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environment.yml
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name: SegFinder
channels:
- conda-forge/label/cf201901
- bioconda/label/cf201901
- conda-forge
- bioconda
- defaults
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/msys2/
- ursky
- r
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/Paddle/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/fastai/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/pytorch/
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_kmp_llvm
- _r-mutex=1.0.1=anacondar_1
- alsa-lib=1.2.3.2=h166bdaf_0
- bedtools=2.30.0=h468198e_3
- binutils_impl_linux-64=2.36.1=h193b22a_2
- binutils_linux-64=2.36=hf3e587d_10
- blas=2.116=openblas
- blas-devel=3.9.0=16_linux64_openblas
- blast=2.13.0=hf3cf87c_0
- bowtie2=2.2.5=py39h7cff6ad_8
- bwidget=1.9.14=ha770c72_1
- bzip2=1.0.8=h7f98852_4
- c-ares=1.18.1=h7f98852_0
- ca-certificates=2024.2.2=hbcca054_0
- cairo=1.16.0=h18b612c_1001
- cd-hit=4.8.1=h5b5514e_7
- cffi=1.15.1=py39he91dace_3
- checkv=1.0.1=pyhdfd78af_0
- collectl=4.0.4=1
- colorama=0.4.6=pyhd8ed1ab_0
- coloredlogs=15.0.1=pyhd8ed1ab_3
- curl=7.87.0=h5eee18b_0
- diamond=0.9.19=hd28b015_2
- entrez-direct=16.2=he881be0_1
- expat=2.5.0=hcb278e6_1
- fasta-splitter=0.2.6=hdfd78af_1
- fastool=0.1.4=he4a0461_8
- fastp=0.22.0=h2e03b76_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=hab24e00_0
- fontconfig=2.14.2=h14ed4e7_0
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- freetype=2.12.1=hca18f0e_1
- fribidi=1.0.10=h36c2ea0_0
- future=0.18.3=pyhd8ed1ab_0
- gcc_impl_linux-64=11.2.0=h82a94d6_16
- gcc_linux-64=11.2.0=h39a9532_10
- gettext=0.21.1=h27087fc_0
- gfortran_impl_linux-64=11.2.0=h7a446d4_16
- gfortran_linux-64=11.2.0=h777b47f_10
- giflib=5.2.1=h0b41bf4_3
- glib=2.74.1=h6239696_0
- glib-tools=2.74.1=h6239696_0
- glpk=5.0=h445213a_0
- gmp=6.2.1=h58526e2_0
- gmpy2=2.1.2=py39h376b7d2_1
- graphite2=1.3.14=h295c915_1
- gsl=2.7=he838d99_0
- gxx_impl_linux-64=11.2.0=h82a94d6_16
- gxx_linux-64=11.2.0=hacbe6df_10
- harfbuzz=4.3.0=hf52aaf7_1
- hmmer=3.3.2=h87f3376_2
- htslib=1.17=h6bc39ce_1
- humanfriendly=10.0=py39hf3d152e_4
- icu=58.2=hf484d3e_1000
- importlib-metadata=6.1.0=pyha770c72_0
- iqtree=2.2.3=h21ec9f0_0
- java-jdk=7.0.91=1
- jellyfish=2.2.10=h6bb024c_1
- jemalloc=5.3.0=hcb278e6_0
- jpeg=9e=h0b41bf4_3
- kcounter=0.1.1=py39hbf8eff0_1
- kernel-headers_linux-64=2.6.32=he073ed8_15
- keyutils=1.6.1=h166bdaf_0
- kmer-jellyfish=2.3.0=h9f5acd7_3
- krb5=1.19.3=h3790be6_0
- ld_impl_linux-64=2.36.1=hea4e1c9_2
- lerc=4.0.0=h27087fc_0
- libblas=3.9.0=16_linux64_openblas
- libboost=1.73.0=h28710b8_12
- libcblas=3.9.0=16_linux64_openblas
- libcurl=7.87.0=h91b91d3_0
- libdeflate=1.14=h166bdaf_0
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=h516909a_1
- libexpat=2.5.0=hcb278e6_1
- libffi=3.4.2=h7f98852_5
- libgcc=7.2.0=h69d50b8_2
- libgcc-devel_linux-64=11.2.0=h0952999_16
- libgcc-ng=12.2.0=h65d4601_19
- libgfortran-ng=12.2.0=h69a702a_19
- libgfortran5=12.2.0=h337968e_19
- libglib=2.74.1=h7a41b64_0
- libgomp=12.2.0=h65d4601_19
- libiconv=1.17=h166bdaf_0
- libidn2=2.3.4=h166bdaf_0
- libjemalloc=5.3.0=hcb278e6_0
- liblapack=3.9.0=16_linux64_openblas
- liblapacke=3.9.0=16_linux64_openblas
- libnghttp2=1.46.0=hce63b2e_0
- libnsl=2.0.0=h7f98852_0
- libopenblas=0.3.21=pthreads_h78a6416_3
- libpng=1.6.39=h753d276_0
- libprotobuf=3.20.3=h3eb15da_0
- libsanitizer=11.2.0=he4da1e4_16
- libsqlite=3.40.0=h753d276_0
- libssh2=1.10.0=haa6b8db_3
- libstdcxx-devel_linux-64=11.2.0=h0952999_16
- libstdcxx-ng=12.2.0=h46fd767_19
- libtiff=4.4.0=h82bc61c_5
- libunistring=0.9.10=h7f98852_0
- libuuid=2.38.1=h0b41bf4_0
- libwebp-base=1.3.0=h0b41bf4_0
- libxcb=1.13=h7f98852_1004
- libxml2=2.9.14=h74e7548_0
- libzlib=1.2.13=h166bdaf_4
- llvm-openmp=16.0.0=h417c0b6_0
- mafft=7.520=h031d066_2
- make=4.3=hd18ef5c_1
- megahit=1.2.9=h2e03b76_1
- mpc=1.3.1=hfe3b2da_0
- mpfr=4.2.0=hb012696_0
- mpmath=1.3.0=pyhd8ed1ab_0
- muscle=5.1=h9f5acd7_1
- ncbi-vdb=3.0.10=hdbdd923_0
- ncurses=6.3=h27087fc_1
- ninja=1.11.1=h924138e_0
- numpy=1.24.2=py39h7360e5f_0
- onnxruntime=1.14.1=py39hd32e49d_0
- openblas=0.3.21=pthreads_h320a7e8_3
- openjdk=11.0.1=h516909a_1016
- openssl=1.1.1w=hd590300_0
- ossuuid=1.6.2=hf484d3e_1000
- packaging=23.1=pyhd8ed1ab_0
- pandas=2.0.0=py39h2ad29b5_0
- pandoc=2.5=0
- pango=1.50.7=h05da053_0
- parafly=r2013_01_21=0
- pcre=8.45=h9c3ff4c_0
- pcre2=10.37=hc3806b6_1
- perl=5.32.1=2_h7f98852_perl5
- perl-alien-build=2.48=pl5321hec16e2b_0
- perl-alien-libxml2=0.17=pl5321hec16e2b_0
- perl-archive-tar=2.40=pl5321hdfd78af_0
- perl-business-isbn=3.007=pl5321hd8ed1ab_0
- perl-business-isbn-data=20210112.006=pl5321hd8ed1ab_0
- perl-capture-tiny=0.48=pl5321ha770c72_1
- perl-carp=1.50=pl5321hd8ed1ab_0
- perl-common-sense=3.75=pl5321hd8ed1ab_0
- perl-compress-raw-bzip2=2.201=pl5321h166bdaf_0
- perl-compress-raw-zlib=2.202=pl5321h166bdaf_0
- perl-constant=1.33=pl5321hd8ed1ab_0
- perl-data-dumper=2.183=pl5321h166bdaf_0
- perl-encode=3.19=pl5321h166bdaf_0
- perl-exporter=5.74=pl5321hd8ed1ab_0
- perl-exporter-tiny=1.002002=pl5321hd8ed1ab_0
- perl-extutils-makemaker=7.70=pl5321hd8ed1ab_0
- perl-ffi-checklib=0.28=pl5321hdfd78af_0
- perl-file-chdir=0.1011=pl5321hd8ed1ab_0
- perl-file-path=2.18=pl5321hd8ed1ab_0
- perl-file-temp=0.2304=pl5321hd8ed1ab_0
- perl-file-util=4.201720=pl5321hdfd78af_0
- perl-file-which=1.24=pl5321hd8ed1ab_0
- perl-importer=0.026=pl5321hd8ed1ab_0
- perl-io-compress=2.201=pl5321h87f3376_0
- perl-io-zlib=1.14=pl5321hdfd78af_0
- perl-json=4.10=pl5321hdfd78af_0
- perl-json-xs=2.34=pl5321h9f5acd7_5
- perl-lib=0.63=pl5321hdfd78af_2
- perl-list-moreutils=0.430=pl5321hdfd78af_0
- perl-list-moreutils-xs=0.430=pl5321hec16e2b_1
- perl-mime-base64=3.16=pl5321h166bdaf_0
- perl-parent=0.241=pl5321hd8ed1ab_0
- perl-path-tiny=0.124=pl5321hd8ed1ab_0
- perl-pathtools=3.75=pl5321h166bdaf_0
- perl-scalar-list-utils=1.63=pl5321h166bdaf_0
- perl-scope-guard=0.21=pl5321hd8ed1ab_0
- perl-storable=3.15=pl5321h166bdaf_0
- perl-sub-info=0.002=pl5321hd8ed1ab_0
- perl-term-table=0.016=pl5321hdfd78af_0
- perl-test2-suite=0.000145=pl5321hdfd78af_0
- perl-threaded=5.32.1=hdfd78af_1
- perl-types-serialiser=1.01=pl5321hdfd78af_0
- perl-uri=5.12=pl5321hdfd78af_0
- perl-xml-libxml=2.0207=pl5321h661654b_0
- perl-xml-namespacesupport=1.12=pl5321hd8ed1ab_0
- perl-xml-sax=1.02=pl5321hd8ed1ab_0
- perl-xml-sax-base=1.09=pl5321hd8ed1ab_0
- pigz=2.6=h27826a3_0
- pip=23.0.1=pyhd8ed1ab_0
- pixman=0.38.0=h516909a_1003
- prodigal=2.6.3=hec16e2b_4
- prodigal-gv=2.11.0=h7132678_0
- protobuf=3.20.3=py39h227be39_1
- psutil=5.9.4=py39hb9d737c_0
- pthread-stubs=0.4=h36c2ea0_1001
- pycparser=2.21=pyhd8ed1ab_0
- python=3.9.16=h7a1cb2a_0
- python-dateutil=2.8.2=pyhd8ed1ab_0
- python-flatbuffers=23.1.21=pyhd8ed1ab_0
- python-tzdata=2023.3=pyhd8ed1ab_0
- python_abi=3.9=2_cp39
- pytorch=1.12.1=cpu_py39h9dbd814_1
- pytz=2023.3=pyhd8ed1ab_0
- pyyaml=6.0=py39hb9d737c_5
- r=4.2=r42hd8ed1ab_1006
- r-askpass=1.1=r42h06615bd_3
- r-backports=1.4.1=r42h06615bd_1
- r-base=4.2.0=h1ae530e_0
- r-base64enc=0.1_3=r42h06615bd_1005
- r-bit=4.0.5=r42h06615bd_0
- r-bit64=4.0.5=r42h06615bd_1
- r-blob=1.2.4=r42hc72bb7e_0
- r-boot=1.3_28.1=r42hc72bb7e_0
- r-broom=1.0.4=r42hc72bb7e_0
- r-bslib=0.4.2=r42hc72bb7e_0
- r-cachem=1.0.7=r42h133d619_0
- r-callr=3.7.3=r42hc72bb7e_0
- r-cellranger=1.1.0=r42hc72bb7e_1005
- r-class=7.3_21=r42h133d619_0
- r-cli=3.6.1=r42h38f115c_0
- r-clipr=0.8.0=r42hc72bb7e_1
- r-cluster=2.1.4=r42h8da6f51_0
- r-codetools=0.2_19=r42hc72bb7e_0
- r-colorspace=2.1_0=r42h133d619_0
- r-cpp11=0.4.3=r42hc72bb7e_0
- r-crayon=1.5.2=r42hc72bb7e_1
- r-curl=4.3.3=r42h06615bd_1
- r-data.table=1.14.8=r42h133d619_0
- r-dbi=1.1.3=r42hc72bb7e_1
- r-dbplyr=2.3.2=r42hc72bb7e_0
- r-digest=0.6.31=r42h38f115c_0
- r-dplyr=1.1.1=r42h38f115c_0
- r-dtplyr=1.3.1=r42hc72bb7e_0
- r-ellipsis=0.3.2=r42h06615bd_1
- r-evaluate=0.20=r42hc72bb7e_0
- r-fansi=1.0.4=r42h133d619_0
- r-farver=2.1.1=r42h7525677_1
- r-fastmap=1.1.1=r42h38f115c_0
- r-fontawesome=0.5.0=r42hc72bb7e_0
- r-forcats=1.0.0=r42hc72bb7e_0
- r-foreign=0.8_84=r42h133d619_0
- r-fs=1.6.1=r42h38f115c_0
- r-gargle=1.3.0=r42h785f33e_0
- r-generics=0.1.3=r42hc72bb7e_1
- r-getopt=1.20.3=r42ha770c72_3
- r-ggplot2=3.4.0=r42hc72bb7e_1
- r-ggthemes=4.2.4=r42hc72bb7e_1
- r-glue=1.6.2=r42h06615bd_1
- r-googledrive=2.1.0=r42hc72bb7e_0
- r-googlesheets4=1.1.0=r42h785f33e_0
- r-gtable=0.3.3=r42hc72bb7e_0
- r-haven=2.5.2=r42h38f115c_0
- r-highr=0.10=r42hc72bb7e_0
- r-hms=1.1.3=r42hc72bb7e_0
- r-htmltools=0.5.5=r42h38f115c_0
- r-httr=1.4.5=r42hc72bb7e_0
- r-ids=1.0.1=r42hc72bb7e_2
- r-igraph=1.3.5=r42hb34fc8a_0
- r-isoband=0.2.7=r42h38f115c_1
- r-jquerylib=0.1.4=r42hc72bb7e_1
- r-jsonlite=1.8.4=r42h133d619_0
- r-kernsmooth=2.23_20=r42hd009a43_1
- r-knitr=1.42=r42hc72bb7e_1
- r-labeling=0.4.2=r42hc72bb7e_2
- r-lattice=0.20_45=r42h06615bd_1
- r-lifecycle=1.0.3=r42hc72bb7e_1
- r-lubridate=1.9.2=r42h133d619_1
- r-magrittr=2.0.3=r42h06615bd_1
- r-mass=7.3_58.3=r42h133d619_0
- r-matrix=1.5_3=r42h5f7b363_0
- r-memoise=2.0.1=r42hc72bb7e_1
- r-mgcv=1.8_42=r42he1ae0d6_0
- r-mime=0.12=r42h06615bd_1
- r-mnormt=2.1.1=r42h8da6f51_0
- r-modelr=0.1.11=r42hc72bb7e_0
- r-munsell=0.5.0=r42hc72bb7e_1005
- r-nlme=3.1_162=r42hac0b197_0
- r-nnet=7.3_18=r42h06615bd_1
- r-openssl=2.0.2=r42h76d94ec_0
- r-openxlsx=4.2.5.1=r42h7525677_0
- r-patchwork=1.1.2=r42hc72bb7e_1
- r-pillar=1.9.0=r42hc72bb7e_0
- r-pkgconfig=2.0.3=r42hc72bb7e_2
- r-prettyunits=1.1.1=r42h142f84f_0
- r-processx=3.8.0=r42h06615bd_0
- r-progress=1.2.2=r42hc72bb7e_3
- r-ps=1.7.3=r42h133d619_0
- r-psych=2.2.9=r42hc72bb7e_1
- r-purrr=1.0.1=r42h133d619_0
- r-r6=2.5.1=r42hc72bb7e_1
- r-rappdirs=0.3.3=r42h06615bd_1
- r-rcolorbrewer=1.1_3=r42h785f33e_1
- r-rcpp=1.0.10=r42h38f115c_0
- r-readr=2.1.4=r42h38f115c_0
- r-readxl=1.4.2=r42h81ef4d7_0
- r-recommended=4.2=r42hd8ed1ab_1005
- r-rematch=1.0.1=r42hc72bb7e_1005
- r-rematch2=2.1.2=r42hc72bb7e_2
- r-reprex=2.0.2=r42hc72bb7e_1
- r-rlang=1.1.0=r42h38f115c_0
- r-rmarkdown=2.21=r42hc72bb7e_0
- r-rpart=4.1.19=r42h06615bd_0
- r-rstudioapi=0.14=r42hc72bb7e_1
- r-rvest=1.0.3=r42hc72bb7e_1
- r-sass=0.4.5=r42h38f115c_0
- r-scales=1.2.1=r42hc72bb7e_1
- r-selectr=0.4_2=r42hc72bb7e_2
- r-spatial=7.3_16=r42h133d619_0
- r-stringi=1.7.6=r42h884c59f_0
- r-stringr=1.5.0=r42h785f33e_0
- r-survival=3.5_5=r42h133d619_0
- r-sys=3.4.1=r42h06615bd_0
- r-tibble=3.2.1=r42h133d619_1
- r-tidyr=1.3.0=r42h38f115c_0
- r-tidyselect=1.2.0=r42hc72bb7e_0
- r-tidyverse=1.3.1=r42h6115d3f_0
- r-timechange=0.2.0=r42h38f115c_0
- r-tinytex=0.44=r42hc72bb7e_0
- r-tmvnsim=1.0_2=r42h8da6f51_4
- r-tzdb=0.3.0=r42h7525677_1
- r-utf8=1.2.3=r42h133d619_0
- r-uuid=1.1_0=r42h06615bd_1
- r-vctrs=0.6.1=r42h38f115c_0
- r-viridislite=0.4.1=r42hc72bb7e_1
- r-vroom=1.6.1=r42h38f115c_0
- r-withr=2.5.0=r42hc72bb7e_1
- r-xfun=0.38=r42h38f115c_0
- r-xml2=1.3.3=r42h044e5c7_2
- r-yaml=2.3.7=r42h133d619_0
- r-zip=2.2.2=r42h06615bd_0
- readline=8.2=h8228510_1
- rename=1.601=hdfd78af_1
- ribodetector=0.2.7=pyhdfd78af_0
- rsem=1.2.28=0
- salmon=0.13.1=h86b0361_0
- samtools=1.6=h3f2fef4_8
- sed=4.8=he412f7d_0
- seqkit=2.3.1=h9ee0642_0
- seqtk=1.3=h7132678_4
- setuptools=67.6.1=pyhd8ed1ab_0
- six=1.16.0=pyh6c4a22f_0
- slclust=02022010=1
- spades=3.13.0=0
- sqlite=3.40.1=h5082296_0
- sra-tools=3.0.10=h9f5acd7_0
- sympy=1.11.1=pyh04b8f61_3
- sysroot_linux-64=2.12=he073ed8_15
- taxonkit=0.14.2=h9ee0642_0
- tbb=2020.2=h4bd325d_4
- tk=8.6.12=h27826a3_0
- tktable=2.10=hb7b940f_3
- tqdm=4.65.0=pyhd8ed1ab_1
- trimal=1.4.1=h4ac6f70_8
- trimmomatic=0.39=hdfd78af_2
- trinity=2.1.1=6
- typing-extensions=4.5.0=hd8ed1ab_0
- typing_extensions=4.5.0=pyha770c72_0
- tzdata=2023c=h71feb2d_0
- unzip=6.0=h7f98852_3
- wget=1.20.3=ha56f1ee_1
- wheel=0.40.0=pyhd8ed1ab_0
- xorg-fixesproto=5.0=h7f98852_1002
- xorg-inputproto=2.3.2=h7f98852_1002
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.0.10=h7f98852_0
- xorg-libsm=1.2.3=hd9c2040_1000
- xorg-libx11=1.8.4=h0b41bf4_0
- xorg-libxau=1.0.9=h7f98852_0
- xorg-libxdmcp=1.1.3=h7f98852_0
- xorg-libxext=1.3.4=h0b41bf4_2
- xorg-libxfixes=5.0.3=h7f98852_1004
- xorg-libxi=1.7.10=h7f98852_0
- xorg-libxrender=0.9.10=h7f98852_1003
- xorg-libxt=1.3.0=hd590300_0
- xorg-libxtst=1.2.3=h7f98852_1002
- xorg-recordproto=1.14.2=h7f98852_1002
- xorg-renderproto=0.11.1=h7f98852_1002
- xorg-xextproto=7.3.0=h0b41bf4_1003
- xorg-xproto=7.0.31=h7f98852_1007
- xz=5.2.10=h5eee18b_1
- yaml=0.2.5=h7f98852_2
- zipp=3.15.0=pyhd8ed1ab_0
- zlib=1.2.13=h166bdaf_4
- zstd=1.5.2=h3eb15da_6
- pip:
- biopython==1.77
- nimporter==1.1.0
- regex==2022.10.31
- screed==1.1.1