Dear all,
I am the beginner of bioinformatic and Mac user.
I have been trying to install QIIME2 on my new computer (Mac book pro, M1 max).
Before install, I also install Miniconda3 (Miniconda3 macOS Apple M1 64-bit bash; Python 3.9.12), and wget.
Then, I tried to starting to QIIME2 installation such as following:
a) wget https://data.qiime2.org/distro/core/qiime2-2022.8-py38-osx-conda.yml —> the result was good.
(base) ~Mac Downloads % conda env create -n qiime2-2022.8 --file qiime2-2022.8-py38-osx-conda.yml
Collecting package metadata (repodata.json): done
Solving environment: failed
ResolvePackageNotFound:
perl-compress-raw-bzip2=2.201
xopen=1.6.0
qiime2=2022.8.3
emperor=1.0.3
q2galaxy=2022.8.1
q2-diversity-lib=2022.8.0
htslib=1.15.1
fasttree=2.1.11
r-interp=1.1_3
biom-format=2.1.12
q2-composition=2022.8.0
bioconductor-dada2=1.22.0
q2-gneiss=2022.8.0
perl-encode=3.19
sepp=4.3.10
blast=2.12.0
q2-dada2=2022.8.0
samtools=1.15.1
entrez-direct=16.2
gfortran_impl_osx-64=9.5.0
iqtree=2.2.0.3
r-rcurl=1.98_1.8
scikit-bio=0.5.7
perl-json-xs=2.34
iow=1.0.5
bioconductor-delayedarray=0.20.0
unifrac=1.1.1
cutadapt=4.1
perl-scalar-list-utils=1.63
perl-pathtools=3.75
q2-metadata=2022.8.0
bioconductor-genomicranges=1.46.1
mafft=7.505
q2-taxa=2022.8.0
vsearch=2.21.1
q2-feature-classifier=2022.8.0
sortmerna=2.0
q2-mystery-stew=2022.8.0
bioconductor-zlibbioc=1.40.0
isa-l=2.30.0
q2-fragment-insertion=2022.8.0
raxml=8.2.12
python-isal=1.0.1
r-jpeg=0.1_9
q2-alignment=2022.8.0
r-vegan=2.6_2
bioconductor-rhtslib=1.26.0
q2-deblur=2022.8.0
q2cli=2022.8.0
pbzip2=1.1.13
bioconductor-biocparallel=1.28.3
gfortran_osx-64=9.5.0
bioconductor-s4vectors=0.32.3
q2-cutadapt=2022.8.0
bioconductor-xvector=0.34.0
q2-longitudinal=2022.8.0
q2-demux=2022.8.0
bowtie2=2.4.5
fastcluster=1.2.6
bioconductor-shortread=1.52.0
bioconductor-genomicalignments=1.30.0
q2-sample-classifier=2022.8.0
q2-diversity=2022.8.0
q2-emperor=2022.8.0
q2-phylogeny=2022.8.0
bioconductor-iranges=2.28.0
perl-compress-raw-zlib=2.202
hmmer=3.1b2
q2-quality-filter=2022.8.0
q2templates=2022.8.0
perl-list-moreutils-xs=0.430
q2-vsearch=2022.8.0
bioconductor-biostrings=2.62.0
q2-types=2022.8.0
bioconductor-rsamtools=2.10.0
unifrac-binaries=1.1.1
bioconductor-biobase=2.54.0
dnaio=0.9.1
perl-io-compress=2.106
q2-quality-control=2022.8.0
q2-feature-table=2022.8.1
I tried to re-install another miniconda3 (Miniconda3 macOS Apple M1 ARM 64-bit bash, Python3.8), but didn’t work well.
How can I do next. I wish your comment.
Hi @Hironori_Fukuoka , welcome to
If you search the forum you'll find several threads related to this. You can start here:
Hi @MarcoT ,
There are a couple of ways around this. For example, you'll have to use miniforge if you want to install M1 native conda setup, otherwise miniconda (i.e. Intel version) if using Rosetta. The first link below is quite good. But I'll provide a few other links to help you select which approach might work best for you:
-Mike
lizgehret
(Liz Gehret)
October 12, 2022, 4:11pm
3
Hey @Hironori_Fukuoka !
Piggybacking off of @SoilRotifer - I wanted to share that I submitted an update to our docs that includes install instructions for Macs with M1 chips. You can view that code change here , for reference. Here's how you should install QIIME 2 using conda on an M1 Mac:
wget https://data.qiime2.org/distro/core/qiime2-2022.8-py38-osx-conda.yml
CONDA_SUBDIR=osx-64 conda env create -n qiime2-2022.8 --file qiime2-2022.11-py38-osx-conda.yml
conda activate qiime2-2022.8
conda config --env --set subdir osx-64
Cheers
2 Likes
Dear @lizgehret
Thank you for your kind advice such the following code.
I tried code, but the following message was given.
(base) ~Mac~. % wget https://data.qiime2.org/distro/core/qiime2-2022.8-py38-osx-conda.yml
--2022-10-13 14:15:59-- https://data.qiime2.org/distro/core/qiime2-2022.8-py38-osx-conda.yml
Resolving data.qiime2.org (data.qiime2.org )... 54.200.1.12
Connecting to data.qiime2.org (data.qiime2.org )|54.200.1.12|:443... connected.
HTTP request sent, awaiting response... 302 FOUND
Location: https://raw.githubusercontent.com/qiime2/environment-files/master/2022.8/release/qiime2-2022.8-py38-osx-conda.yml [following]
--2022-10-13 14:15:59-- https://raw.githubusercontent.com/qiime2/environment-files/master/2022.8/release/qiime2-2022.8-py38-osx-conda.yml
Resolving raw.githubusercontent.com (raw.githubusercontent.com )... 2606:50c0:8003::154, 2606:50c0:8002::154, 2606:50c0:8000::154, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com )|2606:50c0:8003::154|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 8573 (8.4K) [text/plain]
Saving to: 'qiime2-2022.8-py38-osx-conda.yml.2'
qiime2-2022.8-py38-osx-conda.yml.2 100%[============================================================================================================================>] 8.37K --.-KB/s in 0s
2022-10-13 14:16:00 (18.2 MB/s) - 'qiime2-2022.8-py38-osx-conda.yml.2' saved [8573/8573]
(base) ~Mac ~ % CONDA_SUBDIR=osx-64 conda env create -n qiime2-2022.8 --file qiime2-2022.11-py38-osx-conda.yml
SpecNotFound: Invalid name 'qiime2-2022.8', try the format: user/package
Do you know where I mistook?
Dear @SoilRotifer
Thank you for your rapid and kind response.
I would try installation via your advise.
Thank you very much.
Fukuoka
1 Like
Dear @SoilRotifer @lizgehret
Thank you for your advice.
Finally I can install qiime2 via the following command.
CONDA_SUBDIR=osx-64 conda env create -n qiime2-2022.8 --file qiime2-2022.8-py38-osx-conda.yml
conda activate qiime2-2022.8
conda config --env --set subdir osx-64
Thank you! If I confuse again, I hope your help again.
Best,
Fukuoka
1 Like
system
(system)
Closed
November 13, 2022, 2:34pm
7
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