Commit 487d4402 authored by Erwan DELAGE's avatar Erwan DELAGE

Passage à Qiime 2019.10

parent fedb8cc6
......@@ -279,7 +279,7 @@ def check_system():
OS = "linux"
# Conda's environment files
qiime2_version = "2019.4-py36"
qiime2_version = "2019.10-py36"
global qiime2_yml
qiime2_yml = "conda/qiime2-" + qiime2_version + "-" + OS + "-conda.yml"
......
channels:
- qiime2/label/r2019.4
- qiime2/label/r2019.10
- conda-forge
- bioconda
- defaults
- conda-forge/label/gcc7
dependencies:
- _r-mutex=1.0.0
- _libgcc_mutex=0.1
- _r-mutex=1.0.1
- alsa-lib=1.1.5
- arb-bio-tools=6.0.6
- asn1crypto=0.24.0
- asn1crypto=1.2.0
- atomicwrites=1.3.0
- attrs=19.1.0
- attrs=19.3.0
- backcall=0.1.0
- bibtexparser=1.1.0
- binutils_impl_linux-64=2.31.1
......@@ -21,7 +22,7 @@ dependencies:
- bioconductor-dada2=1.10.0
- bioconductor-delayedarray=0.8.0
- bioconductor-genomeinfodb=1.18.1
- bioconductor-genomeinfodbdata=1.2.0
- bioconductor-genomeinfodbdata=1.2.1
- bioconductor-genomicalignments=1.18.1
- bioconductor-genomicranges=1.34.0
- bioconductor-iranges=2.16.0
......@@ -32,282 +33,307 @@ dependencies:
- bioconductor-xvector=0.22.0
- bioconductor-zlibbioc=1.28.0
- biom-format=2.1.7
- blas=1.1
- blast=2.7.1
- blas=2.14
- blast=2.9.0
- bleach=3.1.0
- bokeh=1.1.0
- boost=1.67.0
- boost-cpp=1.67.0
- bwidget=1.9.11
- bz2file=0.98
- bzip2=1.0.6
- ca-certificates=2019.3.9
- bokeh=1.3.4
- boost=1.68.0
- boost-cpp=1.68.0
- bwidget=1.9.13
- bzip2=1.0.8
- ca-certificates=2019.9.11
- cachecontrol=0.12.5
- cairo=1.16.0
- certifi=2019.3.9
- cffi=1.12.3
- certifi=2019.9.11
- cffi=1.13.1
- chardet=3.0.4
- click=7.0
- cryptography=2.6.1
- curl=7.64.1
- cutadapt=2.3
- cryptography=2.7
- curl=7.65.3
- cutadapt=2.6
- cycler=0.10.0
- cython=0.29.13
- dbus=1.13.6
- deblur=1.1.0
- decorator=4.4.0
- defusedxml=0.5.0
- dnaio=0.3
- emperor=1.0.0b19
- decorator=4.4.1
- defusedxml=0.6.0
- dendropy=4.4.0
- dnaio=0.4
- emperor=1.0.0b20
- entrypoints=0.3
- expat=2.2.5
- fastcluster=1.1.25
- fasttree=2.1.10
- fontconfig=2.13.1
- freetype=2.10.0
- future=0.17.1
- future=0.18.2
- gcc_impl_linux-64=7.3.0
- gcc_linux-64=7.3.0
- gettext=0.19.8.1
- gfortran_impl_linux-64=7.3.0
- gfortran_linux-64=7.3.0
- giflib=5.1.7
- glib=2.58.3
- gmp=6.1.2
- gneiss=0.4.4
- gnutls=3.5.19
- gneiss=0.4.6
- gnutls=3.6.5
- graphite2=1.3.13
- gsl=2.4
- gst-plugins-base=1.14.4
- gstreamer=1.14.4
- gsl=2.5
- gst-plugins-base=1.14.5
- gstreamer=1.14.5
- gxx_impl_linux-64=7.3.0
- gxx_linux-64=7.3.0
- h5py=2.9.0
- h5py=2.10.0
- harfbuzz=2.4.0
- hdf5=1.10.4
- hdf5=1.10.5
- hdmedians=0.13
- hmmer=3.1b2
- icu=58.2
- idna=2.8
- ijson=2.3
- ipykernel=5.1.0
- ipython=7.5.0
- ijson=2.5
- importlib_metadata=0.23
- ipykernel=5.1.3
- ipython=7.9.0
- ipython_genutils=0.2.0
- ipywidgets=7.4.2
- iqtree=1.6.10
- jedi=0.13.3
- jinja2=2.10.1
- ipywidgets=7.5.1
- iqtree=1.6.12
- jedi=0.15.1
- jinja2=2.10.3
- joblib=0.14.0
- jpeg=9c
- jsonschema=3.0.1
- jupyter_client=5.2.4
- jupyter_core=4.4.0
- jsonschema=3.1.1
- jupyter_client=5.3.3
- jupyter_core=4.5.0
- kiwisolver=1.1.0
- krb5=1.16.3
- lcms2=2.9
- libarbdb=6.0.6
- libcurl=7.64.1
- libblas=3.8.0
- libcblas=3.8.0
- libcurl=7.65.3
- libedit=3.1.20170329
- libffi=3.2.1
- libgcc=7.2.0
- libgcc-ng=8.2.0
- libgcc-ng=9.1.0
- libgfortran-ng=7.3.0
- libiconv=1.15
- libidn2=2.1.1
- liblapack=3.8.0
- liblapacke=3.8.0
- libopenblas=0.3.7
- libpng=1.6.37
- libsodium=1.0.16
- libsodium=1.0.17
- libssh2=1.8.2
- libstdcxx-ng=8.2.0
- libstdcxx-ng=9.1.0
- libtiff=4.0.10
- libunistring=0.9.10
- libuuid=2.32.1
- libxcb=1.13
- libxml2=2.9.9
- lockfile=0.12.2
- lz4-c=1.8.3
- mafft=7.310
- make=4.2.1
- markupsafe=1.1.1
- matplotlib=3.0.3
- matplotlib-base=3.0.3
- matplotlib=3.1.0
- matplotlib-base=3.1.0
- mistune=0.8.4
- more-itertools=4.3.0
- msgpack-python=0.6.1
- more-itertools=7.2.0
- msgpack-python=0.6.2
- natsort=6.0.0
- nbconvert=5.5.0
- nbconvert=5.6.1
- nbformat=4.4.0
- ncurses=6.1
- nettle=3.3
- networkx=2.3
- nettle=3.4.1
- networkx=2.4
- nose=1.3.7
- notebook=5.7.8
- numpy=1.16.2
- notebook=6.0.1
- numpy=1.17.3
- olefile=0.46
- openblas=0.3.3
- openjdk=11.0.1
- openssl=1.1.1b
- packaging=19.0
- pandas=0.24.2
- pandoc=2.7.2
- openssl=1.1.1c
- packaging=19.2
- pandas=0.25.2
- pandoc=2.7.3
- pandocfilters=1.4.2
- pango=1.40.14
- parso=0.4.0
- parso=0.5.1
- patsy=0.5.1
- pcre=8.41
- pcre=8.43
- perl=5.26.2
- perl-archive-tar=2.32
- perl-carp=1.38
- perl-compress-raw-bzip2=2.086
- perl-compress-raw-zlib=2.086
- perl-common-sense=3.74
- perl-compress-raw-bzip2=2.087
- perl-compress-raw-zlib=2.087
- perl-exporter=5.72
- perl-exporter-tiny=1.002001
- perl-extutils-makemaker=7.36
- perl-io-compress=2.086
- perl-io-compress=2.087
- perl-io-zlib=1.10
- perl-json=4.02
- perl-json-xs=2.34
- perl-list-moreutils=0.428
- perl-list-moreutils-xs=0.428
- perl-pathtools=3.75
- perl-scalar-list-utils=1.45
- perl-scalar-list-utils=1.52
- perl-types-serialiser=1.0
- perl-xsloader=0.24
- pexpect=4.7.0
- pickleshare=0.7.5
- pigz=2.3.4
- pillow=6.0.0
- pip=19.1
- pixman=0.34.0
- pluggy=0.11.0
- prometheus_client=0.6.0
- prompt_toolkit=2.0.9
- psutil=5.6.2
- pillow=6.2.1
- pip=19.3.1
- pixman=0.38.0
- pluggy=0.12.0
- prometheus_client=0.7.1
- prompt_toolkit=2.0.10
- psutil=5.6.3
- pthread-stubs=0.4
- ptyprocess=0.6.0
- py=1.8.0
- pycparser=2.19
- pygments=2.4.0
- pygments=2.4.2
- pyopenssl=19.0.0
- pyparsing=2.3.0
- pyparsing=2.4.2
- pyqt=5.9.2
- pyrsistent=0.15.1
- pysocks=1.6.8
- pytest=4.4.2
- pyrsistent=0.15.5
- pysocks=1.7.1
- pytest=5.2.2
- python=3.6.7
- python-dateutil=2.8.0
- pytz=2019.1
- pyyaml=5.1
- pyzmq=18.0.1
- q2-alignment=2019.4.0
- q2-composition=2019.4.0
- q2-cutadapt=2019.4.0
- q2-dada2=2019.4.0
- q2-deblur=2019.4.0
- q2-demux=2019.4.1
- q2-diversity=2019.4.0
- q2-emperor=2019.4.0
- q2-feature-classifier=2019.4.0
- q2-feature-table=2019.4.0
- q2-fragment-insertion=2019.4.0
- q2-gneiss=2019.4.0
- q2-longitudinal=2019.4.0
- q2-metadata=2019.4.0
- q2-phylogeny=2019.4.0
- q2-quality-control=2019.4.0
- q2-quality-filter=2019.4.0
- q2-sample-classifier=2019.4.0
- q2-taxa=2019.4.0
- q2-types=2019.4.1
- q2-vsearch=2019.4.0
- q2cli=2019.4.0
- q2templates=2019.4.0
- qiime2=2019.4.0
- pytz=2019.3
- pyyaml=5.1.2
- pyzmq=18.1.0
- q2-alignment=2019.10.0
- q2-composition=2019.10.0
- q2-cutadapt=2019.10.0
- q2-dada2=2019.10.0
- q2-deblur=2019.10.0
- q2-demux=2019.10.0
- q2-diversity=2019.10.0
- q2-emperor=2019.10.0
- q2-feature-classifier=2019.10.0
- q2-feature-table=2019.10.0
- q2-fragment-insertion=2019.10.0
- q2-gneiss=2019.10.0
- q2-longitudinal=2019.10.0
- q2-metadata=2019.10.0
- q2-phylogeny=2019.10.0
- q2-quality-control=2019.10.0
- q2-quality-filter=2019.10.0
- q2-sample-classifier=2019.10.0
- q2-taxa=2019.10.0
- q2-types=2019.10.0
- q2-vsearch=2019.10.0
- q2cli=2019.10.0
- q2templates=2019.10.0
- qiime2=2019.10.0
- qt=5.9.7
- r-assertthat=0.2.1
- r-backports=1.1.5
- r-base=3.5.1
- r-bh=1.69.0_1
- r-bitops=1.0_6
- r-cli=1.1.0
- r-cluster=2.0.9
- r-cluster=2.1.0
- r-colorspace=1.4_1
- r-crayon=1.3.4
- r-data.table=1.12.2
- r-digest=0.6.18
- r-data.table=1.12.6
- r-digest=0.6.22
- r-ellipsis=0.3.0
- r-fansi=0.4.0
- r-formatr=1.6
- r-formatr=1.7
- r-futile.logger=1.4.3
- r-futile.options=1.0.1
- r-ggplot2=3.1.1
- r-ggplot2=3.2.1
- r-glue=1.3.1
- r-gtable=0.3.0
- r-hwriter=1.3.2
- r-labeling=0.3
- r-lambda.r=1.2.3
- r-lambda.r=1.2.4
- r-lattice=0.20_38
- r-latticeextra=0.6_28
- r-lazyeval=0.2.2
- r-magrittr=1.5
- r-mass=7.3_51.4
- r-matrix=1.2_17
- r-matrixstats=0.54.0
- r-mgcv=1.8_28
- r-matrixstats=0.55.0
- r-mgcv=1.8_29
- r-munsell=0.5.0
- r-nlme=3.1_139
- r-nlme=3.1_141
- r-permute=0.9_5
- r-pillar=1.3.1
- r-pkgconfig=2.0.2
- r-pillar=1.4.2
- r-pkgconfig=2.0.3
- r-plyr=1.8.4
- r-r6=2.4.0
- r-rcolorbrewer=1.1_2
- r-rcpp=1.0.1
- r-rcppparallel=4.4.2
- r-rcpp=1.0.2
- r-rcppparallel=4.4.4
- r-rcurl=1.95_4.12
- r-reshape2=1.4.3
- r-rlang=0.3.4
- r-rlang=0.4.1
- r-scales=1.0.0
- r-snow=0.4_3
- r-stringi=1.4.3
- r-stringr=1.4.0
- r-tibble=2.1.1
- r-tibble=2.1.3
- r-utf8=1.1.4
- r-vegan=2.5_4
- r-vctrs=0.2.0
- r-vegan=2.5_6
- r-viridislite=0.3.0
- r-withr=2.1.2
- r-zeallot=0.1.0
- raxml=8.2.12
- readline=7.0
- requests=2.21.0
- readline=8.0
- requests=2.22.0
- scikit-bio=0.5.5
- scikit-learn=0.20.2
- scipy=1.2.1
- scikit-learn=0.21.2
- scipy=1.3.1
- seaborn=0.9.0
- send2trash=1.5.0
- setuptools=41.0.1
- sina=1.4.0
- sepp=4.3.10
- setuptools=41.6.0
- sina=1.6.0
- sip=4.19.8
- six=1.12.0
- sortmerna=2.0
- sqlite=3.28.0
- statsmodels=0.9.0
- tbb=2019.6
- sqlite=3.30.1
- statsmodels=0.10.1
- tbb=2019.9
- terminado=0.8.2
- testpath=0.4.2
- tk=8.6.9
- tktable=2.10
- tornado=6.0.2
- traitlets=4.3.2
- tzlocal=1.5.1
- unifrac=0.9.3
- urllib3=1.24.2
- tornado=6.0.3
- traitlets=4.3.3
- tzlocal=2.0.0
- unifrac=0.10.0
- urllib3=1.25.6
- vsearch=2.7.0
- wcwidth=0.1.7
- webencodings=0.5.1
- wget=1.20.1
- wheel=0.33.1
- widgetsnbextension=3.4.2
- xopen=0.5.1
- wheel=0.33.6
- widgetsnbextension=3.5.1
- xopen=0.8.4
- xorg-fixesproto=5.0
- xorg-inputproto=2.3.2
- xorg-kbproto=1.0.7
- xorg-libice=1.0.9
- xorg-libice=1.0.10
- xorg-libsm=1.2.3
- xorg-libx11=1.6.7
- xorg-libx11=1.6.9
- 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-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=5.2.4
- yaml=0.1.7
- zeromq=4.3.1
- zeromq=4.3.2
- zipp=0.6.0
- zlib=1.2.11
- zstd=1.4.3
channels:
- qiime2/label/r2019.4
- qiime2/label/r2019.10
- conda-forge
- bioconda
- defaults
- conda-forge/label/gcc7
dependencies:
- _r-mutex=1.0.0
- _r-mutex=1.0.1
- appnope=0.1.0
- arb-bio-tools=6.0.6
- asn1crypto=0.24.0
- asn1crypto=1.2.0
- atomicwrites=1.3.0
- attrs=19.1.0
- attrs=19.3.0
- backcall=0.1.0
- bibtexparser=1.1.0
- bioconductor-biobase=2.42.0
......@@ -20,7 +19,7 @@ dependencies:
- bioconductor-dada2=1.10.0
- bioconductor-delayedarray=0.8.0
- bioconductor-genomeinfodb=1.18.1
- bioconductor-genomeinfodbdata=1.2.0
- bioconductor-genomeinfodbdata=1.2.1
- bioconductor-genomicalignments=1.18.1
- bioconductor-genomicranges=1.34.0
- bioconductor-iranges=2.16.0
......@@ -31,239 +30,260 @@ dependencies:
- bioconductor-xvector=0.22.0
- bioconductor-zlibbioc=1.28.0
- biom-format=2.1.7
- blas=1.1
- blas=2.12
- blast=2.6.0
- bleach=3.1.0
- bokeh=1.1.0
- bokeh=1.3.4
- boost=1.67.0
- boost-cpp=1.67.0
- bwidget=1.9.11
- bz2file=0.98
- bzip2=1.0.6
- ca-certificates=2019.3.9
- bwidget=1.9.13
- bzip2=1.0.8
- ca-certificates=2019.9.11
- cachecontrol=0.12.5
- cairo=1.14.12
- certifi=2019.3.9
- cffi=1.12.3
- cctools=921
- certifi=2019.6.16
- cffi=1.13.1
- chardet=3.0.4
- clang=9.0.0
- clang_osx-64=9.0.0
- clangxx=9.0.0
- clangxx_osx-64=9.0.0
- click=7.0
- cryptography=2.6.1
- curl=7.64.1
- cutadapt=2.3
- compiler-rt=9.0.0
- cryptography=2.7
- curl=7.65.3
- cutadapt=2.6
- cycler=0.10.0
- cython=0.29.13
- deblur=1.1.0
- decorator=4.4.0
- defusedxml=0.5.0
- dnaio=0.3
- emperor=1.0.0b19
- decorator=4.4.1
- defusedxml=0.6.0
- dendropy=4.2.0
- dnaio=0.4
- emperor=1.0.0b20
- entrypoints=0.3
- fastcluster=1.1.25
- fasttree=2.1.10
- fontconfig=2.13.1
- freetype=2.10.0
- future=0.17.1
- future=0.18.2
- gettext=0.19.8.1
- gfortran_osx-64=4.8.5
- glib=2.56.2
- gneiss=0.4.4
- gneiss=0.4.6
- graphite2=1.3.13
- gsl=2.2.1
- h5py=2.9.0
- h5py=2.10.0
- harfbuzz=1.9.0
- hdf5=1.10.4
- hdf5=1.10.5
- hdmedians=0.13
- hmmer=3.1b2
- icu=58.2
- idna=2.8
- ijson=2.3
- ipykernel=5.1.0
- ipython=7.5.0
- ijson=2.5
- importlib_metadata=0.23
- ipykernel=5.1.3
- ipython=7.9.0
- ipython_genutils=0.2.0
- ipywidgets=7.4.2
- iqtree=1.6.10
- jedi=0.13.3
- jinja2=2.10.1
- ipywidgets=7.5.1
- iqtree=1.6.12
- jedi=0.15.1
- jinja2=2.10.3
- joblib=0.14.0
- jpeg=9c
- jsonschema=3.0.1
- jupyter_client=5.2.4
- jupyter_core=4.4.0
- jsonschema=3.1.1
- jupyter_client=5.3.3
- jupyter_core=4.5.0
- kiwisolver=1.1.0
- krb5=1.16.3
- ld64=409.12
- libarbdb=6.0.6
- libcurl=7.64.1
- libcxx=8.0.0
- libcxxabi=8.0.0
- libblas=3.8.0
- libcblas=3.8.0
- libcurl=7.65.3
- libcxx=9.0.0
- libedit=3.1.20170329
- libffi=3.2.1
- libgcc=4.8.5
- libgfortran=3.0.1
- libiconv=1.15
- libidn2=2.1.1
- liblapack=3.8.0
- liblapacke=3.8.0
- libllvm9=9.0.0
- libopenblas=0.3.7
- libpng=1.6.37
- libsodium=1.0.16
- libsodium=1.0.17
- libssh2=1.8.2
- libtiff=4.0.10
- libunistring=0.9.10
- libxml2=2.9.9
- llvm-openmp=8.0.0
- llvm-openmp=8.0.1
- lockfile=0.12.2
- lz4-c=1.8.3
- mafft=7.310
- make=4.2.1
- markupsafe=1.1.1
- matplotlib=3.0.3
- matplotlib-base=3.0.3
- matplotlib=3.1.0
- matplotlib-base=3.1.0
- mistune=0.8.4
- more-itertools=4.3.0
- msgpack-python=0.6.1
- more-itertools=7.2.0
- msgpack-python=0.6.2
- natsort=6.0.0
- nbconvert=5.5.0
- nbconvert=5.6.1
- nbformat=4.4.0
- ncurses=6.1
- networkx=2.3
- networkx=2.4
- nose=1.3.7
- notebook=5.7.8
- numpy=1.16.2
- notebook=6.0.1
- numpy=1.17.3
- olefile=0.46
- openblas=0.3.3
- openjdk=11.0.1
- openmp=8.0.0
- openssl=1.1.1b
- packaging=19.0
- pandas=0.24.2
- pandoc=2.7.2
- openmp=8.0.1
- openssl=1.1.1c
- packaging=19.2
- pandas=0.25.2
- pandoc=2.7.3
- pandocfilters=1.4.2
- pango=1.40.14
- parso=0.4.0
- parso=0.5.1
- patsy=0.5.1
- pcre=8.41
- pcre=8.43
- pexpect=4.7.0
- pickleshare=0.7.5
- pigz=2.3.4
- pillow=6.0.0
- pip=19.1
- pillow=6.2.1
- pip=19.3.1
- pixman=0.34.0
- pluggy=0.11.0
- prometheus_client=0.6.0
- prompt_toolkit=2.0.9
- psutil=5.6.2
- pluggy=0.12.0
- prometheus_client=0.7.1
- prompt_toolkit=2.0.10
- psutil=5.6.3
- ptyprocess=0.6.0
- py=1.8.0
- pycparser=2.19
- pygments=2.4.0
- pygments=2.4.2
- pyopenssl=19.0.0
- pyparsing=2.3.0
- pyrsistent=0.15.1
- pysocks=1.6.8
- pytest=4.4.2
- pyparsing=2.4.2
- pyrsistent=0.15.5
- pysocks=1.7.1
- pytest=5.2.2
- python=3.6.7
- python-dateutil=2.8.0
- pytz=2019.1
- pyyaml=5.1
- pyzmq=18.0.1
- q2-alignment=2019.4.0
- q2-composition=2019.4.0
- q2-cutadapt=2019.4.0
- q2-dada2=2019.4.0
- q2-deblur=2019.4.0
- q2-demux=2019.4.1
- q2-diversity=2019.4.0
- q2-emperor=2019.4.0
- q2-feature-classifier=2019.4.0
- q2-feature-table=2019.4.0
- q2-fragment-insertion=2019.4.0
- q2-gneiss=2019.4.0
- q2-longitudinal=2019.4.0
- q2-metadata=2019.4.0
- q2-phylogeny=2019.4.0
- q2-quality-control=2019.4.0
- q2-quality-filter=2019.4.0
- q2-sample-classifier=2019.4.0
- q2-taxa=2019.4.0
- q2-types=2019.4.1
- q2-vsearch=2019.4.0
- q2cli=2019.4.0