Files
bttoxin-pipeline/tools/base_prokka/0_genomeAnnotation/pixi.toml
zly 8e0deb1691 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>
2026-01-28 20:31:00 +08:00

369 lines
22 KiB
TOML

[workspace]
authors = ["zly <644706215@qq.com>"]
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"]
name = "prokka"
platforms = ["linux-64"]
version = "0.1.0"
[tasks]
[dependencies]
_libgcc_mutex = { version = "==0.1", build = "conda_forge" }
_openmp_mutex = { version = "==4.5", build = "2_gnu" }
alsa-lib = { version = "==1.2.11", build = "hd590300_1" }
aragorn = { version = "==1.2.41", build = "h7b50bb2_5" }
argcomplete = { version = "==3.6.2", build = "pyhd8ed1ab_0" }
argh = { version = "==0.31.3", build = "pyhd8ed1ab_1" }
argtable2 = { version = "==2.13", build = "hd590300_1004" }
aria2 = { version = "==1.23.0", build = "0" }
arpack = { version = "==3.7.0", build = "hdefa2d7_2" }
barrnap = { version = "==0.9", build = "hdfd78af_4" }
bedtools = { version = "==2.31.1", build = "hf5e1c6e_2" }
biocode = { version = "==0.12.1", build = "pyhdfd78af_0" }
biopython = { version = "==1.85", build = "py311h49ec1c0_2" }
blast = { version = "==2.16.0", build = "hc155240_3" }
blast-legacy = { version = "==2.2.26", build = "hf7ff83a_5" }
boost-cpp = { version = "==1.74.0", build = "h75c5d50_8" }
brotli = { version = "==1.1.0", build = "hb03c661_4" }
brotli-bin = { version = "==1.1.0", build = "hb03c661_4" }
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clustalo = { version = "==1.2.4", build = "h503566f_10" }
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fontconfig = { version = "==2.14.2", build = "h14ed4e7_0" }
fonts-conda-ecosystem = { version = "==1", build = "0" }
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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"