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bttoxin-pipeline/tools/base_prokka/0_genomeAnnotation/prokka.yml
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

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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
- ca-certificates=2025.8.3=hbd8a1cb_0
- cairo=1.16.0=hb05425b_5
- capnproto=1.0.2=hfc55251_1
- cd-hit=4.8.1=h43eeafb_11
- certifi=2025.8.3=pyhd8ed1ab_0
- cffi=2.0.0=py311h5b438cf_0
- charset-normalizer=3.4.3=pyhd8ed1ab_0
- clustalo=1.2.4=h503566f_10
- clustalw=2.1=h9948957_12
- colorama=0.4.6=pyhd8ed1ab_1
- consan=1.2=h7b50bb2_7
- contourpy=1.3.3=py311hdf67eae_2
- curl=7.87.0=h6312ad2_0
- cycler=0.12.1=pyhd8ed1ab_1
- dendropy=5.0.8=pyhdfd78af_1
- dialign-tx=1.0.2=h7b50bb2_8
- diamond=2.0.15=hb97b32f_1
- dnspython=2.8.0=pyhcf101f3_0
- easel=0.49=hb6cb901_3
- eggnog-mapper=2.1.13=pyhdfd78af_2
- entrez-direct=22.4=he881be0_0
- expat=2.7.1=hecca717_0
- famsa=2.2.3=h9948957_1
- fasttree=2.2.0=h7b50bb2_0
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- font-ttf-inconsolata=3.000=h77eed37_0
- font-ttf-source-code-pro=2.038=h77eed37_0
- font-ttf-ubuntu=0.83=h77eed37_3
- fontconfig=2.14.2=h14ed4e7_0
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- fonttools=4.60.1=py311h3778330_0
- freetype=2.12.1=h267a509_2
- gawk=5.3.1=hcd3d067_0
- gffutils=0.13=pyh7cba7a3_0
- giflib=5.2.2=hd590300_0
- glib=2.80.2=hf974151_0
- glib-tools=2.80.2=hb6ce0ca_0
- glpk=5.0=h445213a_0
- gmp=6.3.0=hac33072_2
- gnutls=3.8.9=h86084c0_1
- graphite2=1.3.14=hecca717_2
- gsl=2.7=he838d99_0
- h2=4.3.0=pyhcf101f3_0
- harfbuzz=6.0.0=h8e241bc_0
- hmmer=3.4=hb6cb901_4
- hpack=4.1.0=pyhd8ed1ab_0
- hyperframe=6.1.0=pyhd8ed1ab_0
- icu=70.1=h27087fc_0
- idna=3.10=pyhd8ed1ab_1
- importlib-metadata=8.7.0=pyhe01879c_1
- infernal=1.1.5=pl5321h7b50bb2_4
- intbitset=3.0.2=py311h459d7ec_1
- intel-openmp=2023.1.0=hdb19cb5_46306
- jinja2=3.1.6=pyhd8ed1ab_0
- joblib=1.5.2=pyhd8ed1ab_0
- kalign2=2.04=h7b50bb2_8
- keyutils=1.6.3=hb9d3cd8_0
- kiwisolver=1.4.9=py311h724c32c_1
- krb5=1.20.1=hf9c8cef_0
- lcms2=2.16=hb7c19ff_0
- ld_impl_linux-64=2.44=ha97dd6f_2
- lerc=4.0.0=h0aef613_1
- libasprintf=0.25.1=h3f43e3d_1
- libblas=3.9.0=36_h4a7cf45_openblas
- libbrotlicommon=1.1.0=hb03c661_4
- libbrotlidec=1.1.0=hb03c661_4
- libbrotlienc=1.1.0=hb03c661_4
- libcblas=3.9.0=36_h0358290_openblas
- libcups=2.3.3=h36d4200_3
- libcurl=7.87.0=h6312ad2_0
- libdb=6.2.32=h9c3ff4c_0
- libdeflate=1.20=hd590300_0
- libedit=3.1.20250104=pl5321h7949ede_0
- libev=4.33=hd590300_2
- libexpat=2.7.1=hecca717_0
- libffi=3.4.6=h2dba641_1
- libgcc=15.1.0=h767d61c_5
- libgcc-ng=15.1.0=h69a702a_5
- libgettextpo=0.25.1=h3f43e3d_1
- libgfortran=15.1.0=h69a702a_5
- libgfortran-ng=15.1.0=h69a702a_5
- libgfortran5=15.1.0=hcea5267_5
- libglib=2.80.2=hf974151_0
- libgomp=15.1.0=h767d61c_5
- libhwloc=2.9.1=hd6dc26d_0
- libiconv=1.18=h3b78370_2
- libidn11=1.34=h1cef754_0
- libidn2=2.3.8=ha4ef2c3_0
- libjpeg-turbo=3.1.0=hb9d3cd8_0
- liblapack=3.9.0=36_h47877c9_openblas
- liblzma=5.8.1=hb9d3cd8_2
- liblzma-devel=5.8.1=hb9d3cd8_2
- libnghttp2=1.51.0=hdcd2b5c_0
- libnsl=2.0.1=hb9d3cd8_1
- libopenblas=0.3.30=pthreads_h94d23a6_2
- libpng=1.6.43=h2797004_0
- libsqlite=3.46.0=hde9e2c9_0
- libssh2=1.10.0=haa6b8db_3
- libstdcxx=15.1.0=h8f9b012_5
- libstdcxx-ng=15.1.0=h4852527_5
- libtasn1=4.20.0=hb9d3cd8_0
- libtiff=4.6.0=h1dd3fc0_3
- libunistring=0.9.10=h7f98852_0
- libuuid=2.41.2=he9a06e4_0
- libwebp-base=1.6.0=hd42ef1d_0
- libxcb=1.15=h0b41bf4_0
- libxcrypt=4.4.36=hd590300_1
- libxml2=2.10.3=hca2bb57_4
- libzlib=1.2.13=h4ab18f5_6
- llvmlite=0.44.0=py311hc1e8f15_1
- mafft=7.526=h4bc722e_0
- markupsafe=3.0.3=py311h3778330_0
- mash=2.3=hc74b729_7
- matplotlib-base=3.10.1=py311h2b939e6_0
- metis=5.1.0=hd0bcaf9_1007
- minced=0.4.2=hdfd78af_1
- mkl=2023.1.0=h213fc3f_46344
- mmseqs2=16.747c6=pl5321h6a68c12_0
- mpfr=4.2.1=h90cbb55_3
- mpi=1.0=openmpi
- munkres=1.0.7=py_1
- muscle=3.8.1551=h9948957_9
- mustang=3.2.4=h9948957_0
- narwhals=2.6.0=pyhcf101f3_0
- ncbi-vdb=3.2.1=h9948957_0
- ncurses=6.5=h2d0b736_3
- nettle=3.10.1=h4a9d5aa_0
- networkx=3.5=pyhe01879c_0
- numba=0.61.2=py311h6220fa4_2
- numpy=2.2.6=py311h5d046bc_0
- openjdk=11.0.1=h516909a_1016
- openjpeg=2.5.2=h488ebb8_0
- openmpi=4.1.6=hc5af2df_101
- openssl=1.1.1w=hd590300_0
- p11-kit=0.24.1=hc5aa10d_0
- packaging=25.0=pyh29332c3_1
- paml=4.10.9=h7b50bb2_1
- panaroo=1.5.2=pyhdfd78af_0
- parallel=20250822=ha770c72_0
- pasta=1.9.2=py311hefa8cab_5
- pcre=8.45=h9c3ff4c_0
- pcre2=10.43=hcad00b1_0
- peewee=3.17.6=py311h26bb8ec_0
- perl=5.32.1=7_hd590300_perl5
- perl-algorithm-diff=1.1903=pl5321hdfd78af_3
- perl-archive-tar=3.04=pl5321hdfd78af_0
- perl-b-cow=0.007=pl5321hb9d3cd8_1
- perl-base=2.23=pl5321hdfd78af_2
- perl-bio-asn1-entrezgene=1.73=pl5321hdfd78af_3
- perl-bio-coordinate=1.007001=pl5321hdfd78af_3
- perl-bio-featureio=1.6.905=pl5321hdfd78af_4
- perl-bio-samtools=1.43=pl5321he4a0461_4
- perl-bio-searchio-hmmer=1.7.3=pl5321hdfd78af_0
- perl-bio-tools-phylo-paml=1.7.3=pl5321hdfd78af_3
- perl-bio-tools-run-alignment-clustalw=1.7.4=pl5321hdfd78af_3
- perl-bio-tools-run-alignment-tcoffee=1.7.4=pl5321hdfd78af_5
- perl-bioperl=1.7.8=hdfd78af_1
- perl-bioperl-core=1.7.8=pl5321hdfd78af_1
- perl-bioperl-run=1.007003=pl5321hdfd78af_0
- perl-business-isbn=3.007=pl5321hdfd78af_0
- perl-business-isbn-data=20210112.006=pl5321hdfd78af_0
- perl-capture-tiny=0.48=pl5321hdfd78af_2
- perl-carp=1.38=pl5321hdfd78af_4
- perl-class-data-inheritable=0.09=pl5321hdfd78af_0
- perl-clone=0.46=pl5321hec16e2b_0
- perl-common-sense=3.75=pl5321hdfd78af_0
- perl-compress-raw-bzip2=2.201=pl5321h87f3376_1
- perl-compress-raw-zlib=2.105=pl5321h87f3376_0
- perl-constant=1.33=pl5321hdfd78af_2
- perl-data-dump=1.25=pl5321h7b50bb2_2
- perl-data-dumper=2.183=pl5321hec16e2b_1
- perl-db_file=1.858=pl5321hb9d3cd8_0
- perl-devel-stacktrace=2.04=pl5321hdfd78af_1
- perl-digest-hmac=1.05=pl5321hdfd78af_0
- perl-digest-md5=2.58=pl5321hec16e2b_1
- perl-encode=3.19=pl5321hec16e2b_1
- perl-encode-locale=1.05=pl5321hdfd78af_7
- perl-exception-class=1.45=pl5321hdfd78af_0
- perl-exporter=5.72=pl5321hdfd78af_2
- perl-exporter-tiny=1.002002=pl5321hdfd78af_0
- perl-extutils-makemaker=7.70=pl5321hd8ed1ab_0
- perl-file-listing=6.16=pl5321hdfd78af_0
- perl-file-path=2.18=pl5321hd8ed1ab_0
- perl-file-slurper=0.014=pl5321hdfd78af_0
- perl-file-sort=1.01=pl5321hdfd78af_3
- perl-file-spec=3.48_01=pl5321hdfd78af_2
- perl-file-temp=0.2304=pl5321hd8ed1ab_0
- perl-getopt-long=2.58=pl5321hdfd78af_0
- perl-html-parser=3.81=pl5321h4ac6f70_1
- perl-html-tagset=3.24=pl5321hdfd78af_0
- perl-http-cookiejar-lwp=0.014=pl5321hdfd78af_0
- perl-http-cookies=6.11=pl5321hdfd78af_0
- perl-http-daemon=6.16=pl5321hdfd78af_0
- perl-http-date=6.06=pl5321hdfd78af_0
- perl-http-message=7.00=pl5321hdfd78af_0
- perl-http-negotiate=6.01=pl5321hdfd78af_4
- perl-inc-latest=0.500=pl5321ha770c72_0
- perl-io-compress=2.201=pl5321h503566f_5
- perl-io-html=1.004=pl5321hdfd78af_0
- perl-io-socket-ssl=2.074=pl5321hdfd78af_0
- perl-io-string=1.08=pl5321hdfd78af_4
- perl-io-tty=1.16=pl5321hec16e2b_1
- perl-io-zlib=1.15=pl5321hdfd78af_1
- perl-ipc-run=20250809.0=pl5321hdfd78af_0
- perl-json=4.10=pl5321hdfd78af_1
- perl-json-xs=4.04=pl5321h9948957_0
- perl-libwww-perl=6.80=pl5321hdfd78af_0
- perl-libxml-perl=0.08=pl5321hdfd78af_3
- perl-list-moreutils=0.430=pl5321hdfd78af_0
- perl-list-moreutils-xs=0.430=pl5321h7b50bb2_5
- perl-lwp-mediatypes=6.04=pl5321hdfd78af_1
- perl-lwp-protocol-https=6.14=pl5321hdfd78af_1
- perl-mime-base64=3.16=pl5321hec16e2b_2
- perl-module-build=0.4234=pl5321ha770c72_1
- perl-module-load=0.34=pl5321hdfd78af_0
- perl-mozilla-ca=20250602=pl5321hdfd78af_0
- perl-net-http=6.24=pl5321hdfd78af_0
- perl-net-ssleay=1.92=pl5321h0e0aaa8_1
- perl-ntlm=1.09=pl5321hdfd78af_5
- perl-parent=0.236=pl5321hdfd78af_2
- perl-pathtools=3.75=pl5321hec16e2b_3
- perl-scalar-list-utils=1.62=pl5321hec16e2b_1
- perl-socket=2.027=pl5321h5c03b87_6
- perl-sub-uplevel=0.2800=pl5321hec16e2b_4
- perl-test-deep=1.130=pl5321hdfd78af_0
- perl-test-differences=0.69=pl5321hdfd78af_0
- perl-test-exception=0.43=pl5321hdfd78af_3
- perl-test-most=0.38=pl5321hdfd78af_0
- perl-test-needs=0.002009=pl5321hdfd78af_0
- perl-test-requiresinternet=0.05=pl5321hdfd78af_1
- perl-test-warn=0.36=pl5321hdfd78af_2
- perl-text-diff=1.45=pl5321hdfd78af_1
- perl-time-local=1.35=pl5321hdfd78af_0
- perl-timedate=2.33=pl5321hdfd78af_2
- perl-tree-dag_node=1.35=pl5321hdfd78af_0
- perl-try-tiny=0.31=pl5321hdfd78af_1
- perl-types-serialiser=1.01=pl5321hdfd78af_0
- perl-uri=5.12=pl5321hdfd78af_0
- perl-url-encode=0.03=pl5321h9ee0642_1
- perl-www-robotrules=6.02=pl5321hdfd78af_4
- perl-xml-dom=1.46=pl5321hdfd78af_1
- perl-xml-dom-xpath=0.14=pl5321hdfd78af_2
- perl-xml-namespacesupport=1.12=pl5321hdfd78af_1
- perl-xml-parser=2.44_01=pl5321hf2e2c51_1004
- perl-xml-regexp=0.04=pl5321hdfd78af_3
- perl-xml-sax=1.02=pl5321hdfd78af_1
- perl-xml-sax-base=1.09=pl5321hdfd78af_1
- perl-xml-sax-expat=0.51=pl5321hdfd78af_4
- perl-xml-simple=2.25=pl5321hdfd78af_2
- perl-xml-xpathengine=0.14=pl5321hdfd78af_3
- phylip=3.697=h7b50bb2_3
- pillow=10.3.0=py311h18e6fac_0
- pip=25.2=pyh8b19718_0
- pixman=0.46.4=h54a6638_1
- plotly=6.3.0=pyhd8ed1ab_0
- poa=2.0=h7b50bb2_6
- prank=170427=h9948957_1
- probcons=1.12=h8b12597_1
- probconsrna=1.10=h9f5acd7_4
- proda=1.0=h503566f_7
- prodigal=2.6.3=h7b50bb2_10
- prokka=1.14.6=pl5321hdfd78af_5
- psutil=7.1.3=py311haee01d2_0
- pthread-stubs=0.4=hb9d3cd8_1002
- pycparser=2.22=pyh29332c3_1
- pyfaidx=0.9.0.3=pyhdfd78af_0
- pymongo=4.14.1=py311h1ddb823_0
- 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
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