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environment.yml
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environment.yml
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name: LongReadQC.v1.1
channels:
- bioconda
- conda-forge
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- _r-mutex=1.0.1=anacondar_1
- aiohttp=3.9.3=py312h98912ed_1
- aiosignal=1.3.1=pyhd8ed1ab_0
- amply=0.1.6=pyhd8ed1ab_0
- appdirs=1.4.4=pyh9f0ad1d_0
- argparse-dataclass=2.0.0=pyhd8ed1ab_0
- attmap=0.13.2=pyhd8ed1ab_0
- attrs=23.2.0=pyh71513ae_0
- binutils_impl_linux-64=2.40=hf600244_0
- bioconductor-biobase=2.62.0=r43ha9d7317_1
- bioconductor-biocgenerics=0.48.1=r43hdfd78af_2
- bioconductor-biocparallel=1.36.0=r43hf17093f_1
- bioconductor-limma=3.58.1=r43ha9d7317_0
- bioconductor-variancepartition=1.32.2=r43hdfd78af_0
- boto=2.49.0=py_0
- boto3=1.34.66=pyhd8ed1ab_0
- botocore=1.34.66=pyge310_1234567_0
- brotli-python=1.1.0=py312h30efb56_1
- bwidget=1.9.14=ha770c72_1
- bz2file=0.98=py_0
- bzip2=1.0.8=hd590300_5
- c-ares=1.27.0=hd590300_0
- ca-certificates=2024.2.2=hbcca054_0
- cachetools=5.3.3=pyhd8ed1ab_0
- cairo=1.18.0=h3faef2a_0
- certifi=2024.2.2=pyhd8ed1ab_0
- cffi=1.16.0=py312hf06ca03_0
- charset-normalizer=3.3.2=pyhd8ed1ab_0
- coin-or-cbc=2.10.10=h9002f0b_0
- coin-or-cgl=0.60.7=h516709c_0
- coin-or-clp=1.17.8=h1ee7a9c_0
- coin-or-osi=0.108.8=ha2443b9_0
- coin-or-utils=2.11.9=hee58242_0
- coincbc=2.10.10=0_metapackage
- colorama=0.4.6=pyhd8ed1ab_0
- conda-inject=1.3.1=pyhd8ed1ab_0
- configargparse=1.7=pyhd8ed1ab_0
- connection_pool=0.0.3=pyhd3deb0d_0
- cryptography=42.0.5=py312h241aef2_0
- curl=8.6.0=hca28451_0
- datrie=0.8.2=py312h98912ed_7
- docutils=0.20.1=py312h7900ff3_3
- dpath=2.1.6=pyha770c72_0
- eido=0.2.2=pyhd8ed1ab_0
- exceptiongroup=1.2.0=pyhd8ed1ab_2
- expat=2.6.2=h59595ed_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_1
- fontconfig=2.14.2=h14ed4e7_0
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- freetype=2.12.1=h267a509_2
- fribidi=1.0.10=h36c2ea0_0
- frozenlist=1.4.1=py312h98912ed_0
- gcc_impl_linux-64=13.2.0=h338b0a0_5
- gettext=0.21.1=h27087fc_0
- gfortran_impl_linux-64=13.2.0=h76e1118_5
- gitdb=4.0.11=pyhd8ed1ab_0
- gitpython=3.1.42=pyhd8ed1ab_0
- google-api-core=2.17.1=pyhd8ed1ab_0
- google-auth=2.28.2=pyhca7485f_0
- google-cloud-core=2.4.1=pyhd8ed1ab_0
- google-cloud-storage=2.16.0=pyhca7485f_0
- google-crc32c=1.1.2=py312h775cd15_5
- google-resumable-media=2.7.0=pyhd8ed1ab_0
- googleapis-common-protos=1.63.0=pyhd8ed1ab_0
- graphite2=1.3.13=h59595ed_1003
- grpcio=1.62.1=py312hb06c811_0
- gxx_impl_linux-64=13.2.0=h338b0a0_5
- harfbuzz=8.3.0=h3d44ed6_0
- htslib=1.19.1=h81da01d_2
- humanfriendly=10.0=pyhd8ed1ab_6
- icu=73.2=h59595ed_0
- idna=3.6=pyhd8ed1ab_0
- immutables=0.20=py312h98912ed_1
- importlib_resources=6.3.2=pyhd8ed1ab_0
- iniconfig=2.0.0=pyhd8ed1ab_0
- jinja2=3.1.3=pyhd8ed1ab_0
- jmespath=1.0.1=pyhd8ed1ab_0
- joblib=1.3.2=pyhd8ed1ab_0
- jsonschema=4.21.1=pyhd8ed1ab_0
- jsonschema-specifications=2023.12.1=pyhd8ed1ab_0
- jupyter_core=5.7.2=py312h7900ff3_0
- kernel-headers_linux-64=2.6.32=he073ed8_17
- keyutils=1.6.1=h166bdaf_0
- krb5=1.21.2=h659d440_0
- ld_impl_linux-64=2.40=h41732ed_0
- lerc=4.0.0=h27087fc_0
- libabseil=20240116.1=cxx17_h59595ed_2
- libblas=3.9.0=21_linux64_openblas
- libcblas=3.9.0=21_linux64_openblas
- libcrc32c=1.1.2=h9c3ff4c_0
- libcurl=8.6.0=hca28451_0
- libdeflate=1.18=h0b41bf4_0
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=hd590300_2
- libexpat=2.6.2=h59595ed_0
- libffi=3.4.2=h7f98852_5
- libgcc-devel_linux-64=13.2.0=ha9c7c90_105
- libgcc-ng=13.2.0=h807b86a_5
- libgfortran-ng=13.2.0=h69a702a_5
- libgfortran5=13.2.0=ha4646dd_5
- libglib=2.78.1=hebfc3b9_0
- libgomp=13.2.0=h807b86a_5
- libgrpc=1.62.1=h15f2491_0
- libiconv=1.17=hd590300_2
- libjpeg-turbo=2.1.5.1=hd590300_1
- liblapack=3.9.0=21_linux64_openblas
- liblapacke=3.9.0=21_linux64_openblas
- libnghttp2=1.58.0=h47da74e_1
- libnsl=2.0.1=hd590300_0
- libopenblas=0.3.26=pthreads_h413a1c8_0
- libpng=1.6.43=h2797004_0
- libprotobuf=4.25.3=h08a7969_0
- libre2-11=2023.09.01=h5a48ba9_2
- libsanitizer=13.2.0=h7e041cc_5
- libsqlite=3.45.2=h2797004_0
- libssh2=1.11.0=h0841786_0
- libstdcxx-devel_linux-64=13.2.0=ha9c7c90_105
- libstdcxx-ng=13.2.0=h7e041cc_5
- libtiff=4.6.0=h8b53f26_0
- libuuid=2.38.1=h0b41bf4_0
- libwebp-base=1.3.2=hd590300_0
- libxcb=1.15=h0b41bf4_0
- libxcrypt=4.4.36=hd590300_1
- libxml2=2.12.6=h232c23b_1
- libzlib=1.2.13=hd590300_5
- logmuse=0.2.6=pyh8c360ce_0
- make=4.3=hd18ef5c_1
- markdown-it-py=3.0.0=pyhd8ed1ab_0
- markupsafe=2.1.5=py312h98912ed_0
- mdurl=0.1.2=pyhd8ed1ab_0
- multidict=6.0.5=py312h98912ed_0
- nbformat=5.10.3=pyhd8ed1ab_0
- ncurses=6.4.20240210=h59595ed_0
- nlopt=2.7.1=py312hc70d0cb_4
- numpy=1.26.4=py312heda63a1_0
- openssl=3.2.1=hd590300_1
- packaging=24.0=pyhd8ed1ab_0
- pandas=2.2.1=py312hfb8ada1_0
- pango=1.50.14=ha41ecd1_2
- pcre2=10.40=hc3806b6_0
- peppy=0.40.1=pyhd8ed1ab_0
- pip=24.0=pyhd8ed1ab_0
- pixman=0.43.2=h59595ed_0
- pkgutil-resolve-name=1.3.10=pyhd8ed1ab_1
- plac=1.4.3=pyhd8ed1ab_0
- platformdirs=4.2.0=pyhd8ed1ab_0
- pluggy=1.4.0=pyhd8ed1ab_0
- protobuf=4.25.3=py312h72fbbdf_0
- psutil=5.9.8=py312h98912ed_0
- pthread-stubs=0.4=h36c2ea0_1001
- pulp=2.8.0=py312h7900ff3_0
- pyasn1=0.5.1=pyhd8ed1ab_0
- pyasn1-modules=0.3.0=pyhd8ed1ab_0
- pycparser=2.21=pyhd8ed1ab_0
- pygments=2.17.2=pyhd8ed1ab_0
- pyopenssl=24.0.0=pyhd8ed1ab_0
- pyparsing=3.1.2=pyhd8ed1ab_0
- pysocks=1.7.1=pyha2e5f31_6
- pytest=8.1.1=pyhd8ed1ab_0
- python=3.12.2=hab00c5b_0_cpython
- python-dateutil=2.9.0=pyhd8ed1ab_0
- python-fastjsonschema=2.19.1=pyhd8ed1ab_0
- python-tzdata=2024.1=pyhd8ed1ab_0
- python_abi=3.12=4_cp312
- pytz=2024.1=pyhd8ed1ab_0
- pyu2f=0.1.5=pyhd8ed1ab_0
- pyyaml=6.0.1=py312h98912ed_1
- r=4.3=r43hd8ed1ab_1007
- r-aod=1.3.3=r43ha770c72_0
- r-backports=1.4.1=r43h57805ef_2
- r-base=4.3.1=h639d9d3_5
- r-bh=1.84.0_0=r43hc72bb7e_0
- r-bitops=1.0_7=r43h57805ef_2
- r-boot=1.3_30=r43hc72bb7e_0
- r-broom=1.0.5=r43hc72bb7e_1
- r-catools=1.18.2=r43ha503ecb_2
- r-class=7.3_22=r43h57805ef_1
- r-cli=3.6.2=r43ha503ecb_0
- r-cluster=2.1.6=r43h61816a4_0
- r-codetools=0.2_20=r43hc72bb7e_0
- r-colorspace=2.1_0=r43h57805ef_1
- r-corpcor=1.6.10=r43hc72bb7e_2
- r-cpp11=0.4.7=r43hc72bb7e_0
- r-crayon=1.5.2=r43hc72bb7e_2
- r-dplyr=1.1.4=r43ha503ecb_0
- r-ellipsis=0.3.2=r43h57805ef_2
- r-envstats=2.8.1=r43ha770c72_0
- r-evaluate=0.23=r43hc72bb7e_0
- r-fancova=0.6_1=r43hc72bb7e_1
- r-fansi=1.0.6=r43h57805ef_0
- r-farver=2.1.1=r43ha503ecb_2
- r-foreign=0.8_86=r43h57805ef_0
- r-formatr=1.14=r43hc72bb7e_1
- r-futile.logger=1.4.3=r43hc72bb7e_1005
- r-futile.options=1.0.1=r43hc72bb7e_1004
- r-gbrd=0.4_11=r43hc72bb7e_1005
- r-generics=0.1.3=r43hc72bb7e_2
- r-ggplot2=3.5.0=r43hc72bb7e_0
- r-glue=1.7.0=r43h57805ef_0
- r-gplots=3.1.3.1=r43hc72bb7e_0
- r-gtable=0.3.4=r43hc72bb7e_0
- r-gtools=3.9.5=r43h57805ef_0
- r-highr=0.10=r43hc72bb7e_1
- r-isoband=0.2.7=r43ha503ecb_2
- r-iterators=1.0.14=r43hc72bb7e_2
- r-kernsmooth=2.23_22=r43h13b3f57_0
- r-knitr=1.45=r43hc72bb7e_1
- r-labeling=0.4.3=r43hc72bb7e_0
- r-lambda.r=1.2.4=r43hc72bb7e_3
- r-lattice=0.22_6=r43h57805ef_0
- r-lifecycle=1.0.4=r43hc72bb7e_0
- r-lme4=1.1_35.2=r43ha503ecb_0
- r-lmertest=3.1_3=r43hc72bb7e_2
- r-magrittr=2.0.3=r43h57805ef_2
- r-mass=7.3_60=r43h57805ef_1
- r-matrix=1.6_5=r43h316c678_0
- r-matrixstats=1.2.0=r43h57805ef_0
- r-mgcv=1.9_1=r43h316c678_0
- r-minqa=1.2.6=r43hcf54a89_0
- r-munsell=0.5.0=r43hc72bb7e_1006
- r-mvtnorm=1.2_4=r43hd9ac46e_0
- r-nlme=3.1_164=r43h61816a4_0
- r-nloptr=2.0.3=r43hcf54a89_2
- r-nnet=7.3_19=r43h57805ef_1
- r-nortest=1.0_4=r43hc72bb7e_1005
- r-numderiv=2016.8_1.1=r43hc72bb7e_5
- r-pbkrtest=0.5.2=r43hc72bb7e_1
- r-pillar=1.9.0=r43hc72bb7e_1
- r-pkgconfig=2.0.3=r43hc72bb7e_3
- r-plyr=1.8.9=r43ha503ecb_0
- r-purrr=1.0.2=r43h57805ef_0
- r-r6=2.5.1=r43hc72bb7e_2
- r-rbibutils=2.2.16=r43h57805ef_0
- r-rcolorbrewer=1.1_3=r43h785f33e_2
- r-rcpp=1.0.12=r43h7df8631_0
- r-rcpparmadillo=0.12.8.1.0=r43h08d816e_0
- r-rcppeigen=0.3.4.0.0=r43h08d816e_0
- r-rdpack=2.6=r43hc72bb7e_0
- r-recommended=4.3=r43hd8ed1ab_1006
- r-remacor=0.0.18=r43h08d816e_0
- r-reshape2=1.4.4=r43ha503ecb_3
- r-rhpcblasctl=0.23_42=r43h57805ef_1
- r-rlang=1.1.3=r43ha503ecb_0
- r-rpart=4.1.23=r43h57805ef_0
- r-scales=1.3.0=r43hc72bb7e_0
- r-snow=0.4_4=r43hc72bb7e_2
- r-spatial=7.3_17=r43h57805ef_0
- r-statmod=1.5.0=r43hd8f1df9_1
- r-stringi=1.8.3=r43h9facbd6_0
- r-stringr=1.5.1=r43h785f33e_0
- r-survival=3.5_8=r43h57805ef_0
- r-tibble=3.2.1=r43h57805ef_2
- r-tidyr=1.3.1=r43ha503ecb_0
- r-tidyselect=1.2.0=r43hc72bb7e_1
- r-utf8=1.2.4=r43h57805ef_0
- r-vctrs=0.6.5=r43ha503ecb_0
- r-viridislite=0.4.2=r43hc72bb7e_1
- r-withr=3.0.0=r43hc72bb7e_0
- r-xfun=0.43=r43ha503ecb_0
- r-xml2=1.3.6=r43hbfba7a4_1
- r-yaml=2.3.8=r43h57805ef_0
- re2=2023.09.01=h7f4b329_2
- readline=8.2=h8228510_1
- referencing=0.34.0=pyhd8ed1ab_0
- requests=2.31.0=pyhd8ed1ab_0
- reretry=0.11.8=pyhd8ed1ab_0
- rich=13.7.1=pyhd8ed1ab_0
- rpds-py=0.18.0=py312h4b3b743_0
- rsa=4.9=pyhd8ed1ab_0
- s3transfer=0.10.1=pyhd8ed1ab_0
- samtools=1.19.2=h50ea8bc_1
- scikit-learn=1.4.1.post1=py312h394d371_0
- scipy=1.12.0=py312heda63a1_2
- sed=4.8=he412f7d_0
- setuptools=69.2.0=pyhd8ed1ab_0
- six=1.16.0=pyh6c4a22f_0
- slack-sdk=3.27.1=pyha770c72_0
- slack_sdk=3.27.1=hd8ed1ab_0
- smart_open=3.0.0=pyh9f0ad1d_0
- smmap=5.0.0=pyhd8ed1ab_0
- snakemake=8.9.0=hdfd78af_0
- snakemake-interface-common=1.17.1=pyhdfd78af_0
- snakemake-interface-executor-plugins=9.0.0=pyhdfd78af_0
- snakemake-interface-report-plugins=1.0.0=pyhdfd78af_0
- snakemake-interface-storage-plugins=3.1.1=pyhdfd78af_0
- snakemake-minimal=8.9.0=pyhdfd78af_0
- stopit=1.1.2=py_0
- sysroot_linux-64=2.12=he073ed8_17
- tabulate=0.9.0=pyhd8ed1ab_1
- threadpoolctl=3.4.0=pyhc1e730c_0
- throttler=1.2.2=pyhd8ed1ab_0
- tk=8.6.13=noxft_h4845f30_101
- tktable=2.10=h0c5db8f_5
- tomli=2.0.1=pyhd8ed1ab_0
- toposort=1.10=pyhd8ed1ab_0
- traitlets=5.14.2=pyhd8ed1ab_0
- typing_extensions=4.10.0=pyha770c72_0
- tzdata=2024a=h0c530f3_0
- ubiquerg=0.7.0=pyhd8ed1ab_0
- urllib3=2.2.1=pyhd8ed1ab_0
- veracitools=0.1.3=py_0
- wheel=0.42.0=pyhd8ed1ab_0
- wrapt=1.16.0=py312h98912ed_0
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.1.1=hd590300_0
- xorg-libsm=1.2.4=h7391055_0
- xorg-libx11=1.8.7=h8ee46fc_0
- xorg-libxau=1.0.11=hd590300_0
- xorg-libxdmcp=1.1.3=h7f98852_0
- xorg-libxext=1.3.4=h0b41bf4_2
- xorg-libxrender=0.9.11=hd590300_0
- xorg-libxt=1.3.0=hd590300_1
- xorg-renderproto=0.11.1=h7f98852_1002
- xorg-xextproto=7.3.0=h0b41bf4_1003
- xorg-xproto=7.0.31=h7f98852_1007
- xz=5.2.6=h166bdaf_0
- yaml=0.2.5=h7f98852_2
- yarl=1.9.4=py312h98912ed_0
- yte=1.5.4=pyha770c72_0
- zipp=3.17.0=pyhd8ed1ab_0
- zlib=1.2.13=hd590300_5
- zstd=1.5.5=hfc55251_0
- pip:
- contourpy==1.2.0
- cycler==0.12.1
- fonttools==4.50.0
- kiwisolver==1.4.5
- matplotlib==3.8.3
- pillow==10.2.0
- seaborn==0.13.2
prefix: /home/isaid42/mambaforge/envs/LongReadQC.v1.1