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Add a YAML file with the exact Conda environment (package/software ve…
…rsions) used for SCAN2
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Joe Luquette
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Joe Luquette
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May 9, 2022
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,345 @@ | ||
| name: scansnv-pta | ||
| channels: | ||
| - dranew | ||
| - soil | ||
| - conda-forge/label/cf201901 | ||
| - jluquette | ||
| - conda-forge | ||
| - bioconda | ||
| - defaults | ||
| dependencies: | ||
| - _libgcc_mutex=0.1=main | ||
| - _r-mutex=1.0.0=anacondar_1 | ||
| - aioeasywebdav=2.2.0=py36_0 | ||
| - aiohttp=3.4.4=py36h470a237_0 | ||
| - anaconda-client=1.7.1=py_0 | ||
| - appdirs=1.4.3=py_1 | ||
| - asn1crypto=0.24.0=py36_1003 | ||
| - async-timeout=3.0.1=py_1000 | ||
| - attrs=18.2.0=py_0 | ||
| - bcrypt=3.1.4=py36h470a237_0 | ||
| - beautifulsoup4=4.6.3=py36_1000 | ||
| - bedtools=2.27.1=he941832_2 | ||
| - bioconductor-annotationdbi=1.42.1=r351_0 | ||
| - bioconductor-annotationfilter=1.4.0=r351_0 | ||
| - bioconductor-biobase=2.40.0=r351ha44fe06_1 | ||
| - bioconductor-biocgenerics=0.26.0=r351_0 | ||
| - bioconductor-biocparallel=1.14.2=r351h26a2512_0 | ||
| - bioconductor-biomart=2.36.1=r351_0 | ||
| - bioconductor-biostrings=2.48.0=r351h470a237_0 | ||
| - bioconductor-biovizbase=1.28.2=r351h470a237_0 | ||
| - bioconductor-bsgenome=1.48.0=r351_0 | ||
| - bioconductor-bsgenome.hsapiens.ucsc.hg19=1.4.0=r351_4 | ||
| - bioconductor-delayedarray=0.6.6=r351_0 | ||
| - bioconductor-ensembldb=2.4.1=r351_0 | ||
| - bioconductor-genomeinfodb=1.16.0=r351_0 | ||
| - bioconductor-genomeinfodbdata=1.1.0=r351_0 | ||
| - bioconductor-genomicalignments=1.16.0=r351h470a237_0 | ||
| - bioconductor-genomicfeatures=1.32.3=r351_0 | ||
| - bioconductor-genomicranges=1.32.7=r351h470a237_0 | ||
| - bioconductor-gviz=1.24.0=r351_0 | ||
| - bioconductor-iranges=2.14.12=r351h470a237_0 | ||
| - bioconductor-protgenerics=1.12.0=r351_0 | ||
| - bioconductor-rsamtools=1.32.3=r351hfc679d8_0 | ||
| - bioconductor-rtracklayer=1.40.6=r351h470a237_0 | ||
| - bioconductor-s4vectors=0.18.3=r351h470a237_0 | ||
| - bioconductor-summarizedexperiment=1.10.1=r351_0 | ||
| - bioconductor-variantannotation=1.26.1=r351h470a237_0 | ||
| - bioconductor-xvector=0.20.0=r351h470a237_0 | ||
| - bioconductor-zlibbioc=1.26.0=r351h470a237_0 | ||
| - blas=1.0=mkl | ||
| - boost=1.66.0=py36_1 | ||
| - boost-cpp=1.66.0=1 | ||
| - boto3=1.7.84=py_0 | ||
| - botocore=1.10.84=py_0 | ||
| - bwidget=1.9.11=1 | ||
| - bzip2=1.0.6=h470a237_2 | ||
| - ca-certificates=2018.11.29=ha4d7672_0 | ||
| - cachetools=2.1.0=py_0 | ||
| - cairo=1.14.12=h276e583_5 | ||
| - certifi=2018.11.29=py36_1000 | ||
| - cffi=1.11.5=py36h5e8e0c9_1 | ||
| - chardet=3.0.4=py36_1003 | ||
| - clyent=1.2.2=py_1 | ||
| - conda=4.5.12=py36_1000 | ||
| - conda-build=3.17.5=py36_0 | ||
| - conda-env=2.6.0=1 | ||
| - configargparse=0.13.0=py_1 | ||
| - cryptography=2.3.1=py36hdffb7b8_0 | ||
| - cryptography-vectors=2.3.1=py36_1000 | ||
| - curl=7.63.0=h74213dd_0 | ||
| - datrie=0.7.1=py36h7b6447c_1 | ||
| - decorator=4.3.0=py_0 | ||
| - docutils=0.14=py36_1001 | ||
| - dropbox=7.3.1=py36_0 | ||
| - eagle-phase=2.3.5=0 | ||
| - expat=2.2.5=hfc679d8_2 | ||
| - filechunkio=1.6=py36_0 | ||
| - filelock=3.0.10=py_0 | ||
| - fontconfig=2.13.1=h65d0f4c_0 | ||
| - freetype=2.9.1=h6debe1e_4 | ||
| - ftputil=3.2=py36_0 | ||
| - gatk=3.8=py36_0 | ||
| - gettext=0.19.8.1=h5e8e0c9_1 | ||
| - gitdb2=2.0.5=py_0 | ||
| - gitpython=2.1.11=py_0 | ||
| - glib=2.56.2=h464dc38_1 | ||
| - glob2=0.6=py_0 | ||
| - google-auth=1.2.1=py_0 | ||
| - google-auth-httplib2=0.0.3=py_2 | ||
| - google-cloud-core=0.24.1=py36_0 | ||
| - google-cloud-storage=1.1.1=py36_0 | ||
| - google-resumable-media=0.0.2=py36_0 | ||
| - googleapis-common-protos=1.5.5=py_0 | ||
| - graphite2=1.3.12=hfc679d8_1 | ||
| - graphviz=2.38.0=h08bfae6_9 | ||
| - gsl=2.2.1=h0c605f7_3 | ||
| - harfbuzz=1.9.0=h04dbb29_1 | ||
| - htslib=1.9=h47928c2_5 | ||
| - httplib2=0.12.0=py36_1000 | ||
| - icu=58.2=hfc679d8_0 | ||
| - idna=2.8=py36_1000 | ||
| - idna_ssl=1.0.0=0 | ||
| - intel-openmp=2019.1=144 | ||
| - ipython_genutils=0.2.0=py_1 | ||
| - jinja2=2.10=py_1 | ||
| - jmespath=0.9.3=py_1 | ||
| - jpeg=9c=h470a237_1 | ||
| - jsonschema=3.0.0a3=py36_1000 | ||
| - jupyter_core=4.4.0=py_0 | ||
| - krb5=1.16.2=hbb41f41_0 | ||
| - libarchive=3.3.3=h823be47_0 | ||
| - libcurl=7.63.0=hbdb9355_0 | ||
| - libdeflate=1.0=h470a237_0 | ||
| - libedit=3.1.20170329=h6b74fdf_2 | ||
| - libffi=3.2.1=hd88cf55_4 | ||
| - libgcc-ng=8.2.0=hdf63c60_1 | ||
| - libgfortran=3.0.0=1 | ||
| - libgfortran-ng=7.2.0=hdf63c60_3 | ||
| - libiconv=1.15=h470a237_3 | ||
| - liblief=0.9.0=h7725739_1 | ||
| - libpng=1.6.36=ha92aebf_0 | ||
| - libprotobuf=3.6.1=hd28b015_0 | ||
| - libssh2=1.8.0=h5b517e9_3 | ||
| - libstdcxx-ng=8.2.0=hdf63c60_1 | ||
| - libtiff=4.0.10=he6b73bb_1 | ||
| - libtool=2.4.6=h470a237_2 | ||
| - libuuid=2.32.1=h470a237_2 | ||
| - libxcb=1.13=h470a237_2 | ||
| - libxml2=2.9.8=h422b904_5 | ||
| - make=4.2.1=h470a237_1002 | ||
| - markupsafe=1.1.0=py36h470a237_0 | ||
| - mkl=2019.1=144 | ||
| - mkl_fft=1.0.10=py36_0 | ||
| - mkl_random=1.0.2=py36_0 | ||
| - multidict=4.5.1=py36h470a237_0 | ||
| - nbformat=4.4.0=py_1 | ||
| - ncurses=6.1=hf484d3e_0 | ||
| - networkx=2.2=py_1 | ||
| - numpy=1.15.4=py36h7e9f1db_0 | ||
| - numpy-base=1.15.4=py36hde5b4d6_0 | ||
| - openblas=0.3.4=ha44fe06_0 | ||
| - openjdk=8.0.192=h470a237_2 | ||
| - openssl=1.0.2p=h470a237_1 | ||
| - pandas=0.23.4=py36hf8a1672_0 | ||
| - pango=1.40.14=he752989_2 | ||
| - paramiko=2.4.2=py36_1000 | ||
| - patchelf=0.9=hfc679d8_2 | ||
| - pcre=8.41=hfc679d8_3 | ||
| - picard=2.18.23=0 | ||
| - pip=18.1=py36_1000 | ||
| - pixman=0.34.0=h470a237_3 | ||
| - pkginfo=1.4.2=py_1 | ||
| - prettytable=0.7.2=py_2 | ||
| - protobuf=3.6.1=py36hfc679d8_1 | ||
| - psutil=5.4.8=py36h470a237_0 | ||
| - pthread-stubs=0.4=h470a237_1 | ||
| - py-lief=0.9.0=py36h7725739_1 | ||
| - pyasn1=0.4.4=py_1 | ||
| - pyasn1-modules=0.0.5=py36_0 | ||
| - pycosat=0.6.3=py36h470a237_1 | ||
| - pycparser=2.19=py_0 | ||
| - pygraphviz=1.3.1=py36_0 | ||
| - pynacl=1.3.0=py36h470a237_0 | ||
| - pyopenssl=18.0.0=py36_1000 | ||
| - pyrsistent=0.14.7=py36h470a237_0 | ||
| - pysftp=0.2.9=py36_0 | ||
| - pysocks=1.6.8=py36_1002 | ||
| - python=3.6.6=h5001a0f_3 | ||
| - python-dateutil=2.7.5=py_0 | ||
| - python-irodsclient=0.7.0=py_0 | ||
| - python-libarchive-c=2.8=py36_1004 | ||
| - pytz=2018.7=py_0 | ||
| - pyyaml=3.13=py36h470a237_1 | ||
| - r-acepack=1.4.1=r35h9bbef5b_1004 | ||
| - r-assertthat=0.2.0=r351h6115d3f_1001 | ||
| - r-backports=1.1.5=r35hcdcec82_0 | ||
| - r-base=3.5.1=h391c2eb_4 | ||
| - r-base64enc=0.1_3=r35hcdcec82_1003 | ||
| - r-bh=1.66.0_1=r351_2001 | ||
| - r-bindr=0.1.1=r351h6115d3f_1001 | ||
| - r-bindrcpp=0.2.2=r351h9d2a408_1 | ||
| - r-bit=1.1_12=r351h470a237_2 | ||
| - r-bit64=0.9_7=r351hc070d10_0 | ||
| - r-bitops=1.0_6=r351hc070d10_2 | ||
| - r-blob=1.1.1=r351_1001 | ||
| - r-callr=3.4.2=r35h6115d3f_0 | ||
| - r-checkmate=2.0.0=r35hcdcec82_0 | ||
| - r-cli=1.0.1=r351h6115d3f_1000 | ||
| - r-clipr=0.7.0=r35h6115d3f_0 | ||
| - r-clisymbols=1.2.0=r35h6115d3f_1002 | ||
| - r-cluster=2.1.0=r35h9bbef5b_2 | ||
| - r-colorspace=1.4_1=r35hcdcec82_1 | ||
| - r-crayon=1.3.4=r351h6115d3f_1001 | ||
| - r-curl=4.3=r35hcdcec82_0 | ||
| - r-data.table=1.12.8=r35hcdcec82_0 | ||
| - r-dbi=1.0.0=r351h6115d3f_1001 | ||
| - r-dbplyr=1.2.2=r351h6115d3f_1001 | ||
| - r-desc=1.2.0=r35h6115d3f_1002 | ||
| - r-devtools=2.0.2=r351h6115d3f_0 | ||
| - r-dichromat=2.0_0=r35_2001 | ||
| - r-digest=0.6.18=r351hc070d10_0 | ||
| - r-dplyr=0.7.8=r351h9d2a408_0 | ||
| - r-evaluate=0.14=r35h6115d3f_1 | ||
| - r-fansi=0.3.0=r351hc070d10_0 | ||
| - r-fastghquad=1.0=r351h29659fb_0 | ||
| - r-foreign=0.8_76=r35hcdcec82_0 | ||
| - r-formatr=1.5=r351h6115d3f_1001 | ||
| - r-formula=1.2_3=r35h6115d3f_1002 | ||
| - r-fs=1.3.2=r35h0357c0b_0 | ||
| - r-futile.logger=1.4.3=r351h6115d3f_1001 | ||
| - r-futile.options=1.0.1=r351h6115d3f_1000 | ||
| - r-ggplot2=3.3.0=r35h6115d3f_0 | ||
| - r-gh=1.1.0=r35h6115d3f_0 | ||
| - r-git2r=0.24.0=r351h47c54a8_1 | ||
| - r-glue=1.3.0=r351h470a237_2 | ||
| - r-gridextra=2.3=r35h6115d3f_1002 | ||
| - r-gtable=0.3.0=r35h6115d3f_2 | ||
| - r-highr=0.8=r35h6115d3f_1 | ||
| - r-hmisc=4.4_0=r35h9bbef5b_0 | ||
| - r-hms=0.4.2=r351h6115d3f_1000 | ||
| - r-htmltable=1.13.3=r35h6115d3f_0 | ||
| - r-htmltools=0.4.0=r35h0357c0b_0 | ||
| - r-htmlwidgets=1.5.1=r35h6115d3f_0 | ||
| - r-httr=1.4.1=r35h6115d3f_1 | ||
| - r-ini=0.3.1=r35h6115d3f_1002 | ||
| - r-isoband=0.2.1=r35h0357c0b_0 | ||
| - r-jsonlite=1.6.1=r35hcdcec82_0 | ||
| - r-knitr=1.28=r35h6115d3f_0 | ||
| - r-labeling=0.3=r35h6115d3f_1002 | ||
| - r-lambda.r=1.2.3=r351h6115d3f_1000 | ||
| - r-lattice=0.20_38=r351hc070d10_0 | ||
| - r-latticeextra=0.6_28=r35h6115d3f_1002 | ||
| - r-lazyeval=0.2.2=r35hcdcec82_1 | ||
| - r-magrittr=1.5=r351h6115d3f_1001 | ||
| - r-markdown=1.1=r35hcdcec82_0 | ||
| - r-mass=7.3_51.5=r35hcdcec82_0 | ||
| - r-matrix=1.2_15=r351hc070d10_0 | ||
| - r-matrixstats=0.54.0=r351hc070d10_0 | ||
| - r-memoise=1.1.0=r351h6115d3f_1001 | ||
| - r-mgcv=1.8_31=r35hcdcec82_0 | ||
| - r-mime=0.9=r35hcdcec82_0 | ||
| - r-munsell=0.5.0=r35h6115d3f_1002 | ||
| - r-nlme=3.1_147=r35h9bbef5b_0 | ||
| - r-nnet=7.3_13=r35hcdcec82_0 | ||
| - r-openssl=1.1=r351hff1dc39_1001 | ||
| - r-pillar=1.3.0=r351h6115d3f_1000 | ||
| - r-pkgbuild=1.0.6=r35h6115d3f_0 | ||
| - r-pkgconfig=2.0.2=r351h6115d3f_1001 | ||
| - r-pkgload=1.0.2=r35h0357c0b_1001 | ||
| - r-plogr=0.2.0=r351h6115d3f_1001 | ||
| - r-praise=1.0.0=r35h6115d3f_1003 | ||
| - r-prettyunits=1.0.2=r351h6115d3f_1001 | ||
| - r-processx=3.4.2=r35hcdcec82_0 | ||
| - r-progress=1.2.2=r35h6115d3f_1 | ||
| - r-ps=1.3.2=r35hcdcec82_0 | ||
| - r-purrr=0.2.5=r351hc070d10_2 | ||
| - r-r6=2.2.2=r351h6115d3f_1001 | ||
| - r-rappdirs=0.3.1=r35hcdcec82_1003 | ||
| - r-rcmdcheck=1.3.2=r351h6115d3f_1000 | ||
| - r-rcolorbrewer=1.1_2=r35h6115d3f_1002 | ||
| - r-rcpp=1.0.0=r351h9d2a408_0 | ||
| - r-rcurl=1.95_4.11=r351hc070d10_3 | ||
| - r-remotes=2.1.1=r35h6115d3f_0 | ||
| - r-reticulate=1.14=r35h0357c0b_0 | ||
| - r-rlang=0.3.0.1=r351h470a237_0 | ||
| - r-rpart=4.1_15=r35hcdcec82_1 | ||
| - r-rprojroot=1.3_2=r35h6115d3f_1002 | ||
| - r-rsqlite=2.1.1=r351h9d2a408_0 | ||
| - r-rstudioapi=0.11=r35h6115d3f_0 | ||
| - r-scales=1.0.0=r35h0357c0b_1002 | ||
| - r-scansnv=0.1=r351hf484d3e_0 | ||
| - r-sessioninfo=1.1.1=r35h6115d3f_1001 | ||
| - r-snow=0.4_3=r351h6115d3f_1000 | ||
| - r-stringi=1.4.3=r35h0357c0b_2 | ||
| - r-stringr=1.4.0=r35h6115d3f_1 | ||
| - r-survival=3.1_12=r35hcdcec82_0 | ||
| - r-testthat=2.2.1=r35h0357c0b_0 | ||
| - r-tibble=1.4.2=r351hc070d10_2 | ||
| - r-tidyselect=0.2.5=r351h9d2a408_0 | ||
| - r-usethis=1.5.1=r35h6115d3f_1 | ||
| - r-utf8=1.1.4=r351hc070d10_0 | ||
| - r-viridis=0.5.1=r35h6115d3f_1003 | ||
| - r-viridislite=0.3.0=r35h6115d3f_1002 | ||
| - r-whisker=0.4=r35h6115d3f_0 | ||
| - r-withr=2.1.2=r35h6115d3f_1001 | ||
| - r-xfun=0.13=r35h6115d3f_0 | ||
| - r-xml=3.98_1.16=r351hc070d10_0 | ||
| - r-xopen=1.0.0=r35h6115d3f_1002 | ||
| - r-yaml=2.2.1=r35hcdcec82_0 | ||
| - ratelimiter=1.2.0=py36_1000 | ||
| - readline=7.0=h7b6447c_5 | ||
| - requests=2.13.0=py36_0 | ||
| - rpy2=2.9.4=py36r351h941a26a_1 | ||
| - rsa=3.1.4=py36_0 | ||
| - ruamel_yaml=0.15.71=py36h470a237_0 | ||
| - s3transfer=0.1.13=py36_1001 | ||
| - samtools=1.9=h8ee4bcc_1 | ||
| - scansnv=1.0=0 | ||
| - setuptools=40.6.3=py36_0 | ||
| - shapeit=2.r837=0 | ||
| - shyaml=0.6.1=py_0 | ||
| - six=1.12.0=py36_1000 | ||
| - smmap2=2.0.5=py_0 | ||
| - snakemake=5.3.1=0 | ||
| - snakemake-minimal=5.3.1=py_0 | ||
| - sqlite=3.25.3=h7b6447c_0 | ||
| - tk=8.6.8=hbc83047_0 | ||
| - tktable=2.10=h14c3975_0 | ||
| - tqdm=4.28.1=py_0 | ||
| - traitlets=4.3.2=py36_1000 | ||
| - tzlocal=1.5.1=py_0 | ||
| - urllib3=1.12=py36_0 | ||
| - wget=1.19.5=h1ad7b7a_0 | ||
| - wheel=0.32.3=py36_0 | ||
| - wrapt=1.10.11=py36h470a237_1 | ||
| - xmlrunner=1.7.7=py_0 | ||
| - xorg-kbproto=1.0.7=h470a237_2 | ||
| - xorg-libice=1.0.9=h470a237_4 | ||
| - xorg-libsm=1.2.3=h8c8a85c_0 | ||
| - xorg-libx11=1.6.6=h470a237_0 | ||
| - xorg-libxau=1.0.8=h470a237_6 | ||
| - xorg-libxdmcp=1.1.2=h470a237_7 | ||
| - xorg-libxext=1.3.3=h470a237_4 | ||
| - xorg-libxpm=3.5.12=h470a237_2 | ||
| - xorg-libxrender=0.9.10=h470a237_2 | ||
| - xorg-libxt=1.1.5=h470a237_2 | ||
| - xorg-renderproto=0.11.1=h470a237_2 | ||
| - xorg-xextproto=7.3.0=h470a237_2 | ||
| - xorg-xproto=7.0.31=h470a237_7 | ||
| - xz=5.2.4=h14c3975_4 | ||
| - yaml=0.1.7=had09818_2 | ||
| - yarl=1.3.0=py36h470a237_0 | ||
| - zlib=1.2.11=ha838bed_2 | ||
| - pip: | ||
| - cycler==0.10.0 | ||
| - drmaa==0.7.9 | ||
| - kiwisolver==1.1.0 | ||
| - matplotlib==3.2.1 | ||
| - patsy==0.5.1 | ||
| - pyparsing==2.4.6 | ||
| - scipy==1.4.1 | ||
| - sigprofilermatrixgenerator==1.1.9 | ||
| - sigprofilerplotting==1.1.0 | ||
| - statsmodels==0.11.1 | ||
| prefix: /home/ljl11/.conda/envs/scansnv-pta |