Unverified Commit b4858860 authored by Michal Ziemski's avatar Michal Ziemski
Browse files

Add environment spec file

Took 56 minutes
parent f05003c1
Pipeline #137969 passed with stages
in 18 minutes and 49 seconds
......@@ -11,7 +11,8 @@ RUN chmod 644 /usr/local/share/ca-certificates/* && update-ca-certificates
RUN apt-get update && apt-get upgrade -y && apt-get install -y zip
RUN wget https://data.qiime2.org/distro/core/qiime2-2022.2-py38-linux-conda.yml
#RUN wget https://data.qiime2.org/distro/core/qiime2-2022.2-py38-linux-conda.yml
COPY qiime2-2022.2-py38-linux-conda.yml .
RUN mamba env update -n base --file qiime2-2022.2-py38-linux-conda.yml
RUN rm qiime2-2022.2-py38-linux-conda.yml
......
channels:
- qiime2/label/r2022.2
- https://packages.qiime2.org/qiime2/2022.2/passed/core/
- conda-forge
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1
- _openmp_mutex=4.5
- _r-mutex=1.0.1
- alsa-lib=1.2.3.2
- argon2-cffi=21.3.0
- argon2-cffi-bindings=21.2.0
- asttokens=2.0.5
- attr=2.5.1
- attrs=21.4.0
- backcall=0.2.0
- backports=1.0
- backports.functools_lru_cache=1.6.4
- beautifulsoup4=4.11.1
- bibtexparser=1.1.0
- binutils_impl_linux-64=2.36.1
- binutils_linux-64=2.36
- bioconductor-biobase=2.54.0
- bioconductor-biocgenerics=0.40.0
- bioconductor-biocparallel=1.28.3
- bioconductor-biostrings=2.62.0
- bioconductor-dada2=1.22.0
- bioconductor-delayedarray=0.20.0
- bioconductor-genomeinfodb=1.30.0
- bioconductor-genomeinfodbdata=1.2.7
- bioconductor-genomicalignments=1.30.0
- bioconductor-genomicranges=1.46.1
- bioconductor-iranges=2.28.0
- bioconductor-matrixgenerics=1.6.0
- bioconductor-rhtslib=1.26.0
- bioconductor-rsamtools=2.10.0
- bioconductor-s4vectors=0.32.3
- bioconductor-shortread=1.52.0
- bioconductor-summarizedexperiment=1.24.0
- bioconductor-xvector=0.34.0
- bioconductor-zlibbioc=1.40.0
- biom-format=2.1.10
- blast=2.12.0
- bleach=5.0.0
- bokeh=2.4.3
- bowtie2=2.4.5
- brotli=1.0.9
- brotli-bin=1.0.9
- brotlipy=0.7.0
- bwidget=1.9.14
- bzip2=1.0.8
- c-ares=1.18.1
- ca-certificates=2022.5.18.1
- cachecontrol=0.12.11
- cached-property=1.5.2
- cached_property=1.5.2
- cairo=1.16.0
- certifi=2022.5.18.1
- cffi=1.15.0
- charset-normalizer=2.0.12
- click=7.1.2
- colorama=0.4.4
- cryptography=37.0.2
- curl=7.83.1
- cutadapt=4.0
- cycler=0.11.0
- cython=0.29.30
- dbus=1.13.6
- deblur=1.1.0
- debugpy=1.6.0
- decorator=4.4.2
- defusedxml=0.7.1
- dendropy=4.5.2
- dill=0.3.5.1
- dnaio=0.9.0
- emperor=1.0.3
- entrez-direct=16.2
- entrypoints=0.4
- executing=0.8.3
- expat=2.4.8
- fastcluster=1.2.6
- fasttree=2.1.10
- fftw=3.3.10
- flit-core=3.7.1
- font-ttf-dejavu-sans-mono=2.37
- font-ttf-inconsolata=3.000
- font-ttf-source-code-pro=2.038
- font-ttf-ubuntu=0.83
- fontconfig=2.14.0
- fonts-conda-ecosystem=1
- fonts-conda-forge=1
- fonttools=4.33.3
- freetype=2.10.4
- fribidi=1.0.10
- future=0.18.2
- gcc_impl_linux-64=10.3.0
- gcc_linux-64=10.3.0
- gettext=0.19.8.1
- gfortran_impl_linux-64=10.3.0
- gfortran_linux-64=10.3.0
- giflib=5.2.1
- gneiss=0.4.6
- graphite2=1.3.13
- gsl=2.7
- gst-plugins-base=1.20.2
- gstreamer=1.20.2
- gxx_impl_linux-64=10.3.0
- gxx_linux-64=10.3.0
- h5py=3.6.0
- harfbuzz=4.3.0
- hdf5=1.12.1
- hdmedians=0.14.2
- hmmer=3.1b2
- htslib=1.15.1
- icu=70.1
- idna=3.3
- ijson=3.1.3
- importlib-metadata=4.11.4
- importlib_resources=5.7.1
- iniconfig=1.1.1
- ipykernel=6.13.0
- ipython=8.4.0
- ipython_genutils=0.2.0
- ipywidgets=7.7.0
- iqtree=2.2.0_beta
- isa-l=2.30.0
- jack=1.9.18
- jedi=0.18.1
- jinja2=3.1.2
- joblib=1.1.0
- jpeg=9e
- jsonschema=4.5.1
- jupyter_client=7.3.1
- jupyter_core=4.10.0
- jupyterlab_pygments=0.2.2
- jupyterlab_widgets=1.1.0
- kernel-headers_linux-64=2.6.32
- keyutils=1.6.1
- kiwisolver=1.4.2
- krb5=1.19.3
- lcms2=2.12
- ld_impl_linux-64=2.36.1
- lerc=3.0
- libblas=3.9.0
- libbrotlicommon=1.0.9
- libbrotlidec=1.0.9
- libbrotlienc=1.0.9
- libcap=2.64
- libcblas=3.9.0
- libclang=14.0.4
- libclang13=14.0.4
- libcups=2.3.3
- libcurl=7.83.1
- libdb=6.2.32
- libdeflate=1.10
- libedit=3.1.20191231
- libev=4.33
- libevent=2.1.10
- libffi=3.4.2
- libflac=1.3.4
- libgcc=7.2.0
- libgcc-devel_linux-64=10.3.0
- libgcc-ng=12.1.0
- libgfortran-ng=12.1.0
- libgfortran5=12.1.0
- libglib=2.70.2
- libgomp=12.1.0
- libiconv=1.16
- liblapack=3.9.0
- libllvm10=10.0.1
- libllvm14=14.0.4
- libnghttp2=1.47.0
- libnsl=2.0.0
- libogg=1.3.4
- libopenblas=0.3.20
- libopus=1.3.1
- libpng=1.6.37
- libpq=14.3
- libsanitizer=10.3.0
- libsndfile=1.0.31
- libsodium=1.0.18
- libssh2=1.10.0
- libstdcxx-devel_linux-64=10.3.0
- libstdcxx-ng=12.1.0
- libtiff=4.3.0
- libtool=2.4.6
- libudev1=249
- libuuid=2.32.1
- libvorbis=1.3.7
- libwebp=1.2.2
- libwebp-base=1.2.2
- libxcb=1.13
- libxkbcommon=1.0.3
- libxml2=2.9.14
- libxslt=1.1.33
- libzlib=1.2.11
- llvmlite=0.36.0
- lockfile=0.12.2
- lxml=4.8.0
- lz4=4.0.0
- lz4-c=1.9.3
- mafft=7.505
- make=4.3
- markupsafe=2.1.1
- matplotlib=3.5.2
- matplotlib-base=3.5.2
- matplotlib-inline=0.1.3
- mistune=0.8.4
- msgpack-python=1.0.3
- munkres=1.1.4
- mysql-common=8.0.29
- mysql-libs=8.0.29
- natsort=8.1.0
- nbclient=0.6.3
- nbconvert=6.5.0
- nbconvert-core=6.5.0
- nbconvert-pandoc=6.5.0
- nbformat=5.4.0
- ncurses=6.3
- nest-asyncio=1.5.5
- networkx=2.8.2
- nose=1.3.7
- notebook=6.4.11
- nspr=4.32
- nss=3.78
- numba=0.53.1
- numpy=1.22.4
- openjdk=11.0.9.1
- openjpeg=2.4.0
- openssl=1.1.1o
- packaging=21.3
- pandas=1.2.5
- pandoc=2.18
- pandocfilters=1.5.0
- pango=1.50.7
- parso=0.8.3
- patsy=0.5.2
- pbzip2=1.1.13
- pcre=8.45
- pcre2=10.37
- perl=5.32.1
- perl-archive-tar=2.40
- perl-carp=1.50
- perl-common-sense=3.75
- perl-compress-raw-bzip2=2.103
- perl-compress-raw-zlib=2.105
- perl-encode=3.17
- perl-exporter=5.74
- perl-exporter-tiny=1.002002
- perl-extutils-makemaker=7.64
- perl-io-compress=2.106
- perl-io-zlib=1.11
- perl-json=4.06
- perl-json-xs=2.34
- perl-list-moreutils=0.430
- perl-list-moreutils-xs=0.430
- perl-parent=0.238
- perl-pathtools=3.75
- perl-scalar-list-utils=1.62
- perl-types-serialiser=1.01
- pexpect=4.8.0
- pickleshare=0.7.5
- pigz=2.6
- pillow=9.1.1
- pip=22.1.1
- pixman=0.40.0
- pluggy=1.0.0
- prometheus_client=0.14.1
- prompt-toolkit=3.0.29
- psutil=5.9.1
- pthread-stubs=0.4
- ptyprocess=0.7.0
- pulseaudio=14.0
- pure_eval=0.2.2
- py=1.11.0
- pycparser=2.21
- pygments=2.12.0
- pynndescent=0.5.7
- pyopenssl=22.0.0
- pyparsing=3.0.9
- pyqt=5.15.4
- pyqt5-sip=12.9.0
- pyrsistent=0.18.1
- pysocks=1.7.1
- pytest=7.1.2
- python=3.8.13
- python-dateutil=2.8.2
- python-fastjsonschema=2.15.3
- python-isal=0.11.1
- python_abi=3.8
- pytz=2022.1
- pyyaml=6.0
- pyzmq=23.0.0
- q2-alignment=2022.2.0
- q2-composition=2022.2.0
- q2-cutadapt=2022.2.0
- q2-dada2=2022.2.0
- q2-deblur=2022.2.0
- q2-demux=2022.2.0
- q2-diversity=2022.2.1
- q2-diversity-lib=2022.2.1
- q2-emperor=2022.2.0
- q2-feature-classifier=2022.2.0
- q2-feature-table=2022.2.0
- q2-fragment-insertion=2022.2.0
- q2-gneiss=2022.2.0
- q2-longitudinal=2022.2.0
- q2-metadata=2022.2.0
- q2-mystery-stew=2022.2.0
- q2-phylogeny=2022.2.0
- q2-quality-control=2022.2.0
- q2-quality-filter=2022.2.0
- q2-sample-classifier=2022.2.0
- q2-taxa=2022.2.0
- q2-types=2022.2.0
- q2-vsearch=2022.2.0
- q2cli=2022.2.0
- q2galaxy=2022.2.0
- q2templates=2022.2.0
- qiime2=2022.2.1
- qt-main=5.15.3
- r-backports=1.4.1
- r-base=4.1.3
- r-bh=1.78.0_0
- r-bitops=1.0_7
- r-brio=1.1.3
- r-callr=3.7.0
- r-cli=3.3.0
- r-cluster=2.1.3
- r-colorspace=2.0_3
- r-crayon=1.5.1
- r-desc=1.4.1
- r-diffobj=0.3.5
- r-digest=0.6.29
- r-ellipsis=0.3.2
- r-evaluate=0.15
- r-fansi=1.0.3
- r-farver=2.1.0
- r-formatr=1.12
- r-futile.logger=1.4.3
- r-futile.options=1.0.1
- r-ggplot2=3.3.6
- r-glue=1.6.2
- r-gtable=0.3.0
- r-hwriter=1.3.2.1
- r-isoband=0.2.5
- r-jpeg=0.1_9
- r-jsonlite=1.8.0
- r-labeling=0.4.2
- r-lambda.r=1.2.4
- r-lattice=0.20_45
- r-latticeextra=0.6_29
- r-lifecycle=1.0.1
- r-magrittr=2.0.3
- r-mass=7.3_57
- r-matrix=1.4_1
- r-matrixstats=0.62.0
- r-mgcv=1.8_40
- r-munsell=0.5.0
- r-nlme=3.1_157
- r-permute=0.9_7
- r-pillar=1.7.0
- r-pkgconfig=2.0.3
- r-pkgload=1.2.4
- r-plyr=1.8.7
- r-png=0.1_7
- r-praise=1.0.0
- r-processx=3.5.3
- r-ps=1.7.0
- r-r6=2.5.1
- r-rcolorbrewer=1.1_3
- r-rcpp=1.0.8.3
- r-rcppparallel=5.1.5
- r-rcurl=1.98_1.6
- r-rematch2=2.1.2
- r-reshape2=1.4.4
- r-rlang=1.0.2
- r-rprojroot=2.0.3
- r-rstudioapi=0.13
- r-scales=1.2.0
- r-snow=0.4_4
- r-stringi=1.7.6
- r-stringr=1.4.0
- r-testthat=3.1.4
- r-tibble=3.1.7
- r-utf8=1.2.2
- r-vctrs=0.4.1
- r-vegan=2.6_2
- r-viridislite=0.4.0
- r-waldo=0.4.0
- r-withr=2.5.0
- raxml=8.2.12
- readline=8.1
- requests=2.27.1
- samtools=1.15.1
- scikit-bio=0.5.6
- scikit-learn=0.24.1
- scipy=1.8.1
- seaborn=0.11.2
- seaborn-base=0.11.2
- sed=4.8
- send2trash=1.8.0
- sepp=4.3.10
- setuptools=59.8.0
- sip=6.5.1
- six=1.16.0
- sortmerna=2.0
- soupsieve=2.3.1
- sqlite=3.38.5
- stack_data=0.2.0
- statsmodels=0.13.2
- sysroot_linux-64=2.12
- tbb=2020.2
- terminado=0.15.0
- threadpoolctl=3.1.0
- tinycss2=1.1.1
- tk=8.6.12
- tktable=2.10
- toml=0.10.2
- tomli=2.0.1
- tornado=6.1
- tqdm=4.64.0
- traitlets=5.2.1.post0
- typing_extensions=4.2.0
- tzlocal=2.1
- umap-learn=0.5.3
- unicodedata2=14.0.0
- unifrac=0.20.3
- urllib3=1.26.9
- vsearch=2.7.0
- wcwidth=0.2.5
- webencodings=0.5.1
- wheel=0.37.1
- widgetsnbextension=3.6.0
- xopen=1.5.0
- xorg-fixesproto=5.0
- xorg-inputproto=2.3.2
- xorg-kbproto=1.0.7
- xorg-libice=1.0.10
- xorg-libsm=1.2.3
- xorg-libx11=1.7.2
- xorg-libxau=1.0.9
- xorg-libxdmcp=1.1.3
- xorg-libxext=1.3.4
- xorg-libxfixes=5.0.3
- xorg-libxi=1.7.10
- xorg-libxrender=0.9.10
- xorg-libxt=1.2.1
- xorg-libxtst=1.2.3
- xorg-recordproto=1.14.2
- xorg-renderproto=0.11.1
- xorg-xextproto=7.3.0
- xorg-xproto=7.0.31
- xz=5.2.5
- yaml=0.2.5
- zeromq=4.3.4
- zipp=3.8.0
- zlib=1.2.11
- zstd=1.5.2
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