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environment.yml
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environment.yml
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name: synth4bench
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- _r-mutex=1.0.1=anacondar_1
- _sysroot_linux-64_curr_repodata_hack=4=h5bd9786_17
- alsa-lib=1.2.12=h4ab18f5_0
- argcomplete=3.4.0=pyhd8ed1ab_0
- bc=1.07.1=h7f98852_0
- bcftools=1.17=h3cc50cf_1
- binutils_impl_linux-64=2.36.1=h193b22a_2
- binutils_linux-64=2.36=hf3e587d_10
- bioconductor-biobase=2.58.0=r42ha9d7317_1
- bioconductor-biocgenerics=0.44.0=r42hdfd78af_0
- bioconductor-biocparallel=1.32.5=r42hf17093f_1
- bioconductor-biostrings=2.66.0=r42ha9d7317_1
- bioconductor-data-packages=20231203=hdfd78af_0
- bioconductor-delayedarray=0.24.0=r42ha9d7317_1
- bioconductor-genomeinfodb=1.34.9=r42hdfd78af_0
- bioconductor-genomeinfodbdata=1.2.9=r42hdfd78af_0
- bioconductor-genomicalignments=1.34.0=r42ha9d7317_1
- bioconductor-genomicranges=1.50.0=r42ha9d7317_1
- bioconductor-iranges=2.32.0=r42ha9d7317_1
- bioconductor-matrixgenerics=1.10.0=r42hdfd78af_0
- bioconductor-rhtslib=2.0.0=r42ha9d7317_1
- bioconductor-rsamtools=2.14.0=r42hf17093f_1
- bioconductor-s4vectors=0.36.0=r42ha9d7317_1
- bioconductor-summarizedexperiment=1.28.0=r42hdfd78af_0
- bioconductor-xvector=0.38.0=r42ha9d7317_1
- bioconductor-zlibbioc=1.44.0=r42ha9d7317_2
- blas=1.1=openblas
- bwa=0.7.18=he4a0461_0
- bwidget=1.9.14=ha770c72_1
- bzip2=1.0.8=hd590300_5
- c-ares=1.32.0=h4ab18f5_0
- ca-certificates=2024.7.4=hbcca054_0
- cairo=1.16.0=h18b612c_1001
- curl=7.88.1=h37d81fd_2
- eigen=3.4.0=h00ab1b0_0
- exonerate=2.4.0=h09da616_5
- 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_2
- fontconfig=2.14.2=h14ed4e7_0
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- freebayes=1.3.6=hb0f3ef8_7
- freetype=2.12.1=h267a509_2
- fribidi=1.0.10=h36c2ea0_0
- gatk4=4.3.0.0=py36hdfd78af_0
- gcc_impl_linux-64=11.2.0=h82a94d6_16
- gcc_linux-64=11.2.0=h39a9532_10
- gettext=0.22.5=h59595ed_2
- gettext-tools=0.22.5=h59595ed_2
- gfortran_impl_linux-64=11.2.0=h7a446d4_16
- gfortran_linux-64=11.2.0=h777b47f_10
- giflib=5.2.2=hd590300_0
- glib=2.74.1=h6239696_0
- glib-tools=2.74.1=h6239696_0
- 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
- htslib=1.17=h6bc39ce_1
- icu=58.2=hf484d3e_1000
- jpeg=9e=h0b41bf4_3
- jq=1.7.1=hd590300_0
- jsoncpp=1.9.5=h4bd325d_1
- kernel-headers_linux-64=2.6.32=he073ed8_17
- keyutils=1.6.1=h166bdaf_0
- krb5=1.20.1=hf9c8cef_0
- lcms2=2.12=hddcbb42_0
- ld_impl_linux-64=2.36.1=hea4e1c9_2
- lerc=4.0.0=h27087fc_0
- libasprintf=0.22.5=h661eb56_2
- libasprintf-devel=0.22.5=h661eb56_2
- libblas=3.9.0=22_linux64_openblas
- libcblas=3.9.0=22_linux64_openblas
- libcups=2.3.3=h36d4200_3
- libcurl=7.88.1=h91b91d3_2
- libdeflate=1.20=hd590300_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=11.2.0=h0952999_16
- libgcc-ng=14.1.0=h77fa898_0
- libgettextpo=0.22.5=h59595ed_2
- libgettextpo-devel=0.22.5=h59595ed_2
- libgfortran-ng=14.1.0=h69a702a_0
- libgfortran5=14.1.0=hc5f4f2c_0
- libglib=2.74.1=h7a41b64_0
- libgomp=14.1.0=h77fa898_0
- libiconv=1.17=hd590300_2
- liblapack=3.9.0=22_linux64_openblas
- libnghttp2=1.52.0=ha637b67_1
- libnsl=2.0.1=hd590300_0
- libopenblas=0.3.27=pthreads_hac2b453_1
- libpng=1.6.43=h2797004_0
- libsanitizer=11.2.0=he4da1e4_16
- libsqlite=3.46.0=hde9e2c9_0
- libssh2=1.10.0=haa6b8db_3
- libstdcxx-devel_linux-64=11.2.0=h0952999_16
- libstdcxx-ng=14.1.0=hc0a3c3a_0
- libtiff=4.2.0=hf544144_3
- libuuid=2.38.1=h0b41bf4_0
- libwebp-base=1.4.0=hd590300_0
- libxcb=1.16=hd590300_0
- libxcrypt=4.4.36=hd590300_1
- libxml2=2.9.9=h13577e0_2
- libzlib=1.2.13=h4ab18f5_6
- lofreq=2.1.5=py310h47ef89e_10
- make=4.3=hd18ef5c_1
- ncurses=6.5=h59595ed_0
- oniguruma=6.9.9=hd590300_0
- openblas=0.3.27=pthreads_h9eca1d5_1
- openjdk=11.0.1=h516909a_1016
- openssl=1.1.1w=hd590300_0
- pango=1.50.7=hbd2fdc8_0
- parallel=20240522=ha770c72_0
- pcre=8.45=h9c3ff4c_0
- pcre2=10.37=hc3806b6_1
- perl=5.32.1=7_hd590300_perl5
- picard=3.0.0=hdfd78af_0
- pip=24.0=pyhd8ed1ab_0
- pixman=0.38.0=h516909a_1003
- pthread-stubs=0.4=h36c2ea0_1001
- python=3.10.8=h257c98d_0_cpython
- python_abi=3.10=4_cp310
- pyyaml=6.0.1=py310h2372a71_1
- r-ape=5.8=r42h08d816e_0
- r-assertthat=0.2.1=r42hc72bb7e_4
- r-backports=1.5.0=r42hb1dbf0f_0
- r-base=4.2.0=h1ae530e_0
- r-bh=1.84.0_0=r42hc72bb7e_0
- r-bitops=1.0_7=r42h57805ef_2
- r-brio=1.1.5=r42hb1dbf0f_0
- r-callr=3.7.6=r42hc72bb7e_0
- r-cli=3.6.3=r42ha18555a_0
- r-cluster=2.1.6=r42h61816a4_0
- r-codetools=0.2_20=r42hc72bb7e_0
- r-colorspace=2.1_0=r42h57805ef_1
- r-cpp11=0.4.7=r42hc72bb7e_0
- r-crayon=1.5.3=r42hc72bb7e_0
- r-data.table=1.15.2=r42h029312a_0
- r-desc=1.4.3=r42hc72bb7e_0
- r-diffobj=0.3.5=r42h57805ef_2
- r-digest=0.6.36=r42ha18555a_0
- r-dplyr=1.1.4=r42ha503ecb_0
- r-ellipsis=0.3.2=r42h57805ef_2
- r-evaluate=0.24.0=r42hc72bb7e_0
- r-fansi=1.0.6=r42h57805ef_0
- r-farver=2.1.2=r42ha18555a_0
- r-formatr=1.14=r42hc72bb7e_1
- r-fs=1.6.4=r42ha18555a_0
- r-futile.logger=1.4.3=r42hc72bb7e_1005
- r-futile.options=1.0.1=r42hc72bb7e_1004
- r-generics=0.1.3=r42hc72bb7e_2
- r-getopt=1.20.4=r42ha770c72_0
- r-ggforce=0.4.2=r42ha503ecb_0
- r-ggplot2=3.5.1=r42hc72bb7e_0
- r-ggsci=3.2.0=r42hc72bb7e_0
- r-ggvenn=0.1.10=r42hc72bb7e_1
- r-glue=1.7.0=r42h57805ef_0
- r-gtable=0.3.5=r42hc72bb7e_0
- r-isoband=0.2.7=r42ha503ecb_2
- r-jsonlite=1.8.8=r42h57805ef_0
- r-labeling=0.4.3=r42hc72bb7e_0
- r-lambda.r=1.2.4=r42hc72bb7e_3
- r-lattice=0.22_6=r42h57805ef_0
- r-lifecycle=1.0.4=r42hc72bb7e_0
- r-magrittr=2.0.3=r42h57805ef_2
- r-mass=7.3_60.0.1=r42h57805ef_0
- r-matrix=1.6_5=r42h316c678_0
- r-matrixstats=1.3.0=r42h57805ef_0
- r-memuse=4.2_3=r42h57805ef_1
- r-mgcv=1.9_1=r42h316c678_0
- r-munsell=0.5.1=r42hc72bb7e_0
- r-nlme=3.1_165=r42hbcb9c34_0
- r-optparse=1.7.5=r42hc72bb7e_0
- r-patchwork=1.2.0=r42hc72bb7e_0
- r-permute=0.9_7=r42hc72bb7e_2
- r-pillar=1.9.0=r42hc72bb7e_1
- r-pinfsc50=1.3.0=r42ha770c72_0
- r-pkgbuild=1.4.4=r42hc72bb7e_0
- r-pkgconfig=2.0.3=r42hc72bb7e_3
- r-pkgload=1.3.4=r42hc72bb7e_0
- r-polyclip=1.10_6=r42ha503ecb_0
- r-praise=1.0.0=r42hc72bb7e_1007
- r-prettyunits=1.2.0=r42hc72bb7e_0
- r-processx=3.8.4=r42h57805ef_0
- r-ps=1.7.6=r42h57805ef_0
- r-purrr=1.0.2=r42h57805ef_0
- r-r6=2.5.1=r42hc72bb7e_2
- r-rcolorbrewer=1.1_3=r42h785f33e_2
- r-rcpp=1.0.12=r42h7df8631_0
- r-rcppeigen=0.3.4.0.0=r42h08d816e_0
- r-rcurl=1.98_1.12=r42h133d619_0
- r-rematch2=2.1.2=r42hc72bb7e_3
- r-rlang=1.1.4=r42ha18555a_0
- r-rprojroot=2.0.4=r42hc72bb7e_0
- r-rstudioapi=0.16.0=r42hc72bb7e_0
- r-scales=1.3.0=r42hc72bb7e_0
- r-snow=0.4_4=r42hc72bb7e_2
- r-stringi=1.7.6=r42h884c59f_0
- r-stringr=1.5.1=r42h785f33e_0
- r-systemfonts=1.1.0=r42h6e55c91_0
- r-testthat=3.2.1.1=r42ha503ecb_0
- r-tibble=3.2.1=r42h57805ef_2
- r-tidyselect=1.2.1=r42hc72bb7e_0
- r-tweenr=2.0.3=r42ha503ecb_0
- r-utf8=1.2.4=r42h57805ef_0
- r-vcfr=1.15.0=r42h33b523d_0
- r-vctrs=0.6.5=r42ha503ecb_0
- r-vegan=2.6_6.1=r42hc29710b_0
- r-viridislite=0.4.2=r42hc72bb7e_1
- r-waldo=0.5.2=r42hc72bb7e_0
- r-withr=3.0.0=r42hc72bb7e_0
- readline=8.2=h8228510_1
- samtools=1.18=hd87286a_0
- sed=4.8=he412f7d_0
- setuptools=70.2.0=pyhd8ed1ab_0
- sysroot_linux-64=2.12=he073ed8_17
- tabixpp=1.1.2=hd68fcf3_1
- tk=8.6.13=noxft_h4845f30_101
- tktable=2.10=h8bc8fbc_6
- toml=0.10.2=pyhd8ed1ab_0
- tomlkit=0.13.0=pyha770c72_0
- tzdata=2024a=h0c530f3_0
- vardict-java=1.8.3=hdfd78af_0
- varscan=2.4.6=hdfd78af_0
- vcflib=1.0.9=h146fbdb_4
- velvet=1.2.10=he4a0461_7
- wfa2-lib=2.3.5=h4ac6f70_0
- wheel=0.43.0=pyhd8ed1ab_1
- xmltodict=0.13.0=pyhd8ed1ab_0
- xorg-fixesproto=5.0=h7f98852_1002
- xorg-inputproto=2.3.2=h7f98852_1002
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.1.1=hd590300_0
- xorg-libsm=1.2.4=h7391055_0
- xorg-libx11=1.8.9=hb711507_1
- xorg-libxau=1.0.11=hd590300_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=0.9.11=hd590300_0
- xorg-libxt=1.3.0=hd590300_1
- 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=5.2.6=h166bdaf_0
- yaml=0.2.5=h7f98852_2
- yq=3.4.3=pyhd8ed1ab_0
- zlib=1.2.13=h4ab18f5_6
- zstd=1.5.6=ha6fb4c9_0
- pip:
- biopython==1.80
- contourpy==1.0.6
- cycler==0.11.0
- fonttools==4.38.0
- kiwisolver==1.4.4
- matplotlib==3.6.2
- matplotlib-venn==0.11.7
- numpy==1.24.0
- packaging==22.0
- pandas==1.5.2
- pillow==9.3.0
- pyparsing==3.0.9
- pysam==0.19.1
- python-dateutil==2.8.2
- pytz==2022.7
- scipy==1.9.3
- six==1.16.0