Installation of qiime2 with Anaconda on Windows

Hi!

I have spent the last 3 years learning and practicing data analysis in Python to prepare myself to microbiome data analysis. I’m using Jupiter notebook via Anaconda on Windows. After gaining some experience with Biopython, I would like to start my journey with Qiime2.

Unfortunately, I failed to install qiime using osx/linux yml files found on Qiime2 site. Is it possible to use qiime as a Python library in Jupiter notebooks on Windows?

Hi @jakub.ruszkowski!

Wow!

What did you do? What kind of error did you see? Can you provide more details?

Yes, using a VM, or using the Windows Subsystem for Linux. I think there is a tutorial for WSL somewhere in this forum, give it a quick search!

:qiime2:

I downloaded yml files from Qiime2 site and tried to use them in terminal of Jupiter notebook :

PS C:\Users\jakub\Downloads> conda env create -n qiime2-2020.2 --file qiime2-2020.2-py36-linux-conda.yml
Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound:
  - q2-feature-classifier=2020.2.0
  - qiime2=2020.2.0
  - bioconductor-genomicalignments=1.18.1
  - bioconductor-zlibbioc=1.28.0
  - q2-deblur=2020.2.0
  - perl-scalar-list-utils=1.52
  - tktable=2.10
  - lcms2=2.9
  - perl-xsloader=0.24
  - binutils_impl_linux-64=2.33.1
  - gfortran_impl_linux-64=7.3.0
  - sortmerna=2.0
  - gxx_linux-64=7.3.0
  - perl-pathtools=3.75
  - perl-extutils-makemaker=7.36
  - _openmp_mutex=4.5
  - q2-quality-control=2020.2.0
  - gxx_impl_linux-64=7.3.0
  - bioconductor-shortread=1.40.0
  - readline=8.0
  - vsearch=2.7.0
  - q2-feature-table=2020.2.0
  - perl-compress-raw-bzip2=2.087
  - q2-longitudinal=2020.2.0
  - libgcc=7.2.0
  - perl-compress-raw-zlib=2.087
  - libuuid=2.32.1
  - q2-types=2020.2.0
  - perl-types-serialiser=1.0
  - libgcc-ng=9.2.0
  - blast=2.9.0
  - q2-diversity=2020.2.0
  - q2-phylogeny=2020.2.0
  - pango=1.40.14
  - perl-json=4.02
  - bioconductor-rsamtools=1.34.0
  - q2-metadata=2020.2.0
  - ncurses=6.1
  - fasttree=2.1.10
  - perl-io-zlib=1.10
  - libstdcxx-ng=9.2.0
  - perl-io-compress=2.087
  - libedit=3.1.20170329
  - q2-sample-classifier=2020.2.0
  - bioconductor-biobase=2.42.0
  - perl-common-sense=3.74
  - perl-list-moreutils-xs=0.428
  - scikit-bio=0.5.5
  - gst-plugins-base=1.14.5
  - q2-alignment=2020.2.0
  - perl-json-xs=2.34
  - libgfortran-ng=7.3.0
  - gmp=6.2.0
  - q2-cutadapt=2020.2.0
  - emperor=1.0.0
  - bioconductor-s4vectors=0.20.1
  - perl-exporter=5.72
  - bioconductor-dada2=1.10.0
  - q2-composition=2020.2.0
  - q2-gneiss=2020.2.0
  - bwidget=1.9.14
  - iqtree=1.6.12
  - libgomp=9.2.0
  - perl-exporter-tiny=1.002001
  - dnaio=0.4.1
  - bioconductor-biocparallel=1.16.6
  - q2-taxa=2020.2.0
  - q2cli=2020.2.0
  - gcc_impl_linux-64=7.3.0
  - sepp=4.3.10
  - gfortran_linux-64=7.3.0
  - bioconductor-delayedarray=0.8.0
  - dbus=1.13.6
  - ld_impl_linux-64=2.33.1
  - binutils_linux-64=2.33.1
  - unifrac=0.10.0
  - q2-demux=2020.2.0
  - perl-archive-tar=2.32
  - q2-quality-filter=2020.2.0
  - perl-list-moreutils=0.428
  - sina=1.6.0
  - q2-dada2=2020.2.0
  - bioconductor-genomicranges=1.34.0
  - hdmedians=0.13
  - bioconductor-xvector=0.22.0
  - bioconductor-biostrings=2.50.2
  - hmmer=3.1b2
  - libarbdb=6.0.6
  - arb-bio-tools=6.0.6
  - cutadapt=2.8
  - q2-fragment-insertion=2020.2.0
  - gcc_linux-64=7.3.0
  - alsa-lib=1.1.5
  - gnutls=3.6.5
  - mafft=7.310
  - raxml=8.2.12
  - bioconductor-iranges=2.16.0
  - nettle=3.4.1
  - perl-carp=1.38
  - q2-vsearch=2020.2.0
  - q2templates=2020.2.0
  - gstreamer=1.14.5
  - q2-emperor=2020.2.0

And:

PS C:\Users\jakub\Downloads> conda env update -f qiime2-2020.2-py36-osx-conda.yml
Collecting package metadata (repodata.json): done
Solving environment: failed

ResolvePackageNotFound:
  - dnaio=0.4.1
  - iqtree=1.6.12
  - readline=7.0
  - q2-demux=2020.2.0
  - bwidget=1.9.14
  - raxml=8.2.12
  - emperor=1.0.0
  - bioconductor-biostrings=2.50.2
  - q2-feature-table=2020.2.0
  - bioconductor-s4vectors=0.20.1
  - q2-vsearch=2020.2.0
  - bioconductor-biobase=2.42.0
  - pango=1.40.14
  - mafft=7.310
  - hmmer=3.1b2
  - unifrac=0.10.0
  - fasttree=2.1.10
  - q2-quality-control=2020.2.0
  - q2cli=2020.2.0
  - bioconductor-xvector=0.22.0
  - q2-alignment=2020.2.0
  - bioconductor-zlibbioc=1.28.0
  - libcxx=9.0.1
  - q2-emperor=2020.2.0
  - tktable=2.10
  - q2-dada2=2020.2.0
  - bioconductor-biocparallel=1.16.6
  - q2-phylogeny=2020.2.0
  - q2-diversity=2020.2.0
  - bioconductor-shortread=1.40.0
  - bioconductor-rsamtools=1.34.0
  - q2-gneiss=2020.2.0
  - sepp=4.3.10
  - libgcc=4.8.5
  - appnope=0.1.0
  - clang_osx-64=9.0.1
  - libgfortran=3.0.1
  - libedit=3.1.20170329
  - ncurses=6.1
  - libarbdb=6.0.6
  - bioconductor-dada2=1.10.0
  - tapi=1000.10.8
  - q2-types=2020.2.0
  - q2-cutadapt=2020.2.0
  - gfortran_osx-64=4.8.5
  - bioconductor-delayedarray=0.8.0
  - q2-deblur=2020.2.0
  - bioconductor-genomicalignments=1.18.1
  - q2-metadata=2020.2.0
  - bioconductor-genomicranges=1.34.0
  - ld64=450.3
  - qiime2=2020.2.0
  - q2-quality-filter=2020.2.0
  - cutadapt=2.8
  - sortmerna=2.0
  - clangxx_osx-64=9.0.1
  - cctools=927.0.2
  - hdmedians=0.13
  - blast=2.6.0
  - q2-composition=2020.2.0
  - arb-bio-tools=6.0.6
  - bioconductor-iranges=2.16.0
  - q2-feature-classifier=2020.2.0
  - q2-fragment-insertion=2020.2.0
  - q2-longitudinal=2020.2.0
  - q2-sample-classifier=2020.2.0
  - q2templates=2020.2.0
  - sina=1.4.0
  - scikit-bio=0.5.5
  - q2-taxa=2020.2.0
  - vsearch=2.7.0

I used to try to use VirtualBox but it was very slow. The fact that I’m currently using better hardware so it should work better… Thank you for the recommendation of WSL! I’ll try :slight_smile:

Thanks for explaining - the commands you showed above aren't expected to work on a vanilla windows host - you will need to use the WSL or another VM.

:qiime2: