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environment.yml
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environment.yml
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name: mybase
channels:
- genomedk
- pytorch
- hcc
- anaconda
- conda-forge
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_gnu
- apipkg=1.5=py_0
- argcomplete=1.12.0=pyh9f0ad1d_0
- argh=0.26.2=pyh9f0ad1d_1002
- attrs=20.1.0=pyh9f0ad1d_0
- bcbio-gff=0.6.8=pyh5e36f6f_0
- biopython=1.77=py38h1e0a361_1
- blas=2.16=mkl
- blast=2.10.1=pl526he19e7b1_3
- boost-cpp=1.74.0=h9d3c048_1
- bx-python=0.8.11=py38h024e602_1
- bzip2=1.0.8=h516909a_2
- c-ares=1.11.0=h470a237_1
- ca-certificates=2021.10.8=ha878542_0
- cairo=1.16.0=h6cf1ce9_1008
- certifi=2021.10.8=py38h578d9bd_1
- contextlib2=0.6.0.post1=py_0
- cudatoolkit=10.2.89=h8f6ccaa_8
- curl=7.71.1=he644dc0_8
- cycler=0.10.0=py_2
- cyrus-sasl=2.1.27=h063b49f_1
- dadi=2.1.1=py38h0b5ebd8_2
- diamond=2.0.11=hdcc8f71_0
- dnspython=1.16.0=py38_0
- entrez-direct=13.9=pl526h375a9b1_0
- et_xmlfile=1.0.1=py_1001
- execnet=1.7.1=py_0
- exonerate=2.4.0=haf93ef1_3
- expat=2.2.9=he1b5a44_2
- fastme=2.1.5=0
- fasttree=2.1.10=h516909a_4
- fontconfig=2.13.1=hba837de_1005
- freetype=2.10.4=h0708190_1
- fribidi=1.0.10=h516909a_0
- future=0.18.2=py38_1
- gawk=5.1.0=h516909a_0
- gethogs=20200225=pyh24bf2e0_0
- gettext=0.19.8.1=h0b5b191_1005
- gffread=0.12.1=h8b12597_0
- gffutils=0.10.1=pyh864c0ab_1
- giflib=5.2.1=h516909a_2
- glib=2.68.1=h36276a3_0
- gmp=6.2.1=h58526e2_0
- graphite2=1.3.14=h23475e2_0
- graphviz=2.42.3=h0511662_0
- harfbuzz=2.8.1=h83ec7ef_0
- hmmer=3.3.2=h1b792b2_1
- icu=68.1=h58526e2_0
- importlib-metadata=1.7.0=py38h32f6830_0
- importlib_metadata=1.7.0=0
- iniconfig=1.0.1=pyh9f0ad1d_0
- intel-openmp=2021.2.0=h06a4308_610
- iqtree=2.0.3=h176a8bc_1
- jdcal=1.4.1=py_0
- joblib=0.17.0=py_0
- jpeg=9d=h516909a_0
- kiwisolver=1.3.1=py38h2531618_0
- krb5=1.17.2=h926e7f8_0
- ld_impl_linux-64=2.34=hc38a660_9
- libblas=3.8.0=16_mkl
- libcblas=3.8.0=16_mkl
- libcurl=7.71.1=hcdd3856_8
- libdb=6.1.26=0
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=h516909a_1
- libevent=2.1.10=hcdb4288_3
- libffi=3.3=h58526e2_2
- libgcc=7.2.0=h69d50b8_2
- libgcc-ng=9.3.0=h24d8f2e_14
- libgd=2.2.5=h8e06009_4
- libgfortran-ng=7.5.0=hdf63c60_14
- libglib=2.68.1=h3e27bee_0
- libgomp=9.3.0=h24d8f2e_14
- libiconv=1.16=h516909a_0
- libidn2=2.3.0=h516909a_0
- liblapack=3.8.0=16_mkl
- liblapacke=3.8.0=16_mkl
- libnghttp2=1.41.0=hab1572f_1
- libntlm=1.4=h7f98852_1002
- libopenblas=0.3.6=h5a2b251_2
- libpng=1.6.37=hed695b0_2
- libprotobuf=3.13.0.1=hd408876_0
- libssh2=1.9.0=hab1572f_5
- libstdcxx-ng=9.3.0=hdf63c60_14
- libtiff=4.1.0=hc3755c2_3
- libtool=2.4.6=h516909a_1003
- libunistring=0.9.10=h14c3975_0
- libuuid=2.32.1=h14c3975_1000
- libuv=1.41.0=h7f98852_0
- libwebp=1.0.2=h56121f0_5
- libxcb=1.13=h14c3975_1002
- libxml2=2.9.12=h72842e0_0
- libxslt=1.1.33=h15afd5d_2
- llvm-meta=7.0.0=0
- lxml=4.6.3=py38hf1fe3a4_0
- lz4-c=1.9.2=he1b5a44_1
- lzo=2.10=h516909a_1000
- mafft=7.475=h516909a_0
- matplotlib-base=3.3.4=py38h0efea84_0
- mcl=14.137=pl526h516909a_5
- mkl=2020.2=256
- mmseqs2=12.113e3=h2d02072_2
- mock=4.0.2=py38h32f6830_0
- more-itertools=8.5.0=py_0
- mpi=1.0=openmpi
- muscle=3.8.1551=hc9558a2_5
- mysql=5.7.24=hbb652a2_0
- mysql-common=8.0.22=ha770c72_1
- mysql-connector-c=6.1.6=2
- mysql-connector-python=8.0.22=py38hf5f182a_0
- mysql-libs=8.0.22=h1fd7589_1
- mysql-server=8.0.22=h72c983a_1
- mysqlclient=2.0.3=py38h709712a_0
- ncurses=6.2=he1b5a44_1
- newick_utils=1.6=h516909a_3
- ninja=1.10.2=h4bd325d_0
- nlopt=2.7.0=py38h6599729_1
- numpy=1.19.1=py38hbc27379_1
- olefile=0.46=pyh9f0ad1d_1
- oma=2.4.1=py27h24bf2e0_0
- openmp=7.0.0=h2d50403_0
- openmpi=4.0.5=hdf1f1ad_1
- openpyxl=3.0.5=py_0
- openssl=1.1.1k=h7f98852_0
- orthofinder=2.5.2=0
- orthomcl=2.0.9=hdfd78af_5
- packaging=20.4=pyh9f0ad1d_0
- paml=4.9=h516909a_5
- pandas=1.1.0=py38h950e882_0
- pango=1.42.4=h7062337_4
- path=15.0.0=py38h32f6830_0
- path.py=12.5.0=0
- pcre=8.44=he1b5a44_0
- perl=5.26.2=h516909a_1006
- perl-aceperl=1.92=pl526_2
- perl-algorithm-munkres=0.08=pl526_1
- perl-apache-test=1.40=pl526_1
- perl-app-cpanminus=1.7044=pl526_1
- perl-appconfig=1.71=pl526_1
- perl-archive-tar=2.32=pl526_0
- perl-array-compare=3.0.1=pl526_1
- perl-autoloader=5.74=pl526_2
- perl-base=2.23=pl526_1
- perl-bio-phylo=0.58=pl526_2
- perl-bioperl-core=1.007002=pl526_2
- perl-business-isbn=3.004=pl526_0
- perl-business-isbn-data=20140910.003=pl526_0
- perl-cache-cache=1.08=pl526_0
- perl-carp=1.38=pl526_3
- perl-cgi=4.44=pl526h14c3975_1
- perl-class-inspector=1.34=pl526_0
- perl-class-load=0.25=pl526_0
- perl-class-load-xs=0.10=pl526h6bb024c_2
- perl-class-method-modifiers=2.12=pl526_0
- perl-clone=0.42=pl526h516909a_0
- perl-common-sense=3.74=pl526_2
- perl-compress-raw-bzip2=2.087=pl526he1b5a44_0
- perl-compress-raw-zlib=2.087=pl526hc9558a2_0
- perl-constant=1.33=pl526_1
- perl-convert-binary-c=0.78=pl526h6bb024c_3
- perl-convert-binhex=1.125=pl526_1
- perl-cpan-meta=2.150010=pl526_0
- perl-cpan-meta-requirements=2.140=pl526_0
- perl-cpan-meta-yaml=0.018=pl526_0
- perl-crypt-rc4=2.02=pl526_1
- perl-data-dumper=2.173=pl526_0
- perl-data-optlist=0.110=pl526_2
- perl-data-stag=0.14=pl526_1
- perl-date-format=2.30=pl526_2
- perl-db-file=1.852=pl526h14c3975_0
- perl-dbd-mysql=4.046=pl526h2d50403_0
- perl-dbd-sqlite=1.64=pl526h516909a_0
- perl-dbi=1.642=pl526_0
- perl-devel-globaldestruction=0.14=pl526_0
- perl-devel-overloadinfo=0.005=pl526_0
- perl-devel-stacktrace=2.04=pl526_0
- perl-digest-hmac=1.03=pl526_3
- perl-digest-md5=2.55=pl526_0
- perl-digest-perl-md5=1.9=pl526_1
- perl-digest-sha1=2.13=pl526h6bb024c_1
- perl-dist-checkconflicts=0.11=pl526_2
- perl-dynaloader=1.25=pl526_1
- perl-email-date-format=1.005=pl526_2
- perl-encode=2.88=pl526_1
- perl-encode-locale=1.05=pl526_6
- perl-error=0.17027=pl526_1
- perl-eval-closure=0.14=pl526h6bb024c_4
- perl-exporter=5.72=pl526_1
- perl-exporter-tiny=1.002001=pl526_0
- perl-extutils-cbuilder=0.280230=pl526_1
- perl-extutils-makemaker=7.36=pl526_1
- perl-extutils-manifest=1.72=pl526_0
- perl-extutils-parsexs=3.35=pl526_0
- perl-file-listing=6.04=pl526_1
- perl-file-path=2.16=pl526_0
- perl-file-slurp-tiny=0.004=pl526_1
- perl-file-temp=0.2304=pl526_2
- perl-file-which=1.23=pl526_0
- perl-font-afm=1.20=pl526_2
- perl-font-ttf=1.06=pl526_0
- perl-gd=2.71=pl526he860b03_0
- perl-getopt-long=2.50=pl526_1
- perl-graph=0.9704=pl526_1
- perl-graphviz=2.24=pl526h734ff71_0
- perl-html-element-extended=1.18=pl526_1
- perl-html-entities-numbered=0.04=pl526_1
- perl-html-formatter=2.16=pl526_0
- perl-html-parser=3.72=pl526h6bb024c_5
- perl-html-tableextract=2.13=pl526_2
- perl-html-tagset=3.20=pl526_3
- perl-html-tidy=1.60=pl526_0
- perl-html-tree=5.07=pl526_1
- perl-html-treebuilder-xpath=0.14=pl526_1
- perl-http-cookies=6.04=pl526_0
- perl-http-daemon=6.01=pl526_1
- perl-http-date=6.02=pl526_3
- perl-http-message=6.18=pl526_0
- perl-http-negotiate=6.01=pl526_3
- perl-image-info=1.38=pl526_1
- perl-image-size=3.300=pl526_2
- perl-io-compress=2.087=pl526he1b5a44_0
- perl-io-html=1.001=pl526_2
- perl-io-sessiondata=1.03=pl526_1
- perl-io-socket-ssl=2.066=pl526_0
- perl-io-string=1.08=pl526_3
- perl-io-stringy=2.111=pl526_1
- perl-io-tty=1.12=pl526_1
- perl-io-zlib=1.10=pl526_2
- perl-ipc-cmd=1.02=pl526_0
- perl-ipc-run=20180523.0=pl526_0
- perl-ipc-sharelite=0.17=pl526h6bb024c_1
- perl-jcode=2.07=pl526_2
- perl-json=4.02=pl526_0
- perl-json-pp=4.04=pl526_0
- perl-json-xs=2.34=pl526h6bb024c_3
- perl-lib=0.63=pl526_1
- perl-libwww-perl=6.39=pl526_0
- perl-libxml-perl=0.08=pl526_2
- perl-list-moreutils=0.428=pl526_1
- perl-list-moreutils-xs=0.428=pl526_0
- perl-locale-maketext-simple=0.21=pl526_2
- perl-lwp-mediatypes=6.04=pl526_0
- perl-lwp-protocol-https=6.07=pl526_4
- perl-lwp-simple=6.15=pl526h470a237_4
- perl-mailtools=2.21=pl526_0
- perl-math-cdf=0.1=pl526h14c3975_5
- perl-math-derivative=1.01=pl526_0
- perl-math-random=0.72=pl526h14c3975_2
- perl-math-spline=0.02=pl526_2
- perl-mime-base64=3.15=pl526_1
- perl-mime-lite=3.030=pl526_1
- perl-mime-tools=5.508=pl526_1
- perl-mime-types=2.17=pl526_0
- perl-mldbm=2.05=pl526_1
- perl-module-build=0.4224=pl526_3
- perl-module-corelist=5.20190524=pl526_0
- perl-module-implementation=0.09=pl526_2
- perl-module-load=0.32=pl526_1
- perl-module-load-conditional=0.68=pl526_2
- perl-module-metadata=1.000036=pl526_0
- perl-module-runtime=0.016=pl526_1
- perl-module-runtime-conflicts=0.003=pl526_0
- perl-moo=2.003004=pl526_0
- perl-moose=2.2011=pl526hf484d3e_1
- perl-mozilla-ca=20180117=pl526_1
- perl-mro-compat=0.13=pl526_0
- perl-net-http=6.19=pl526_0
- perl-net-ssleay=1.88=pl526h90d6eec_0
- perl-ntlm=1.09=pl526_4
- perl-ole-storage_lite=0.19=pl526_3
- perl-package-deprecationmanager=0.17=pl526_0
- perl-package-stash=0.38=pl526hf484d3e_1
- perl-package-stash-xs=0.28=pl526hf484d3e_1
- perl-parallel-forkmanager=2.02=pl526_0
- perl-params-check=0.38=pl526_1
- perl-params-util=1.07=pl526h6bb024c_4
- perl-parent=0.236=pl526_1
- perl-parse-recdescent=1.967015=pl526_0
- perl-pathtools=3.75=pl526h14c3975_1
- perl-pdf-api2=2.035=pl526_0
- perl-perl-ostype=1.010=pl526_1
- perl-pod-escapes=1.07=pl526_1
- perl-pod-usage=1.69=pl526_1
- perl-postscript=0.06=pl526_2
- perl-role-tiny=2.000008=pl526_0
- perl-scalar-list-utils=1.52=pl526h516909a_0
- perl-set-scalar=1.29=pl526_2
- perl-soap-lite=1.19=pl526_1
- perl-socket=2.027=pl526_1
- perl-sort-naturally=1.03=pl526_2
- perl-spreadsheet-parseexcel=0.65=pl526_2
- perl-spreadsheet-writeexcel=2.40=pl526_2
- perl-statistics-descriptive=3.0702=pl526_0
- perl-storable=3.15=pl526h14c3975_0
- perl-sub-exporter=0.987=pl526_2
- perl-sub-exporter-progressive=0.001013=pl526_0
- perl-sub-identify=0.14=pl526h14c3975_0
- perl-sub-install=0.928=pl526_2
- perl-sub-name=0.21=pl526_1
- perl-sub-quote=2.006003=pl526_1
- perl-svg=2.84=pl526_0
- perl-svg-graph=0.02=pl526_3
- perl-task-weaken=1.06=pl526_0
- perl-template-toolkit=2.26=pl526_1
- perl-test=1.26=pl526_1
- perl-test-harness=3.42=pl526_0
- perl-test-leaktrace=0.16=pl526h14c3975_2
- perl-test-requiresinternet=0.05=pl526_0
- perl-text-abbrev=1.02=pl526_0
- perl-text-parsewords=3.30=pl526_0
- perl-tie-ixhash=1.23=pl526_2
- perl-time-hires=1.9760=pl526h14c3975_1
- perl-time-local=1.28=pl526_1
- perl-timedate=2.30=pl526_1
- perl-tree-dag_node=1.31=pl526_0
- perl-try-tiny=0.30=pl526_1
- perl-type-tiny=1.004004=pl526_0
- perl-types-serialiser=1.0=pl526_2
- perl-unicode-map=0.112=pl526h6bb024c_3
- perl-uri=1.76=pl526_0
- perl-version=0.9924=pl526_0
- perl-www-robotrules=6.02=pl526_3
- perl-xml-dom=1.46=pl526_0
- perl-xml-dom-xpath=0.14=pl526_1
- perl-xml-filter-buffertext=1.01=pl526_2
- perl-xml-libxml=2.0132=pl526h7ec2d77_1
- perl-xml-libxslt=1.94=pl526_1
- perl-xml-namespacesupport=1.12=pl526_0
- perl-xml-parser=2.44=pl526h4e0c4b3_7
- perl-xml-regexp=0.04=pl526_2
- perl-xml-sax=1.02=pl526_0
- perl-xml-sax-base=1.09=pl526_0
- perl-xml-sax-expat=0.51=pl526_3
- perl-xml-sax-writer=0.57=pl526_0
- perl-xml-simple=2.25=pl526_1
- perl-xml-twig=3.52=pl526_2
- perl-xml-writer=0.625=pl526_2
- perl-xml-xpath=1.44=pl526_0
- perl-xml-xpathengine=0.14=pl526_2
- perl-xsloader=0.24=pl526_0
- perl-yaml=1.29=pl526_0
- pillow=7.2.0=py38h9776b28_0
- pip=20.2.1=py_0
- pixman=0.40.0=h36c2ea0_0
- pluggy=0.13.1=py38h32f6830_2
- prank=v.170427=hc9558a2_3
- proteinortho=6.0.18=hfd40d39_1
- protobuf=3.13.0.1=py38he6710b0_1
- pthread-stubs=0.4=h14c3975_1001
- py=1.9.0=pyh9f0ad1d_0
- pyfaidx=0.6.3.1=pyh5e36f6f_0
- pyparsing=2.4.7=pyh9f0ad1d_0
- pytest=6.0.1=py38h32f6830_0
- pytest-shutil=1.7.0=py_0
- python=3.8.8=hdb3f193_4
- python-dateutil=2.8.1=py_0
- python-lzo=1.12=py38h86e1cee_1003
- python_abi=3.8=1_cp38
- pytorch=1.8.1=py3.8_cuda10.2_cudnn7.6.5_0
- pytz=2020.1=pyh9f0ad1d_0
- pyxdf=1.16.3=py_0
- raxml=8.2.12=h516909a_2
- raxml-ng=0.6.0=0
- readline=8.0=he28a2e2_2
- scikit-learn=0.23.2=py38h0573a6f_0
- scipy=1.5.2=py38h8c5af15_0
- setuptools=49.2.1=py38h32f6830_0
- simplejson=3.17.2=py38h1e0a361_0
- six=1.15.0=pyh9f0ad1d_0
- sqlite=3.33.0=h62c20be_0
- swipe=2.1.0=h78e549b_1
- tbb=2020.2=h4bd325d_3
- termcolor=1.1.0=py_2
- threadpoolctl=2.1.0=pyh5ca1d4c_0
- tidyp=1.04=h516909a_2
- tk=8.6.10=hed695b0_0
- toml=0.10.1=pyh9f0ad1d_0
- tornado=6.1=py38h497a2fe_1
- typing_extensions=3.7.4.3=py_0
- wget=1.20.1=h22169c7_0
- wheel=0.34.2=py_1
- xlrd=1.2.0=py_0
- xlsxwriter=1.3.9=pyhd8ed1ab_0
- xorg-kbproto=1.0.7=h14c3975_1002
- xorg-libice=1.0.10=h516909a_0
- xorg-libsm=1.2.3=h84519dc_1000
- xorg-libx11=1.6.11=h516909a_0
- xorg-libxau=1.0.9=h14c3975_0
- xorg-libxdmcp=1.1.3=h516909a_0
- xorg-libxext=1.3.4=h516909a_0
- xorg-libxpm=3.5.13=h516909a_0
- xorg-libxrender=0.9.10=h516909a_1002
- xorg-libxt=1.1.5=h516909a_1003
- xorg-renderproto=0.11.1=h14c3975_1002
- xorg-xextproto=7.3.0=h14c3975_1002
- xorg-xproto=7.0.31=h14c3975_1007
- xz=5.2.5=h516909a_1
- zipp=3.1.0=py_0
- zlib=1.2.11=h516909a_1006
- zstd=1.4.5=h6597ccf_2
prefix: /nfs/home/afedorova/.conda/envs/mybase