "==1.34.5", build = "hb9d3cd8_0" }
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ca-certificates = { version = "==2025.8.3", build = "hbd8a1cb_0" }
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cairo = { version = "==1.16.0", build = "hb05425b_5" }
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capnproto = { version = "==1.0.2", build = "hfc55251_1" }
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cd-hit = { version = "==4.8.1", build = "h43eeafb_11" }
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certifi = { version = "==2025.8.3", build = "pyhd8ed1ab_0" }
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cffi = { version = "==2.0.0", build = "py311h5b438cf_0" }
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charset-normalizer = { version = "==3.4.3", build = "pyhd8ed1ab_0" }
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clustalo = { version = "==1.2.4", build = "h503566f_10" }
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clustalw = { version = "==2.1", build = "h9948957_12" }
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colorama = { version = "==0.4.6", build = "pyhd8ed1ab_1" }
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consan = { version = "==1.2", build = "h7b50bb2_7" }
|
||||
contourpy = { version = "==1.3.3", build = "py311hdf67eae_2" }
|
||||
curl = { version = "==7.87.0", build = "h6312ad2_0" }
|
||||
cycler = { version = "==0.12.1", build = "pyhd8ed1ab_1" }
|
||||
dendropy = { version = "==5.0.8", build = "pyhdfd78af_1" }
|
||||
dialign-tx = { version = "==1.0.2", build = "h7b50bb2_8" }
|
||||
diamond = { version = "==2.0.15", build = "hb97b32f_1" }
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dnspython = { version = "==2.8.0", build = "pyhcf101f3_0" }
|
||||
easel = { version = "==0.49", build = "hb6cb901_3" }
|
||||
eggnog-mapper = { version = "==2.1.13", build = "pyhdfd78af_2" }
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||||
entrez-direct = { version = "==22.4", build = "he881be0_0" }
|
||||
expat = { version = "==2.7.1", build = "hecca717_0" }
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famsa = { version = "==2.2.3", build = "h9948957_1" }
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fasttree = { version = "==2.2.0", build = "h7b50bb2_0" }
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font-ttf-dejavu-sans-mono = { version = "==2.37", build = "hab24e00_0" }
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font-ttf-inconsolata = { version = "==3.0", build = "h77eed37_0" }
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font-ttf-source-code-pro = { version = "==2.38", build = "h77eed37_0" }
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font-ttf-ubuntu = { version = "==0.83", build = "h77eed37_3" }
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fontconfig = { version = "==2.14.2", build = "h14ed4e7_0" }
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fonts-conda-ecosystem = { version = "==1", build = "0" }
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fonts-conda-forge = { version = "==1", build = "0" }
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fonttools = { version = "==4.60.1", build = "py311h3778330_0" }
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freetype = { version = "==2.12.1", build = "h267a509_2" }
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||||
gawk = { version = "==5.3.1", build = "hcd3d067_0" }
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||||
gffutils = { version = "==0.13", build = "pyh7cba7a3_0" }
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||||
giflib = { version = "==5.2.2", build = "hd590300_0" }
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||||
glib = { version = "==2.80.2", build = "hf974151_0" }
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glib-tools = { version = "==2.80.2", build = "hb6ce0ca_0" }
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glpk = { version = "==5.0", build = "h445213a_0" }
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gmp = { version = "==6.3.0", build = "hac33072_2" }
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gnutls = { version = "==3.8.9", build = "h86084c0_1" }
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graphite2 = { version = "==1.3.14", build = "hecca717_2" }
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||||
gsl = { version = "==2.7", build = "he838d99_0" }
|
||||
h2 = { version = "==4.3.0", build = "pyhcf101f3_0" }
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||||
harfbuzz = { version = "==6.0.0", build = "h8e241bc_0" }
|
||||
hmmer = { version = "==3.4", build = "hb6cb901_4" }
|
||||
hpack = { version = "==4.1.0", build = "pyhd8ed1ab_0" }
|
||||
hyperframe = { version = "==6.1.0", build = "pyhd8ed1ab_0" }
|
||||
icu = { version = "==70.1", build = "h27087fc_0" }
|
||||
idna = { version = "==3.10", build = "pyhd8ed1ab_1" }
|
||||
importlib-metadata = { version = "==8.7.0", build = "pyhe01879c_1" }
|
||||
infernal = { version = "==1.1.5", build = "pl5321h7b50bb2_4" }
|
||||
intbitset = { version = "==3.0.2", build = "py311h459d7ec_1" }
|
||||
intel-openmp = { version = "==2023.1.0", build = "hdb19cb5_46306" }
|
||||
jinja2 = { version = "==3.1.6", build = "pyhd8ed1ab_0" }
|
||||
joblib = { version = "==1.5.2", build = "pyhd8ed1ab_0" }
|
||||
kalign2 = { version = "==2.4", build = "h7b50bb2_8" }
|
||||
keyutils = { version = "==1.6.3", build = "hb9d3cd8_0" }
|
||||
kiwisolver = { version = "==1.4.9", build = "py311h724c32c_1" }
|
||||
krb5 = { version = "==1.20.1", build = "hf9c8cef_0" }
|
||||
lcms2 = { version = "==2.16", build = "hb7c19ff_0" }
|
||||
ld_impl_linux-64 = { version = "==2.44", build = "ha97dd6f_2" }
|
||||
lerc = { version = "==4.0.0", build = "h0aef613_1" }
|
||||
libasprintf = { version = "==0.25.1", build = "h3f43e3d_1" }
|
||||
libblas = { version = "==3.9.0", build = "36_h4a7cf45_openblas" }
|
||||
libbrotlicommon = { version = "==1.1.0", build = "hb03c661_4" }
|
||||
libbrotlidec = { version = "==1.1.0", build = "hb03c661_4" }
|
||||
libbrotlienc = { version = "==1.1.0", build = "hb03c661_4" }
|
||||
libcblas = { version = "==3.9.0", build = "36_h0358290_openblas" }
|
||||
libcups = { version = "==2.3.3", build = "h36d4200_3" }
|
||||
libcurl = { version = "==7.87.0", build = "h6312ad2_0" }
|
||||
libdb = { version = "==6.2.32", build = "h9c3ff4c_0" }
|
||||
libdeflate = { version = "==1.20", build = "hd590300_0" }
|
||||
libedit = { version = "==3.1.20250104", build = "pl5321h7949ede_0" }
|
||||
libev = { version = "==4.33", build = "hd590300_2" }
|
||||
libexpat = { version = "==2.7.1", build = "hecca717_0" }
|
||||
libffi = { version = "==3.4.6", build = "h2dba641_1" }
|
||||
libgcc = { version = "==15.1.0", build = "h767d61c_5" }
|
||||
libgcc-ng = { version = "==15.1.0", build = "h69a702a_5" }
|
||||
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|
||||
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|
||||
libgfortran-ng = { version = "==15.1.0", build = "h69a702a_5" }
|
||||
libgfortran5 = { version = "==15.1.0", build = "hcea5267_5" }
|
||||
libglib = { version = "==2.80.2", build = "hf974151_0" }
|
||||
libgomp = { version = "==15.1.0", build = "h767d61c_5" }
|
||||
libhwloc = { version = "==2.9.1", build = "hd6dc26d_0" }
|
||||
libiconv = { version = "==1.18", build = "h3b78370_2" }
|
||||
libidn11 = { version = "==1.34", build = "h1cef754_0" }
|
||||
libidn2 = { version = "==2.3.8", build = "ha4ef2c3_0" }
|
||||
libjpeg-turbo = { version = "==3.1.0", build = "hb9d3cd8_0" }
|
||||
liblapack = { version = "==3.9.0", build = "36_h47877c9_openblas" }
|
||||
liblzma = { version = "==5.8.1", build = "hb9d3cd8_2" }
|
||||
liblzma-devel = { version = "==5.8.1", build = "hb9d3cd8_2" }
|
||||
libnghttp2 = { version = "==1.51.0", build = "hdcd2b5c_0" }
|
||||
libnsl = { version = "==2.0.1", build = "hb9d3cd8_1" }
|
||||
libopenblas = { version = "==0.3.30", build = "pthreads_h94d23a6_2" }
|
||||
libpng = { version = "==1.6.43", build = "h2797004_0" }
|
||||
libsqlite = { version = "==3.46.0", build = "hde9e2c9_0" }
|
||||
libssh2 = { version = "==1.10.0", build = "haa6b8db_3" }
|
||||
libstdcxx = { version = "==15.1.0", build = "h8f9b012_5" }
|
||||
libstdcxx-ng = { version = "==15.1.0", build = "h4852527_5" }
|
||||
libtasn1 = { version = "==4.20.0", build = "hb9d3cd8_0" }
|
||||
libtiff = { version = "==4.6.0", build = "h1dd3fc0_3" }
|
||||
libunistring = { version = "==0.9.10", build = "h7f98852_0" }
|
||||
libuuid = { version = "==2.41.2", build = "he9a06e4_0" }
|
||||
libwebp-base = { version = "==1.6.0", build = "hd42ef1d_0" }
|
||||
libxcb = { version = "==1.15", build = "h0b41bf4_0" }
|
||||
libxcrypt = { version = "==4.4.36", build = "hd590300_1" }
|
||||
libxml2 = { version = "==2.10.3", build = "hca2bb57_4" }
|
||||
libzlib = { version = "==1.2.13", build = "h4ab18f5_6" }
|
||||
llvmlite = { version = "==0.44.0", build = "py311hc1e8f15_1" }
|
||||
mafft = { version = "==7.526", build = "h4bc722e_0" }
|
||||
markupsafe = { version = "==3.0.3", build = "py311h3778330_0" }
|
||||
mash = { version = "==2.3", build = "hc74b729_7" }
|
||||
matplotlib-base = { version = "==3.10.1", build = "py311h2b939e6_0" }
|
||||
metis = { version = "==5.1.0", build = "hd0bcaf9_1007" }
|
||||
minced = { version = "==0.4.2", build = "hdfd78af_1" }
|
||||
mkl = { version = "==2023.1.0", build = "h213fc3f_46344" }
|
||||
mmseqs2 = { version = "==16.747c6", build = "pl5321h6a68c12_0" }
|
||||
mpfr = { version = "==4.2.1", build = "h90cbb55_3" }
|
||||
mpi = { version = "==1.0", build = "openmpi" }
|
||||
munkres = { version = "==1.0.7", build = "py_1" }
|
||||
muscle = { version = "==3.8.1551", build = "h9948957_9" }
|
||||
mustang = { version = "==3.2.4", build = "h9948957_0" }
|
||||
narwhals = { version = "==2.6.0", build = "pyhcf101f3_0" }
|
||||
ncbi-vdb = { version = "==3.2.1", build = "h9948957_0" }
|
||||
ncurses = { version = "==6.5", build = "h2d0b736_3" }
|
||||
nettle = { version = "==3.10.1", build = "h4a9d5aa_0" }
|
||||
networkx = { version = "==3.5", build = "pyhe01879c_0" }
|
||||
numba = { version = "==0.61.2", build = "py311h6220fa4_2" }
|
||||
numpy = { version = "==2.2.6", build = "py311h5d046bc_0" }
|
||||
openjdk = { version = "==11.0.1", build = "h516909a_1016" }
|
||||
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|
||||
openmpi = { version = "==4.1.6", build = "hc5af2df_101" }
|
||||
openssl = { version = "==1.1.1w", build = "hd590300_0" }
|
||||
p11-kit = { version = "==0.24.1", build = "hc5aa10d_0" }
|
||||
packaging = { version = "==25.0", build = "pyh29332c3_1" }
|
||||
paml = { version = "==4.10.9", build = "h7b50bb2_1" }
|
||||
panaroo = { version = "==1.5.2", build = "pyhdfd78af_0" }
|
||||
parallel = { version = "==20250822", build = "ha770c72_0" }
|
||||
pasta = { version = "==1.9.2", build = "py311hefa8cab_5" }
|
||||
pcre = { version = "==8.45", build = "h9c3ff4c_0" }
|
||||
pcre2 = { version = "==10.43", build = "hcad00b1_0" }
|
||||
peewee = { version = "==3.17.6", build = "py311h26bb8ec_0" }
|
||||
perl = { version = "==5.32.1", build = "7_hd590300_perl5" }
|
||||
perl-algorithm-diff = { version = "==1.1903", build = "pl5321hdfd78af_3" }
|
||||
perl-archive-tar = { version = "==3.4", build = "pl5321hdfd78af_0" }
|
||||
perl-b-cow = { version = "==0.7", build = "pl5321hb9d3cd8_1" }
|
||||
perl-base = { version = "==2.23", build = "pl5321hdfd78af_2" }
|
||||
perl-bio-asn1-entrezgene = { version = "==1.73", build = "pl5321hdfd78af_3" }
|
||||
perl-bio-coordinate = { version = "==1.7001", build = "pl5321hdfd78af_3" }
|
||||
perl-bio-featureio = { version = "==1.6.905", build = "pl5321hdfd78af_4" }
|
||||
perl-bio-samtools = { version = "==1.43", build = "pl5321he4a0461_4" }
|
||||
perl-bio-searchio-hmmer = { version = "==1.7.3", build = "pl5321hdfd78af_0" }
|
||||
perl-bio-tools-phylo-paml = { version = "==1.7.3", build = "pl5321hdfd78af_3" }
|
||||
perl-bio-tools-run-alignment-clustalw = { version = "==1.7.4", build = "pl5321hdfd78af_3" }
|
||||
perl-bio-tools-run-alignment-tcoffee = { version = "==1.7.4", build = "pl5321hdfd78af_5" }
|
||||
perl-bioperl = { version = "==1.7.8", build = "hdfd78af_1" }
|
||||
perl-bioperl-core = { version = "==1.7.8", build = "pl5321hdfd78af_1" }
|
||||
perl-bioperl-run = { version = "==1.7003", build = "pl5321hdfd78af_0" }
|
||||
perl-business-isbn = { version = "==3.7", build = "pl5321hdfd78af_0" }
|
||||
perl-business-isbn-data = { version = "==20210112.6", build = "pl5321hdfd78af_0" }
|
||||
perl-capture-tiny = { version = "==0.48", build = "pl5321hdfd78af_2" }
|
||||
perl-carp = { version = "==1.38", build = "pl5321hdfd78af_4" }
|
||||
perl-class-data-inheritable = { version = "==0.9", build = "pl5321hdfd78af_0" }
|
||||
perl-clone = { version = "==0.46", build = "pl5321hec16e2b_0" }
|
||||
perl-common-sense = { version = "==3.75", build = "pl5321hdfd78af_0" }
|
||||
perl-compress-raw-bzip2 = { version = "==2.201", build = "pl5321h87f3376_1" }
|
||||
perl-compress-raw-zlib = { version = "==2.105", build = "pl5321h87f3376_0" }
|
||||
perl-constant = { version = "==1.33", build = "pl5321hdfd78af_2" }
|
||||
perl-data-dump = { version = "==1.25", build = "pl5321h7b50bb2_2" }
|
||||
perl-data-dumper = { version = "==2.183", build = "pl5321hec16e2b_1" }
|
||||
perl-db_file = { version = "==1.858", build = "pl5321hb9d3cd8_0" }
|
||||
perl-devel-stacktrace = { version = "==2.4", build = "pl5321hdfd78af_1" }
|
||||
perl-digest-hmac = { version = "==1.5", build = "pl5321hdfd78af_0" }
|
||||
perl-digest-md5 = { version = "==2.58", build = "pl5321hec16e2b_1" }
|
||||
perl-encode = { version = "==3.19", build = "pl5321hec16e2b_1" }
|
||||
perl-encode-locale = { version = "==1.5", build = "pl5321hdfd78af_7" }
|
||||
perl-exception-class = { version = "==1.45", build = "pl5321hdfd78af_0" }
|
||||
perl-exporter = { version = "==5.72", build = "pl5321hdfd78af_2" }
|
||||
perl-exporter-tiny = { version = "==1.2002", build = "pl5321hdfd78af_0" }
|
||||
perl-extutils-makemaker = { version = "==7.70", build = "pl5321hd8ed1ab_0" }
|
||||
perl-file-listing = { version = "==6.16", build = "pl5321hdfd78af_0" }
|
||||
perl-file-path = { version = "==2.18", build = "pl5321hd8ed1ab_0" }
|
||||
perl-file-slurper = { version = "==0.14", build = "pl5321hdfd78af_0" }
|
||||
perl-file-sort = { version = "==1.1", build = "pl5321hdfd78af_3" }
|
||||
perl-file-spec = { version = "==3.48_1", build = "pl5321hdfd78af_2" }
|
||||
perl-file-temp = { version = "==0.2304", build = "pl5321hd8ed1ab_0" }
|
||||
perl-getopt-long = { version = "==2.58", build = "pl5321hdfd78af_0" }
|
||||
perl-html-parser = { version = "==3.81", build = "pl5321h4ac6f70_1" }
|
||||
perl-html-tagset = { version = "==3.24", build = "pl5321hdfd78af_0" }
|
||||
perl-http-cookiejar-lwp = { version = "==0.14", build = "pl5321hdfd78af_0" }
|
||||
perl-http-cookies = { version = "==6.11", build = "pl5321hdfd78af_0" }
|
||||
perl-http-daemon = { version = "==6.16", build = "pl5321hdfd78af_0" }
|
||||
perl-http-date = { version = "==6.6", build = "pl5321hdfd78af_0" }
|
||||
perl-http-message = { version = "==7.0", build = "pl5321hdfd78af_0" }
|
||||
perl-http-negotiate = { version = "==6.1", build = "pl5321hdfd78af_4" }
|
||||
perl-inc-latest = { version = "==0.500", build = "pl5321ha770c72_0" }
|
||||
perl-io-compress = { version = "==2.201", build = "pl5321h503566f_5" }
|
||||
perl-io-html = { version = "==1.4", build = "pl5321hdfd78af_0" }
|
||||
perl-io-socket-ssl = { version = "==2.74", build = "pl5321hdfd78af_0" }
|
||||
perl-io-string = { version = "==1.8", build = "pl5321hdfd78af_4" }
|
||||
perl-io-tty = { version = "==1.16", build = "pl5321hec16e2b_1" }
|
||||
perl-io-zlib = { version = "==1.15", build = "pl5321hdfd78af_1" }
|
||||
perl-ipc-run = { version = "==20250809.0", build = "pl5321hdfd78af_0" }
|
||||
perl-json = { version = "==4.10", build = "pl5321hdfd78af_1" }
|
||||
perl-json-xs = { version = "==4.4", build = "pl5321h9948957_0" }
|
||||
perl-libwww-perl = { version = "==6.80", build = "pl5321hdfd78af_0" }
|
||||
perl-libxml-perl = { version = "==0.8", build = "pl5321hdfd78af_3" }
|
||||
perl-list-moreutils = { version = "==0.430", build = "pl5321hdfd78af_0" }
|
||||
perl-list-moreutils-xs = { version = "==0.430", build = "pl5321h7b50bb2_5" }
|
||||
perl-lwp-mediatypes = { version = "==6.4", build = "pl5321hdfd78af_1" }
|
||||
perl-lwp-protocol-https = { version = "==6.14", build = "pl5321hdfd78af_1" }
|
||||
perl-mime-base64 = { version = "==3.16", build = "pl5321hec16e2b_2" }
|
||||
perl-module-build = { version = "==0.4234", build = "pl5321ha770c72_1" }
|
||||
perl-module-load = { version = "==0.34", build = "pl5321hdfd78af_0" }
|
||||
perl-mozilla-ca = { version = "==20250602", build = "pl5321hdfd78af_0" }
|
||||
perl-net-http = { version = "==6.24", build = "pl5321hdfd78af_0" }
|
||||
perl-net-ssleay = { version = "==1.92", build = "pl5321h0e0aaa8_1" }
|
||||
perl-ntlm = { version = "==1.9", build = "pl5321hdfd78af_5" }
|
||||
perl-parent = { version = "==0.236", build = "pl5321hdfd78af_2" }
|
||||
perl-pathtools = { version = "==3.75", build = "pl5321hec16e2b_3" }
|
||||
perl-scalar-list-utils = { version = "==1.62", build = "pl5321hec16e2b_1" }
|
||||
perl-socket = { version = "==2.27", build = "pl5321h5c03b87_6" }
|
||||
perl-sub-uplevel = { version = "==0.2800", build = "pl5321hec16e2b_4" }
|
||||
perl-test-deep = { version = "==1.130", build = "pl5321hdfd78af_0" }
|
||||
perl-test-differences = { version = "==0.69", build = "pl5321hdfd78af_0" }
|
||||
perl-test-exception = { version = "==0.43", build = "pl5321hdfd78af_3" }
|
||||
perl-test-most = { version = "==0.38", build = "pl5321hdfd78af_0" }
|
||||
perl-test-needs = { version = "==0.2009", build = "pl5321hdfd78af_0" }
|
||||
perl-test-requiresinternet = { version = "==0.5", build = "pl5321hdfd78af_1" }
|
||||
perl-test-warn = { version = "==0.36", build = "pl5321hdfd78af_2" }
|
||||
perl-text-diff = { version = "==1.45", build = "pl5321hdfd78af_1" }
|
||||
perl-time-local = { version = "==1.35", build = "pl5321hdfd78af_0" }
|
||||
perl-timedate = { version = "==2.33", build = "pl5321hdfd78af_2" }
|
||||
perl-tree-dag_node = { version = "==1.35", build = "pl5321hdfd78af_0" }
|
||||
perl-try-tiny = { version = "==0.31", build = "pl5321hdfd78af_1" }
|
||||
perl-types-serialiser = { version = "==1.1", build = "pl5321hdfd78af_0" }
|
||||
perl-uri = { version = "==5.12", build = "pl5321hdfd78af_0" }
|
||||
perl-url-encode = { version = "==0.3", build = "pl5321h9ee0642_1" }
|
||||
perl-www-robotrules = { version = "==6.2", build = "pl5321hdfd78af_4" }
|
||||
perl-xml-dom = { version = "==1.46", build = "pl5321hdfd78af_1" }
|
||||
perl-xml-dom-xpath = { version = "==0.14", build = "pl5321hdfd78af_2" }
|
||||
perl-xml-namespacesupport = { version = "==1.12", build = "pl5321hdfd78af_1" }
|
||||
perl-xml-parser = { version = "==2.44_1", build = "pl5321hf2e2c51_1004" }
|
||||
perl-xml-regexp = { version = "==0.4", build = "pl5321hdfd78af_3" }
|
||||
perl-xml-sax = { version = "==1.2", build = "pl5321hdfd78af_1" }
|
||||
perl-xml-sax-base = { version = "==1.9", build = "pl5321hdfd78af_1" }
|
||||
perl-xml-sax-expat = { version = "==0.51", build = "pl5321hdfd78af_4" }
|
||||
perl-xml-simple = { version = "==2.25", build = "pl5321hdfd78af_2" }
|
||||
perl-xml-xpathengine = { version = "==0.14", build = "pl5321hdfd78af_3" }
|
||||
phylip = { version = "==3.697", build = "h7b50bb2_3" }
|
||||
pillow = { version = "==10.3.0", build = "py311h18e6fac_0" }
|
||||
pip = { version = "==25.2", build = "pyh8b19718_0" }
|
||||
pixman = { version = "==0.46.4", build = "h54a6638_1" }
|
||||
plotly = { version = "==6.3.0", build = "pyhd8ed1ab_0" }
|
||||
poa = { version = "==2.0", build = "h7b50bb2_6" }
|
||||
prank = { version = "==170427", build = "h9948957_1" }
|
||||
probcons = { version = "==1.12", build = "h8b12597_1" }
|
||||
probconsrna = { version = "==1.10", build = "h9f5acd7_4" }
|
||||
proda = { version = "==1.0", build = "h503566f_7" }
|
||||
prodigal = { version = "==2.6.3", build = "h7b50bb2_10" }
|
||||
prokka = { version = "==1.14.6", build = "pl5321hdfd78af_5" }
|
||||
psutil = { version = "==7.1.3", build = "py311haee01d2_0" }
|
||||
pthread-stubs = { version = "==0.4", build = "hb9d3cd8_1002" }
|
||||
pycparser = { version = "==2.22", build = "pyh29332c3_1" }
|
||||
pyfaidx = { version = "==0.9.0.3", build = "pyhdfd78af_0" }
|
||||
pymongo = { version = "==4.14.1", build = "py311h1ddb823_0" }
|
||||
pyparsing = { version = "==3.2.5", build = "pyhcf101f3_0" }
|
||||
pysocks = { version = "==1.7.1", build = "pyha55dd90_7" }
|
||||
python = { version = "==3.11.0", build = "h10a6764_1_cpython" }
|
||||
python-dateutil = { version = "==2.9.0.post0", build = "pyhe01879c_2" }
|
||||
python-edlib = { version = "==1.3.9.post1", build = "py311he264feb_2" }
|
||||
python-igraph = { version = "==0.10.4", build = "py311hcb6f00c_0" }
|
||||
python_abi = { version = "==3.11", build = "8_cp311" }
|
||||
pyvcf3 = { version = "==1.0.4", build = "py311haab0aaa_0" }
|
||||
qhull = { version = "==2020.2", build = "h434a139_5" }
|
||||
raxml = { version = "==8.2.13", build = "h7b50bb2_3" }
|
||||
readline = { version = "==8.2", build = "h8c095d6_2" }
|
||||
requests = { version = "==2.32.5", build = "pyhd8ed1ab_0" }
|
||||
rpsbproc = { version = "==0.5.0", build = "h6a68c12_1" }
|
||||
sap = { version = "==1.1.3", build = "h7b50bb2_5" }
|
||||
scikit-learn = { version = "==1.7.2", build = "py311hc3e1efb_0" }
|
||||
scipy = { version = "==1.16.2", build = "py311h1e13796_0" }
|
||||
setuptools = { version = "==80.9.0", build = "pyhff2d567_0" }
|
||||
simplejson = { version = "==3.20.2", build = "py311h49ec1c0_0" }
|
||||
six = { version = "==1.17.0", build = "pyhe01879c_1" }
|
||||
sniffio = { version = "==1.3.1", build = "pyhd8ed1ab_1" }
|
||||
sqlite = { version = "==3.46.0", build = "h6d4b2fc_0" }
|
||||
suitesparse = { version = "==5.10.1", build = "h9e50725_1" }
|
||||
t-coffee = { version = "==13.46.1.b8b1e6", build = "pl5321hb2a3317_2" }
|
||||
taxadb = { version = "==0.12.1", build = "pyh5e36f6f_0" }
|
||||
tbb = { version = "==2021.9.0", build = "hf52228f_0" }
|
||||
tbl2asn-forever = { version = "==25.7.2f", build = "h7b50bb2_6" }
|
||||
texttable = { version = "==1.7.0", build = "pyhd8ed1ab_1" }
|
||||
threadpoolctl = { version = "==3.6.0", build = "pyhecae5ae_0" }
|
||||
tk = { version = "==8.6.13", build = "noxft_h4845f30_101" }
|
||||
tmalign = { version = "==20220227", build = "h9948957_0" }
|
||||
tqdm = { version = "==4.67.1", build = "pyhd8ed1ab_1" }
|
||||
tzdata = { version = "==2025b", build = "h78e105d_0" }
|
||||
unicodedata2 = { version = "==16.0.0", build = "py311h49ec1c0_1" }
|
||||
urllib3 = { version = "==2.5.0", build = "pyhd8ed1ab_0" }
|
||||
viennarna = { version = "==2.7.0", build = "py311pl5321h0f867f1_0" }
|
||||
wget = { version = "==1.20.3", build = "ha56f1ee_1" }
|
||||
wheel = { version = "==0.45.1", build = "pyhd8ed1ab_1" }
|
||||
xlsxwriter = { version = "==3.2.9", build = "pyhd8ed1ab_0" }
|
||||
xorg-fixesproto = { version = "==5.0", build = "hb9d3cd8_1003" }
|
||||
xorg-inputproto = { version = "==2.3.2", build = "hb9d3cd8_1003" }
|
||||
xorg-kbproto = { version = "==1.0.7", build = "hb9d3cd8_1003" }
|
||||
xorg-libice = { version = "==1.1.2", build = "hb9d3cd8_0" }
|
||||
xorg-libsm = { version = "==1.2.6", build = "he73a12e_0" }
|
||||
xorg-libx11 = { version = "==1.8.9", build = "h8ee46fc_0" }
|
||||
xorg-libxau = { version = "==1.0.12", build = "hb9d3cd8_0" }
|
||||
xorg-libxdmcp = { version = "==1.1.5", build = "hb9d3cd8_0" }
|
||||
xorg-libxext = { version = "==1.3.4", build = "h0b41bf4_2" }
|
||||
xorg-libxfixes = { version = "==5.0.3", build = "h7f98852_1004" }
|
||||
xorg-libxi = { version = "==1.7.10", build = "h4bc722e_1" }
|
||||
xorg-libxrender = { version = "==0.9.11", build = "hd590300_0" }
|
||||
xorg-libxt = { version = "==1.3.0", build = "hd590300_1" }
|
||||
xorg-libxtst = { version = "==1.2.5", build = "h4bc722e_0" }
|
||||
xorg-recordproto = { version = "==1.14.2", build = "hb9d3cd8_1003" }
|
||||
xorg-renderproto = { version = "==0.11.1", build = "hb9d3cd8_1003" }
|
||||
xorg-xextproto = { version = "==7.3.0", build = "hb9d3cd8_1004" }
|
||||
xorg-xproto = { version = "==7.0.31", build = "hb9d3cd8_1008" }
|
||||
xz = { version = "==5.8.1", build = "hbcc6ac9_2" }
|
||||
xz-gpl-tools = { version = "==5.8.1", build = "hbcc6ac9_2" }
|
||||
xz-tools = { version = "==5.8.1", build = "hb9d3cd8_2" }
|
||||
zipp = { version = "==3.23.0", build = "pyhd8ed1ab_0" }
|
||||
zlib = { version = "==1.2.13", build = "h4ab18f5_6" }
|
||||
zstandard = { version = "==0.23.0", build = "py311h49ec1c0_3" }
|
||||
zstd = { version = "==1.5.6", build = "ha6fb4c9_0" }
|
||||
|
||||
[pypi-dependencies]
|
||||
blessed = "==1.25.0"
|
||||
gpustat = "==1.1.1"
|
||||
nvidia-ml-py = "==13.580.82"
|
||||
wcwidth = "==0.2.14"
|
||||
370
tools/base_prokka/0_genomeAnnotation/prokka.yml
Normal file
370
tools/base_prokka/0_genomeAnnotation/prokka.yml
Normal file
@@ -0,0 +1,370 @@
|
||||
name: prokka
|
||||
channels:
|
||||
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
|
||||
- bioconda
|
||||
- conda-forge
|
||||
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
|
||||
- ursky
|
||||
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/
|
||||
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
|
||||
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
|
||||
- defaults
|
||||
dependencies:
|
||||
- _libgcc_mutex=0.1=conda_forge
|
||||
- _openmp_mutex=4.5=2_gnu
|
||||
- alsa-lib=1.2.11=hd590300_1
|
||||
- aragorn=1.2.41=h7b50bb2_5
|
||||
- argcomplete=3.6.2=pyhd8ed1ab_0
|
||||
- argh=0.31.3=pyhd8ed1ab_1
|
||||
- argtable2=2.13=hd590300_1004
|
||||
- aria2=1.23.0=0
|
||||
- arpack=3.7.0=hdefa2d7_2
|
||||
- barrnap=0.9=hdfd78af_4
|
||||
- bedtools=2.31.1=hf5e1c6e_2
|
||||
- biocode=0.12.1=pyhdfd78af_0
|
||||
- biopython=1.85=py311h49ec1c0_2
|
||||
- blast=2.16.0=hc155240_3
|
||||
- blast-legacy=2.2.26=hf7ff83a_5
|
||||
- boost-cpp=1.74.0=h75c5d50_8
|
||||
- brotli=1.1.0=hb03c661_4
|
||||
- brotli-bin=1.1.0=hb03c661_4
|
||||
- brotli-python=1.1.0=py311h1ddb823_4
|
||||
- bzip2=1.0.8=hda65f42_8
|
||||
- c-ares=1.34.5=hb9d3cd8_0
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
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|
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|
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
- perl-xml-xpathengine=0.14=pl5321hdfd78af_3
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
- probconsrna=1.10=h9f5acd7_4
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
- pyparsing=3.2.5=pyhcf101f3_0
|
||||
- pysocks=1.7.1=pyha55dd90_7
|
||||
- python=3.11.0=h10a6764_1_cpython
|
||||
- python-dateutil=2.9.0.post0=pyhe01879c_2
|
||||
- python-edlib=1.3.9.post1=py311he264feb_2
|
||||
- python-igraph=0.10.4=py311hcb6f00c_0
|
||||
- python_abi=3.11=8_cp311
|
||||
- pyvcf3=1.0.4=py311haab0aaa_0
|
||||
- qhull=2020.2=h434a139_5
|
||||
- raxml=8.2.13=h7b50bb2_3
|
||||
- readline=8.2=h8c095d6_2
|
||||
- requests=2.32.5=pyhd8ed1ab_0
|
||||
- rpsbproc=0.5.0=h6a68c12_1
|
||||
- sap=1.1.3=h7b50bb2_5
|
||||
- scikit-learn=1.7.2=py311hc3e1efb_0
|
||||
- scipy=1.16.2=py311h1e13796_0
|
||||
- setuptools=80.9.0=pyhff2d567_0
|
||||
- simplejson=3.20.2=py311h49ec1c0_0
|
||||
- six=1.17.0=pyhe01879c_1
|
||||
- sniffio=1.3.1=pyhd8ed1ab_1
|
||||
- sqlite=3.46.0=h6d4b2fc_0
|
||||
- suitesparse=5.10.1=h9e50725_1
|
||||
- t-coffee=13.46.1.b8b01e06=pl5321hb2a3317_2
|
||||
- taxadb=0.12.1=pyh5e36f6f_0
|
||||
- tbb=2021.9.0=hf52228f_0
|
||||
- tbl2asn-forever=25.7.2f=h7b50bb2_6
|
||||
- texttable=1.7.0=pyhd8ed1ab_1
|
||||
- threadpoolctl=3.6.0=pyhecae5ae_0
|
||||
- tk=8.6.13=noxft_h4845f30_101
|
||||
- tmalign=20220227=h9948957_0
|
||||
- tqdm=4.67.1=pyhd8ed1ab_1
|
||||
- tzdata=2025b=h78e105d_0
|
||||
- unicodedata2=16.0.0=py311h49ec1c0_1
|
||||
- urllib3=2.5.0=pyhd8ed1ab_0
|
||||
- viennarna=2.7.0=py311pl5321h0f867f1_0
|
||||
- wget=1.20.3=ha56f1ee_1
|
||||
- wheel=0.45.1=pyhd8ed1ab_1
|
||||
- xlsxwriter=3.2.9=pyhd8ed1ab_0
|
||||
- xorg-fixesproto=5.0=hb9d3cd8_1003
|
||||
- xorg-inputproto=2.3.2=hb9d3cd8_1003
|
||||
- xorg-kbproto=1.0.7=hb9d3cd8_1003
|
||||
- xorg-libice=1.1.2=hb9d3cd8_0
|
||||
- xorg-libsm=1.2.6=he73a12e_0
|
||||
- xorg-libx11=1.8.9=h8ee46fc_0
|
||||
- xorg-libxau=1.0.12=hb9d3cd8_0
|
||||
- xorg-libxdmcp=1.1.5=hb9d3cd8_0
|
||||
- xorg-libxext=1.3.4=h0b41bf4_2
|
||||
- xorg-libxfixes=5.0.3=h7f98852_1004
|
||||
- xorg-libxi=1.7.10=h4bc722e_1
|
||||
- xorg-libxrender=0.9.11=hd590300_0
|
||||
- xorg-libxt=1.3.0=hd590300_1
|
||||
- xorg-libxtst=1.2.5=h4bc722e_0
|
||||
- xorg-recordproto=1.14.2=hb9d3cd8_1003
|
||||
- xorg-renderproto=0.11.1=hb9d3cd8_1003
|
||||
- xorg-xextproto=7.3.0=hb9d3cd8_1004
|
||||
- xorg-xproto=7.0.31=hb9d3cd8_1008
|
||||
- xz=5.8.1=hbcc6ac9_2
|
||||
- xz-gpl-tools=5.8.1=hbcc6ac9_2
|
||||
- xz-tools=5.8.1=hb9d3cd8_2
|
||||
- zipp=3.23.0=pyhd8ed1ab_0
|
||||
- zlib=1.2.13=h4ab18f5_6
|
||||
- zstandard=0.23.0=py311h49ec1c0_3
|
||||
- zstd=1.5.6=ha6fb4c9_0
|
||||
- pip:
|
||||
- blessed==1.25.0
|
||||
- gpustat==1.1.1
|
||||
- nvidia-ml-py==13.580.82
|
||||
- wcwidth==0.2.14
|
||||
prefix: /home/gzy/miniforge3/envs/prokka
|
||||
3
tools/base_prokka/README.md
Normal file
3
tools/base_prokka/README.md
Normal file
@@ -0,0 +1,3 @@
|
||||
prokka 这个环境，是进行基因组注释的，这是进行原核生物分析的第一步，运行这个后，会得到相应的基因注释文件；
|
||||
后续的crispr鉴定，需要输入的文件有gff、faa文件，这些文件是从prokka的运行得到的；
|
||||
后面bgc的鉴定，也需要prokka的结果文件。
|
||||
1194
tools/base_prokka/data/20141126CLLT035.renamed.fasta
Normal file
1194
tools/base_prokka/data/20141126CLLT035.renamed.fasta
Normal file
File diff suppressed because one or more lines are too long
Reference in New Issue
Block a user