Can you create an instruction on how to setup Qiime on Google Colab? I found this fantastic tutorial from Gibbons Lab. Because I don't know how I often this tutorial will be maintained, I borrowed their setup file and created my own Google Colab setup (see the ipbynb file attached).
It would be nice if something like this can be attached on the Qiime website and be maintained. qiime setup.zip (4.1 KB)
Thanks for the suggestion, @Evil_Puppy! I don't think we have any Google Colab experts on the team, perhaps @seangibbons (I'm assuming this is the same Gibbons Lab referenced above) would be interested in contributing a Community Tutorial here on the forum? Thanks!
:qiime2:
I'm looping in @cdiener who put together that Colab tutorial 
Hi,
The script on Github is maintained. For instance, I just pushed fixes a few days ago.
So running the following in colab should be enough:
!wget https://github.com/Gibbons-Lab/isb_course_2021/raw/main/setup_qiime2
%run setup_qiime2
I do think it is a good idea to port it to its own repository to make it easier to use and more maintainable.
This should work in general with the exception of plugins in the Python interface (things like from qiime2.plugins import feature_table won't work since the notebook runs Python 3.7). Plugins will work in the command line interface though.
Hi,
I wanted to use the most updated version of your course on "Qiime2 with Google Colab", from here:isb_course_2023/16S_2023_solutions.ipynb at main · Gibbons-Lab/isb_course_2023 · GitHub
I faced the following error:
FileNotFoundError: [Errno 2] No such file or directory: 'mamba'
Could you please help me with that?
Thanks a lot,
Sara
Hi @smashha,
What line of the Notebook are you running when you get this error?
Hi,
I used this three command, in three different command cell:
!git clone GitHub - Gibbons-Lab/isb_course_2023: Materials and presentation for the 2023 ISB Microbiome course. materials
%cd materials
%run setup_qiime2
I faced an error after the third one.
Thanks
Sara
Hi,
I tried to use the main code, which it is here:
isb_course_2023/setup_qiime2 at main · Gibbons-Lab/isb_course_2023 · GitHub
and it worked well. I installed it.
Dear all,
I am trying to install qiime2 on google colab using ISB microbiome 2023, yet an error arose while setting up qiime2 command!. any ideas ?
Much appreciated
Hi @Ktalaat55, Did you try the code referred to in this post? Please try that and follow up with specific details on the error message that you're receiving if it didn't/doesn't work by copy/pasting the command that you ran and the error message that it generated.
Hi greg,
thanks for your reply. yes I tried the code and the error was
[20:34:29] could not install Qiime 2 
:60
Looking for: ['_libgcc_mutex=0.1', '_openmp_mutex=4.5',
'_r-mutex=1.0.1', 'alsa-lib=1...........
Hi @cdiener or @seangibbons ,
Do y'all have any ideas what is going on here?
Hmm looks like the env files for 2023.7 are broken, at least with mamba. I will try to update to the new versions.
Here is the full log:
Looking for: ['_libgcc_mutex=0.1', '_openmp_mutex=4.5', '_r-mutex=1.0.1',
'alsa-lib=1.2.8', 'altair=5.0.1', 'anyio=3.7.1', 'appdirs=1.4.4', 'argcomplete=3.1.1',
'argon2-cffi=23.1.0', 'argon2-cffi-bindings=21.2.0', 'arrow=1.2.3', 'astor=0.8.1',
'asttokens=2.2.1', 'atpublic=3.0.1', 'attr=2.5.1', 'attrs=23.1.0', 'backcall=0.2.0',
'backports=1.0', 'backports.functools_lru_cache=1.6.5', 'bcrypt=3.2.2',
'beautifulsoup4=4.12.2', 'bibtexparser=1.4.0', 'binutils_impl_linux-64=2.40',
'bioconductor-ancombc=2.0.1', 'bioconductor-beachmat=2.14.0',
'bioconductor-biobase=2.58.0', 'bioconductor-biocbaseutils=1.0.0',
'bioconductor-biocgenerics=0.44.0', 'bioconductor-biocneighbors=1.16.0',
'bioconductor-biocparallel=1.32.5', 'bioconductor-biocsingular=1.14.0',
'bioconductor-biomformat=1.26.0', 'bioconductor-biostrings=2.66.0',
'bioconductor-dada2=1.26.0', 'bioconductor-data-packages=20230718',
'bioconductor-decipher=2.26.0', 'bioconductor-decontam=1.18.0',
'bioconductor-delayedarray=0.24.0', 'bioconductor-delayedmatrixstats=1.20.0',
'bioconductor-dirichletmultinomial=1.40.0', 'bioconductor-genomeinfodb=1.34.9',
'bioconductor-genomeinfodbdata=1.2.9', 'bioconductor-genomicalignments=1.34.0',
'bioconductor-genomicranges=1.50.0', 'bioconductor-iranges=2.32.0',
'bioconductor-matrixgenerics=1.10.0', 'bioconductor-mia=1.6.0',
'bioconductor-multiassayexperiment=1.24.0', 'bioconductor-multtest=2.54.0',
'bioconductor-phyloseq=1.42.0', 'bioconductor-rhdf5=2.42.0',
'bioconductor-rhdf5filters=1.10.0', 'bioconductor-rhdf5lib=1.20.0',
'bioconductor-rhtslib=2.0.0', 'bioconductor-rsamtools=2.14.0',
'bioconductor-s4vectors=0.36.0', 'bioconductor-scaledmatrix=1.6.0',
'bioconductor-scater=1.26.0', 'bioconductor-scuttle=1.8.0',
'bioconductor-shortread=1.56.0', 'bioconductor-singlecellexperiment=1.20.0',
'bioconductor-sparsematrixstats=1.10.0', 'bioconductor-summarizedexperiment=1.28.0',
'bioconductor-treeio=1.22.0', 'bioconductor-treesummarizedexperiment=2.6.0',
'bioconductor-xvector=0.38.0', 'bioconductor-zlibbioc=1.44.0', 'biom-format=2.1.14',
'blast=2.14.1', 'bleach=6.0.0', 'bokeh=3.1.1', 'bowtie2=2.5.1', 'brotli=1.0.9',
'brotli-bin=1.0.9', 'brotli-python=1.0.9', 'bwidget=1.9.14', 'bzip2=1.0.8',
'c-ares=1.19.1', 'ca-certificates=2023.7.22', 'cachecontrol=0.13.1',
'cached-property=1.5.2', 'cached_property=1.5.2', 'cairo=1.16.0', 'certifi=2023.7.22',
'cffi=1.15.1', 'charset-normalizer=3.2.0', 'click=8.1.7', 'colorama=0.4.6',
'comm=0.1.4', 'conda-pack=0.7.0', 'contourpy=1.1.0', 'cryptography=39.0.0',
'curl=7.88.1', 'cutadapt=4.4', 'cycler=0.11.0', 'cython=3.0.2', 'dbus=1.13.6',
'deblur=1.1.1', 'debugpy=1.6.8', 'decorator=4.4.2', 'defusedxml=0.7.1',
'dendropy=4.5.2', 'dill=0.3.7', 'dnaio=0.10.0', 'emperor=1.0.3', 'entrez-direct=16.2',
'entrypoints=0.4', 'exceptiongroup=1.1.3', 'executing=1.2.0', 'expat=2.5.0',
'fastcluster=1.2.6', 'fasttree=2.1.11', 'fftw=3.3.10', 'flufl.lock=7.1',
'font-ttf-dejavu-sans-mono=2.37', 'font-ttf-inconsolata=3.000',
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'fonts-conda-ecosystem=1', 'fonts-conda-forge=1', 'fonttools=4.42.1', 'formulaic=0.6.4',
'fqdn=1.5.1', 'freetype=2.12.1', 'fribidi=1.0.10', 'future=0.18.3',
'gcc_impl_linux-64=13.1.0', 'gettext=0.21.1', 'gfortran_impl_linux-64=13.1.0',
'giflib=5.2.1', 'glib=2.76.4', 'glib-tools=2.76.4', 'globus-sdk=3.27.0', 'glpk=5.0',
'gmp=6.2.1', 'gneiss=0.4.6', 'graphite2=1.3.13', 'graphlib-backport=1.0.3', 'gsl=2.7',
'gst-plugins-base=1.21.3', 'gstreamer=1.21.3', 'gstreamer-orc=0.4.34',
'gxx_impl_linux-64=13.1.0', 'h5py=3.8.0', 'harfbuzz=6.0.0', 'hdf5=1.14.0',
'hdmedians=0.14.2', 'hmmer=3.1b2', 'htslib=1.17', 'icu=70.1', 'idna=3.4', 'ijson=3.2.3',
'importlib-metadata=6.8.0', 'importlib_resources=6.0.1', 'iniconfig=2.0.0',
'interface_meta=1.3.0', 'iow=1.0.5', 'ipykernel=6.25.1', 'ipython=8.12.2',
'ipython_genutils=0.2.0', 'ipywidgets=8.1.0', 'iqtree=2.2.3', 'isa-l=2.30.0',
'isoduration=20.11.0', 'jack=1.9.22', 'jedi=0.19.0', 'jinja2=3.1.2', 'joblib=1.3.2',
'jpeg=9e', 'jq=1.6', 'jsonpointer=2.0', 'jsonschema=4.19.0',
'jsonschema-specifications=2023.7.1', 'jsonschema-with-format-nongpl=4.19.0',
'jupyter_client=7.4.9', 'jupyter_core=5.3.0', 'jupyter_events=0.7.0',
'jupyter_server=2.7.1', 'jupyter_server_terminals=0.4.4', 'jupyterlab_pygments=0.2.2',
'jupyterlab_widgets=3.0.8', 'kernel-headers_linux-64=2.6.32', 'keyutils=1.6.1',
'kiwisolver=1.4.5', 'krb5=1.20.1', 'lame=3.100', 'lcms2=2.15', 'ld_impl_linux-64=2.40',
'lerc=4.0.0', 'libaec=1.0.6', 'libblas=3.9.0', 'libbrotlicommon=1.0.9',
'libbrotlidec=1.0.9', 'libbrotlienc=1.0.9', 'libcap=2.66', 'libcblas=3.9.0',
'libclang=15.0.7', 'libclang13=15.0.7', 'libcups=2.3.3', 'libcurl=7.88.1',
'libdb=6.2.32', 'libdeflate=1.17', 'libedit=3.1.20191231', 'libev=4.33',
'libevent=2.1.10', 'libexpat=2.5.0', 'libffi=3.4.2', 'libflac=1.4.3',
'libgcc-devel_linux-64=13.1.0', 'libgcc-ng=13.1.0', 'libgcrypt=1.10.1',
'libgfortran-ng=13.1.0', 'libgfortran5=13.1.0', 'libglib=2.76.4', 'libgomp=13.1.0',
'libgpg-error=1.47', 'libhwloc=2.9.1', 'libiconv=1.17', 'libidn2=2.3.4',
'liblapack=3.9.0', 'liblapacke=3.9.0', 'libllvm14=14.0.6', 'libllvm15=15.0.7',
'libnghttp2=1.52.0', 'libnsl=2.0.0', 'libogg=1.3.4', 'libopenblas=0.3.23',
'libopus=1.3.1', 'libpng=1.6.39', 'libpq=15.1', 'libsanitizer=13.1.0',
'libsndfile=1.2.2', 'libsodium=1.0.18', 'libsqlite=3.43.0', 'libssh2=1.10.0',
'libstdcxx-devel_linux-64=13.1.0', 'libstdcxx-ng=13.1.0', 'libsystemd0=252',
'libtiff=4.5.0', 'libtool=2.4.7', 'libudev1=253', 'libunistring=0.9.10',
'libuuid=2.38.1', 'libvorbis=1.3.7', 'libwebp-base=1.3.1', 'libxcb=1.13',
'libxkbcommon=1.5.0', 'libxml2=2.10.3', 'libxslt=1.1.37', 'libzlib=1.2.13',
'llvmlite=0.40.1', 'lockfile=0.12.2', 'lxml=4.9.2', 'lz4=4.3.2', 'lz4-c=1.9.4',
'mafft=7.520', 'make=4.3', 'markupsafe=2.1.3', 'matplotlib=3.6.0',
'matplotlib-base=3.6.0', 'matplotlib-inline=0.1.6', 'mistune=3.0.1', 'mpfr=4.2.0',
'mpg123=1.31.3', 'msgpack-python=1.0.5', 'munkres=1.1.4', 'mypy=1.5.1',
'mypy_extensions=1.0.0', 'mysql-common=8.0.32', 'mysql-libs=8.0.32', 'natsort=8.4.0',
'nbclassic=1.0.0', 'nbclient=0.8.0', 'nbconvert=7.7.4', 'nbconvert-core=7.7.4',
'nbconvert-pandoc=7.7.4', 'nbformat=5.9.2', 'ncbi-vdb=3.0.0', 'ncurses=6.4',
'nest-asyncio=1.5.6', 'networkx=3.1', 'nlopt=2.7.1', 'nose=1.3.7', 'notebook=6.5.5',
'notebook-shim=0.2.3', 'nspr=4.35', 'nss=3.92', 'numba=0.57.1', 'numpy=1.24.4',
'oniguruma=6.9.8', 'openjdk=17.0.3', 'openjpeg=2.5.0', 'openssl=1.1.1v',
'overrides=7.4.0', 'packaging=23.1', 'pandas=1.5.3', 'pandoc=3.1.3',
'pandocfilters=1.5.0', 'pango=1.50.14', 'paramiko=3.3.1', 'parsl=2023.8.28',
'parso=0.8.3', 'patsy=0.5.3', 'pbzip2=1.1.13', 'pcre=8.45', 'pcre2=10.40',
'perl=5.32.1', 'perl-archive-tar=2.40', 'perl-carp=1.50', 'perl-common-sense=3.75',
'perl-compress-raw-bzip2=2.201', 'perl-compress-raw-zlib=2.202', 'perl-encode=3.19',
'perl-exporter=5.74', 'perl-exporter-tiny=1.002002', 'perl-extutils-makemaker=7.70',
'perl-io-compress=2.201', 'perl-io-zlib=1.14', 'perl-json=4.10', 'perl-json-xs=2.34',
'perl-list-moreutils=0.430', 'perl-list-moreutils-xs=0.430', 'perl-parent=0.241',
'perl-pathtools=3.75', 'perl-scalar-list-utils=1.63', 'perl-storable=3.15',
'perl-types-serialiser=1.01', 'pexpect=4.8.0', 'pickleshare=0.7.5', 'pigz=2.6',
'pillow=9.4.0', 'pip=23.2.1', 'pixman=0.40.0', 'pkgutil-resolve-name=1.3.10',
'platformdirs=3.10.0', 'pluggy=1.3.0', 'ply=3.11', 'pooch=1.7.0',
'prometheus_client=0.17.1', 'prompt-toolkit=3.0.39', 'prompt_toolkit=3.0.39',
'provenance-lib=2023.7.1', 'psutil=5.9.5', 'pthread-stubs=0.4', 'ptyprocess=0.7.0',
'pulseaudio=16.1', 'pure_eval=0.2.2', 'pycparser=2.21', 'pygments=2.16.1',
'pyjwt=2.8.0', 'pynacl=1.5.0', 'pynndescent=0.5.10', 'pyparsing=3.1.1', 'pyqt=5.15.7',
'pyqt5-sip=12.11.0', 'pysocks=1.7.1', 'pytest=7.4.0', 'python=3.8.15',
'python-dateutil=2.8.2', 'python-fastjsonschema=2.18.0', 'python-isal=1.2.0',
'python-json-logger=2.0.7', 'python_abi=3.8', 'pytz=2023.3', 'pyyaml=6.0.1',
'pyzmq=24.0.1', 'q2-alignment=2023.7.0', 'q2-composition=2023.7.0',
'q2-cutadapt=2023.7.0', 'q2-dada2=2023.7.0', 'q2-deblur=2023.7.0', 'q2-demux=2023.7.0',
'q2-diversity=2023.7.0', 'q2-diversity-lib=2023.7.0', 'q2-emperor=2023.7.0',
'q2-feature-classifier=2023.7.0', 'q2-feature-table=2023.7.0',
'q2-fragment-insertion=2023.7.0', 'q2-gneiss=2023.7.0', 'q2-longitudinal=2023.7.0',
'q2-metadata=2023.7.0', 'q2-mystery-stew=2023.7.0', 'q2-phylogeny=2023.7.0',
'q2-quality-control=2023.7.0', 'q2-quality-filter=2023.7.0',
'q2-sample-classifier=2023.7.0', 'q2-taxa=2023.7.0', 'q2-types=2023.7.0',
'q2-vsearch=2023.7.0', 'q2cli=2023.7.0', 'q2galaxy=2023.7.0', 'q2templates=2023.7.0',
'qiime2=2023.7.0', 'qt-main=5.15.6', 'r-ade4=1.7_22', 'r-ape=5.7_1', 'r-askpass=1.1',
'r-assertthat=0.2.1', 'r-backports=1.4.1', 'r-base=4.2.2', 'r-base64enc=0.1_3',
'r-beeswarm=0.4.0', 'r-bh=1.81.0_1', 'r-bibtex=0.5.1', 'r-bit=4.0.5', 'r-bit64=4.0.5',
'r-bitops=1.0_7', 'r-blob=1.2.4', 'r-boot=1.3_28.1', 'r-broom=1.0.5', 'r-bslib=0.5.1',
'r-cachem=1.0.8', 'r-cairo=1.6_0', 'r-callr=3.7.3', 'r-cellranger=1.1.0',
'r-checkmate=2.2.0', 'r-class=7.3_22', 'r-cli=3.6.1', 'r-clipr=0.8.0',
'r-cluster=2.1.4', 'r-codetools=0.2_19', 'r-colorspace=2.1_0', 'r-conflicted=1.2.0',
'r-cpp11=0.4.6', 'r-crayon=1.5.2', 'r-curl=4.3.3', 'r-cvxr=1.0_11',
'r-data.table=1.14.8', 'r-dbi=1.1.3', 'r-dbplyr=2.3.3', 'r-deldir=1.0_9',
'r-desctools=0.99.49', 'r-digest=0.6.33', 'r-doparallel=1.0.17', 'r-dorng=1.8.6',
'r-dplyr=1.1.2', 'r-dqrng=0.3.0', 'r-dtplyr=1.3.1', 'r-e1071=1.7_13',
'r-ecosolver=0.5.5', 'r-ellipsis=0.3.2', 'r-emmeans=1.8.8', 'r-energy=1.7_11',
'r-estimability=1.4.1', 'r-evaluate=0.21', 'r-exact=3.2', 'r-expm=0.999_7',
'r-fansi=1.0.4', 'r-farver=2.1.1', 'r-fastmap=1.1.1', 'r-fnn=1.1.3.2',
'r-fontawesome=0.5.2', 'r-forcats=1.0.0', 'r-foreach=1.5.2', 'r-foreign=0.8_84',
'r-formatr=1.14', 'r-formula=1.2_5', 'r-frictionless=1.0.2', 'r-fs=1.6.3',
'r-futile.logger=1.4.3', 'r-futile.options=1.0.1', 'r-gargle=1.5.2', 'r-gbrd=0.4_11',
'r-generics=0.1.3', 'r-getopt=1.20.3', 'r-ggbeeswarm=0.7.2', 'r-ggplot2=3.4.3',
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'r-gtable=0.3.4', 'r-haven=2.5.3', 'r-highr=0.10', 'r-hmisc=5.1_0', 'r-hms=1.1.3',
'r-htmltable=2.4.1', 'r-htmltools=0.5.6', 'r-htmlwidgets=1.6.2', 'r-httr=1.4.7',
'r-hwriter=1.3.2.1', 'r-ids=1.0.1', 'r-igraph=1.4.2', 'r-interp=1.1_4',
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'r-lambda.r=1.2.4', 'r-lattice=0.21_8', 'r-latticeextra=0.6_30', 'r-lazyeval=0.2.2',
'r-lifecycle=1.0.3', 'r-lme4=1.1_34', 'r-lmertest=3.1_3', 'r-lmom=3.0',
'r-lubridate=1.9.2', 'r-magrittr=2.0.3', 'r-mass=7.3_60', 'r-matrix=1.6_1',
'r-matrixstats=1.0.0', 'r-memoise=2.0.1', 'r-mgcv=1.9_0', 'r-mime=0.12',
'r-minqa=1.2.5', 'r-modelr=0.1.11', 'r-munsell=0.5.0', 'r-mvtnorm=1.2_3',
'r-nlme=3.1_163', 'r-nloptr=2.0.3', 'r-nnet=7.3_19', 'r-numderiv=2016.8_1.1',
'r-openssl=2.0.5', 'r-optparse=1.7.3', 'r-osqp=0.6.0.8', 'r-permute=0.9_7',
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'r-ps=1.7.5', 'r-purrr=1.0.1', 'r-r6=2.5.1', 'r-ragg=1.2.5', 'r-rappdirs=0.3.3',
'r-rbibutils=2.2.15', 'r-rcolorbrewer=1.1_3', 'r-rcpp=1.0.11', 'r-rcppannoy=0.0.21',
'r-rcppeigen=0.3.3.9.3', 'r-rcpphnsw=0.4.1', 'r-rcppml=0.3.7', 'r-rcppparallel=5.1.6',
'r-rcppprogress=0.4.2', 'r-rcurl=1.98_1.12', 'r-rdpack=2.5', 'r-readr=2.1.4',
'r-readxl=1.4.3', 'r-registry=0.5_1', 'r-rematch=1.0.1', 'r-rematch2=2.1.2',
'r-reprex=2.0.2', 'r-reshape2=1.4.4', 'r-rlang=1.1.1', 'r-rmarkdown=2.24',
'r-rmpfr=0.9_3', 'r-rngtools=1.5.2', 'r-rootsolve=1.8.2.3', 'r-rpart=4.1.19',
'r-rsqlite=2.3.1', 'r-rstudioapi=0.15.0', 'r-rsvd=1.0.5', 'r-rtsne=0.16',
'r-rvest=1.0.3', 'r-sass=0.4.7', 'r-scales=1.2.1', 'r-scs=3.2.4', 'r-selectr=0.4_2',
'r-sitmo=2.0.2', 'r-snow=0.4_4', 'r-sp=2.0_0', 'r-statmod=1.5.0', 'r-stringi=1.7.12',
'r-stringr=1.5.0', 'r-survival=3.5_7', 'r-sys=3.4.2', 'r-systemfonts=1.0.4',
'r-textshaping=0.3.6', 'r-tibble=3.2.1', 'r-tidyr=1.3.0', 'r-tidyselect=1.2.0',
'r-tidytree=0.4.5', 'r-tidyverse=2.0.0', 'r-timechange=0.2.0', 'r-tinytex=0.46',
'r-tzdb=0.4.0', 'r-utf8=1.2.3', 'r-uuid=1.1_1', 'r-uwot=0.1.16', 'r-vctrs=0.6.3',
'r-vegan=2.6_4', 'r-vipor=0.4.5', 'r-viridis=0.6.4', 'r-viridislite=0.4.2',
'r-vroom=1.6.3', 'r-withr=2.5.0', 'r-xfun=0.40', 'r-xml2=1.3.3', 'r-xtable=1.8_4',
'r-yaml=2.3.7', 'r-yulab.utils=0.0.8', 'raxml=8.2.12', 'readline=8.2',
'referencing=0.30.2', 'requests=2.31.0', 'rfc3339-validator=0.1.4',
'rfc3986-validator=0.1.1', 'rpds-py=0.10.0', 'samtools=1.17', 'scikit-bio=0.5.8',
'scikit-learn=0.24.1', 'scipy=1.10.0', 'seaborn=0.12.2', 'seaborn-base=0.12.2',
'sed=4.8', 'send2trash=1.8.2', 'sepp=4.3.10', 'setproctitle=1.3.2', 'setuptools=68.1.2',
'sip=6.7.11', 'six=1.16.0', 'sniffio=1.3.0', 'sortmerna=2.0', 'soupsieve=2.3.2.post1',
'stack_data=0.6.2', 'statsmodels=0.14.0', 'sysroot_linux-64=2.12', 'tbb=2021.9.0',
'tblib=1.7.0', 'terminado=0.17.1', 'threadpoolctl=3.2.0', 'tinycss2=1.2.1', 'tk=8.6.12',
'tktable=2.10', 'toml=0.10.2', 'tomli=2.0.1', 'tomlkit=0.12.1', 'toolz=0.12.0',
'tornado=6.3.3', 'tqdm=4.66.1', 'traitlets=5.9.0', 'typeguard=2.13.3',
'typing-extensions=4.7.1', 'typing_extensions=4.7.1', 'typing_utils=0.1.0',
'tzlocal=2.1', 'umap-learn=0.5.3', 'unicodedata2=15.0.0', 'unifrac=1.3',
'unifrac-binaries=1.3.1', 'uri-template=1.3.0', 'urllib3=2.0.4', 'vsearch=2.22.1',
'wcwidth=0.2.6', 'webcolors=1.13', 'webencodings=0.5.1', 'websocket-client=1.6.2',
'wget=1.20.3', 'wheel=0.41.2', 'widgetsnbextension=4.0.8', 'wrapt=1.15.0',
'xcb-util=0.4.0', 'xcb-util-image=0.4.0', 'xcb-util-keysyms=0.4.0',
'xcb-util-renderutil=0.3.9', 'xcb-util-wm=0.4.1', 'xkeyboard-config=2.38',
'xmltodict=0.13.0', 'xopen=1.7.0', '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=1.8.4',
'xorg-libxau=1.0.11', '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=1.3.0', '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',
'xyzservices=2023.7.0', 'xz=5.2.6', 'yaml=0.2.5', 'yq=3.2.2', 'zeromq=4.3.4',
'zipp=3.16.2', 'zlib=1.2.13', 'zstandard=0.19.0', 'zstd=1.5.5']
Could not solve for environment specs
The following packages are incompatible
├─ fontconfig 2.14.2** is installable and it requires
│ └─ libuuid >=2.32.1,<3.0a0 , which can be installed;
├─ libffi 3.4.2** is requested and can be installed;
├─ libsqlite 3.43.0** is requested and can be installed;
├─ ncurses 6.4** is requested and can be installed;
├─ openssl 1.1.1v** is requested and can be installed;
├─ python 3.8.15** is installable with the potential options
│ ├─ python [3.10.7|3.10.8|3.10.9|3.11.0|3.8.15] would require
│ │ └─ openssl >=3.0.7,<4.0a0 , which conflicts with any installable versions
previously reported;
│ └─ python 3.8.15, which can be installed;
└─ truststore is not installable because there are no viable options
├─ truststore [0.7.0|0.8.0] would require
│ └─ python >=3.10 but there are no viable options
│ ├─ python [3.10.0|3.10.1|3.10.2] would require
│ │ └─ openssl >=3.0.0,<4.0a0 , which conflicts with any installable versions
previously reported;
│ ├─ python [3.10.0|3.10.1|...|3.10.8] conflicts with any installable versions
previously reported;
│ ├─ python 3.10.2 would require
│ │ └─ ncurses >=6.2,<6.3.0a0 , which conflicts with any installable versions
previously reported;
│ ├─ python 3.10.4 would require
│ │ └─ openssl >=3.0.2,<4.0a0 , which conflicts with any installable versions
previously reported;
│ ├─ python 3.10.5 would require
│ │ └─ openssl >=3.0.3,<4.0a0 , which conflicts with any installable versions
previously reported;
│ ├─ python [3.10.6|3.11.0] would require
│ │ └─ openssl >=3.0.5,<4.0a0 , which conflicts with any installable versions
previously reported;
│ ├─ python 3.11.0 conflicts with any installable versions previously reported;
│ ├─ python [3.10.10|3.10.11|3.11.1|3.11.2|3.11.3] would require
│ │ └─ openssl >=3.1.0,<4.0a0 , which conflicts with any installable versions
previously reported;
│ ├─ python [3.10.12|3.11.4] would require
│ │ └─ openssl >=3.1.1,<4.0a0 , which conflicts with any installable versions
previously reported;
│ ├─ python 3.10.13 would require
│ │ └─ libsqlite >=3.43.2,<4.0a0 , which conflicts with any installable versions
previously reported;
│ ├─ python [3.10.13|3.11.7|3.12.1] would require
│ │ └─ libsqlite >=3.44.2,<4.0a0 , which conflicts with any installable versions
previously reported;
│ ├─ python [3.10.7|3.10.8|3.10.9|3.11.0|3.8.15], which cannot be installed (as
previously explained);
│ ├─ python 3.11.5 would require
│ │ └─ openssl >=3.1.2,<4.0a0 , which conflicts with any installable versions
previously reported;
│ ├─ python [3.11.6|3.12.0] would require
│ │ └─ openssl >=3.1.3,<4.0a0 , which conflicts with any installable versions
previously reported;
│ ├─ python 3.12.0rc3 would require
│ │ └─ _python_rc, which does not exist (perhaps a missing channel);
│ ├─ python [3.10.0|3.10.3|3.10.4|3.10.6|3.10.8] would require
│ │ └─ libffi >=3.3,<3.4.0a0 , which conflicts with any installable versions
previously reported;
│ └─ python [3.10.10|3.10.11|...|3.12.1] would require
│ └─ libuuid >=1.41.5,<2.0a0 , which conflicts with any installable versions
previously reported;
├─ truststore 0.8.0 would require
│ └─ python >=3.10,<3.11.0a0 but there are no viable options
│ ├─ python [3.10.0|3.10.1|3.10.2], which cannot be installed (as previously
explained);
│ ├─ python [3.10.0|3.10.1|...|3.10.8] conflicts with any installable versions
previously reported;
│ ├─ python 3.10.2, which cannot be installed (as previously explained);
│ ├─ python 3.10.4, which cannot be installed (as previously explained);
│ ├─ python 3.10.5, which cannot be installed (as previously explained);
│ ├─ python [3.10.6|3.11.0], which cannot be installed (as previously explained);
│ ├─ python [3.10.10|3.10.11|3.11.1|3.11.2|3.11.3], which cannot be installed (as
previously explained);
│ ├─ python [3.10.12|3.11.4], which cannot be installed (as previously
explained);
│ ├─ python 3.10.13, which cannot be installed (as previously explained);
│ ├─ python [3.10.13|3.11.7|3.12.1], which cannot be installed (as previously
explained);
│ ├─ python [3.10.7|3.10.8|3.10.9|3.11.0|3.8.15], which cannot be installed (as
previously explained);
│ ├─ python [3.10.0|3.10.3|3.10.4|3.10.6|3.10.8], which cannot be installed (as
previously explained);
│ └─ python [3.10.10|3.10.11|...|3.12.1], which cannot be installed (as
previously explained);
├─ truststore 0.8.0 would require
│ └─ python >=3.11,<3.12.0a0 but there are no viable options
│ ├─ python [3.10.6|3.11.0], which cannot be installed (as previously explained);
│ ├─ python 3.11.0 conflicts with any installable versions previously reported;
│ ├─ python [3.10.10|3.10.11|3.11.1|3.11.2|3.11.3], which cannot be installed (as
previously explained);
│ ├─ python [3.10.12|3.11.4], which cannot be installed (as previously
explained);
│ ├─ python [3.10.13|3.11.7|3.12.1], which cannot be installed (as previously
explained);
│ ├─ python [3.10.7|3.10.8|3.10.9|3.11.0|3.8.15], which cannot be installed (as
previously explained);
│ ├─ python 3.11.5, which cannot be installed (as previously explained);
│ ├─ python [3.11.6|3.12.0], which cannot be installed (as previously explained);
│ └─ python [3.10.10|3.10.11|...|3.12.1], which cannot be installed (as
previously explained);
└─ truststore 0.8.0 would require
└─ python >=3.12,<3.13.0a0 , which cannot be installed (as previously explained).
Hi @cdiener,
It might have something to do with this: Recommendations for installing older versions of QIIME 2. I am not sure!
Thanks for the help @cdiener
@cherman2 Yeah I guess so, though it's a bit odd because the same env worked with mamba before.
Okay, that one was a weird one. Had nothing to do with libmamba in the end. The script usually updates a conda base environment with the Qiime2 distribution. That's not possible anymore because conda and mamba now require python>=3.10 (due to trustdb dependency) so the environment update would fail.
I deployed a fix to the github repo so the updated script should work again. I ran the 2023 course materials and they worked fine.
Thank you so much for your work on this @cdiener!
Thank you so much for your help
An off-topic reply has been split into a new topic: generate taxa-stacked bar plots
Please keep replies on-topic in the future.
Hello everyone,
I am new with bioinformatics and I'm trying to work Qiime2 in Google Colab. I am trying other options to run my 16S sequencing apart from the terminal in local computer.
However, the codes to install Qiime2 in Colab (isb_course_2023/setup_qiime2 at main · Gibbons-Lab/isb_course_2023 · GitHub) are not running well for me. Perhaps I'm doing something wrong...
The error message that I get is:
An exception has occurred, use %tb to see the full traceback.
SystemExit: 1
/usr/local/lib/python3.10/dist-packages/IPython/core/interactiveshell.py:3561: UserWarning: To exit: use 'exit', 'quit', or Ctrl-D.
** warn("To exit: use 'exit', 'quit', or Ctrl-D.", stacklevel=1)**
and when I use %tb:
/usr/local/lib/python3.10/dist-packages/IPython/core/magics/execution.py:508: UserWarning: Error changing user exception modes.
Unrecognized mode in FormattedTB: <Setup_qiime2>
Valid modes: ['Plain', 'Context', 'Verbose', 'Minimal']
** warn('Error changing %s exception modes.\n%s' %**
Could someone explain me what is the issue?
I appreciate your help!!!!