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environments.yml
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name: tpd
channels:
- bioconda
- conda-forge
- r
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_gnu
- abricate=1.0.1=h1341992_0
- any2fasta=0.4.2=2
- aragorn=1.2.38=h516909a_3
- barrnap=0.9=3
- bbmap=38.89=h1296035_0
- bedtools=2.30.0=hc088bd4_0
- binutils_impl_linux-64=2.35.1=h193b22a_1
- binutils_linux-64=2.35=hc3fd857_29
- biopython=1.78=py37h5e8e339_2
- blast=2.10.1=pl526he19e7b1_3
- boost=1.74.0=py37h6dcda5c_3
- boost-cpp=1.74.0=h9359b55_0
- bzip2=1.0.8=h7f98852_4
- c-ares=1.11.0=h470a237_1
- ca-certificates=2020.12.5=ha878542_0
- cairo=1.16.0=h9f066cc_1006
- certifi=2020.12.5=py37h89c1867_1
- click=7.1.2=pyh9f0ad1d_0
- clustalw=2.1=hc9558a2_5
- crisper_recognition_tool=1.2=1
- csvtk=0.22.0=0
- curl=7.71.1=he644dc0_8
- dfast=1.2.12=h8b12597_0
- emboss=6.6.0=h6debe1e_0
- entrez-direct=13.9=pl526h375a9b1_0
- expat=2.2.10=h9c3ff4c_0
- fontconfig=2.13.1=hba837de_1004
- freetype=2.10.4=h0708190_1
- fribidi=1.0.10=h36c2ea0_0
- gcc_impl_linux-64=9.3.0=h70c0ae5_18
- gcc_linux-64=9.3.0=h7247604_29
- gdbm=1.18=h0a1914f_2
- gettext=0.19.8.1=hf34092f_1004
- ghostx=1.3.7=hfc679d8_1
- giflib=5.2.1=h36c2ea0_2
- gmp=6.2.1=h58526e2_0
- graphite2=1.3.13=h58526e2_1001
- graphviz=2.42.3=h0511662_0
- gxx_impl_linux-64=9.3.0=hd87eabc_18
- gxx_linux-64=9.3.0=h0d07fa4_29
- harfbuzz=2.7.2=ha5b49bf_1
- hmmer=3.3.1=he1b5a44_0
- htslib=1.9=ha228f0b_7
- icu=67.1=he1b5a44_0
- intervaltree=3.0.2=py_0
- joblib=1.0.0=pyhd8ed1ab_0
- jpeg=9d=h36c2ea0_0
- k8=0.2.5=he513fc3_0
- kernel-headers_linux-64=2.6.32=h77966d4_13
- kofamscan=1.3.0=0
- krb5=1.17.2=h926e7f8_0
- ld_impl_linux-64=2.35.1=hea4e1c9_1
- libblas=3.9.0=7_openblas
- libcblas=3.9.0=7_openblas
- libcurl=7.71.1=hcdd3856_8
- libdb=6.1.26=0
- libdeflate=1.0=h14c3975_1
- libedit=3.1.20191231=h46ee950_2
- libev=4.33=h516909a_1
- libffi=3.2.1=he1b5a44_1007
- libgcc=7.2.0=h69d50b8_2
- libgcc-devel_linux-64=9.3.0=h7864c58_18
- libgcc-ng=9.3.0=h5dbcf3e_17
- libgd=2.3.0=h6e6070c_0
- libgfortran-ng=9.3.0=he4bcb1c_17
- libgfortran5=9.3.0=he4bcb1c_17
- libglib=2.66.3=hbe7bbb4_0
- libgomp=9.3.0=h5dbcf3e_17
- libiconv=1.16=h516909a_0
- liblapack=3.9.0=7_openblas
- libnghttp2=1.41.0=hab1572f_1
- libopenblas=0.3.12=pthreads_h4812303_1
- libpng=1.6.37=h21135ba_2
- libssh2=1.9.0=hab1572f_5
- libstdcxx-devel_linux-64=9.3.0=hb016644_18
- libstdcxx-ng=9.3.0=h2ae2ef3_17
- libtiff=4.2.0=hdc55705_0
- libtool=2.4.6=h58526e2_1007
- libuuid=2.32.1=h7f98852_1000
- libwebp=1.1.0=h76fa15c_4
- libwebp-base=1.1.0=h36c2ea0_3
- libxcb=1.13=h7f98852_1003
- libxml2=2.9.10=h68273f3_2
- libxslt=1.1.33=hf705e74_1
- lz4-c=1.9.3=h9c3ff4c_0
- metagene_annotator=1.0=h516909a_3
- minimap2=2.17=hed695b0_3
- mummer=3.23=4
- ncurses=6.1=hf484d3e_1002
- numpy=1.19.5=py37haa41c4c_1
- openjdk=10.0.2=h14c3975_1015
- openssl=1.1.1k=h7f98852_0
- paml=4.9=h516909a_5
- pandas=1.2.1=py37hdc94413_0
- pango=1.42.4=h69149e4_5
- parallel=20201122=ha770c72_0
- pbzip2=1.1.13=0
- pcre=8.44=he1b5a44_0
- perl=5.26.2=h36c2ea0_1008
- perl-aceperl=1.92=pl526_2
- perl-algorithm-diff=1.1903=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-asn1-entrezgene=1.73=pl526_1
- perl-bio-coordinate=1.007001=pl526_1
- perl-bio-featureio=1.6.905=pl526_2
- perl-bio-phylo=0.58=pl526_2
- perl-bio-samtools=1.43=pl526h1341992_1
- perl-bio-tools-phylo-paml=1.7.3=pl526_1
- perl-bio-tools-run-alignment-clustalw=1.7.4=pl526_1
- perl-bio-tools-run-alignment-tcoffee=1.7.4=pl526_2
- perl-bioperl=1.7.2=pl526_11
- perl-bioperl-core=1.007002=pl526_2
- perl-bioperl-run=1.007002=pl526_4
- perl-business-isbn=3.004=pl526_0
- perl-business-isbn-data=20140910.003=pl526_0
- perl-cache-cache=1.08=pl526_0
- perl-capture-tiny=0.48=pl526_0
- perl-carp=1.38=pl526_3
- perl-cgi=4.44=pl526h14c3975_1
- perl-class-data-inheritable=0.08=pl526_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-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-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-exception-class=1.44=pl526_0
- perl-exporter=5.72=pl526_1
- perl-exporter-tiny=1.002001=pl526_0
- perl-extutils-makemaker=7.36=pl526_1
- perl-file-listing=6.04=pl526_1
- perl-file-path=2.16=pl526_0
- perl-file-slurp=9999.27=pl526_0
- perl-file-slurp-tiny=0.004=pl526_1
- perl-file-sort=1.01=pl526_2
- perl-file-spec=3.48_01=pl526_1
- perl-file-temp=0.2304=pl526_2
- perl-file-which=1.23=pl526_0
- perl-findbin=1.51=pl526_2
- perl-font-afm=1.20=pl526_2
- perl-font-ttf=1.06=pl526_0
- perl-gd=2.68=pl526he941832_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-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-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-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-implementation=0.09=pl526_2
- 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-params-util=1.07=pl526h6bb024c_4
- perl-parent=0.236=pl526_1
- perl-parse-recdescent=1.967015=pl526_0
- perl-path-tiny=0.108=pl526_0
- perl-pathtools=3.75=pl526h14c3975_1
- perl-pdf-api2=2.035=pl526_0
- 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-sub-uplevel=0.2800=pl526h14c3975_2
- 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-deep=1.128=pl526_1
- perl-test-differences=0.67=pl526_0
- perl-test-exception=0.43=pl526_2
- perl-test-harness=3.42=pl526_0
- perl-test-leaktrace=0.16=pl526h14c3975_2
- perl-test-most=0.35=pl526_0
- perl-test-requiresinternet=0.05=pl526_0
- perl-test-warn=0.36=pl526_1
- perl-text-csv=2.00=pl526_0
- perl-text-diff=1.45=pl526_0
- perl-threaded=5.26.0=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-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
- phispy=4.2.6=py37h9a982cc_0
- pip=20.3.3=pyhd8ed1ab_0
- pixman=0.40.0=h36c2ea0_0
- pthread-stubs=0.4=h36c2ea0_1001
- pyfastaq=3.17.0=py_2
- pymummer=0.11.0=py_0
- pysam=0.15.3=py37hda2845c_1
- python=3.7.8=h6f2ec95_1_cpython
- python-dateutil=2.8.1=py_0
- python_abi=3.7=1_cp37m
- pytz=2020.5=pyhd8ed1ab_0
- ragtag=1.0.2=pyh7b7c402_0
- readline=8.0=h46ee950_1
- ruby=2.6.6=hebe951e_0
- samtools=1.9=h10a08f8_12
- scikit-learn=0.24.1=py37h69acf81_0
- scipy=1.6.0=py37h14a347d_0
- setuptools=49.6.0=py37h89c1867_3
- six=1.15.0=pyh9f0ad1d_0
- sortedcontainers=2.3.0=pyhd8ed1ab_0
- sqlite=3.32.3=hcee41ef_1
- sysroot_linux-64=2.12=h77966d4_13
- t_coffee=11.0.8=py37hea885bf_8
- tgs-gapcloser=1.0.3=hf484d3e_0
- threadpoolctl=2.1.0=pyh5ca1d4c_0
- tidyp=1.04=h516909a_2
- tk=8.6.10=h21135ba_1
- unzip=6.0=h7f98852_2
- wheel=0.36.2=pyhd3deb0d_0
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.0.10=h516909a_0
- xorg-libsm=1.2.3=h84519dc_1000
- xorg-libx11=1.6.12=h516909a_0
- xorg-libxau=1.0.9=h7f98852_0
- xorg-libxdmcp=1.1.3=h7f98852_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=h7f98852_1002
- xorg-xproto=7.0.31=h7f98852_1007
- xz=5.2.5=h516909a_1
- yaml=0.2.5=h516909a_0
- zlib=1.2.11=h516909a_1010
- zstd=1.4.8=ha95c52a_1