Qiime 2 installation issue on mac

#Qiime 2 installation issue on macOS

Hi,
I am a beginner of Qiime2. I have natively installed Miniconda and Qiime2 by following the instructions on https://docs.qiime2.org/2019.7/install/native/#install-qiime-2-within-a-conda-environment

Everything works fine. However, when I test my installation by typing qiime --help, it said command not found. How can I solve this issue? Here are the infor:

the version that I installed: qiime2 2019.7
the error:

Last login: Thu Sep 5 18:28:21 on ttys000

(base) Godrics-MacBook-Pro:~ godric$ qiime --help

-bash: qiime: command not found
(base) Godrics-MacBook-Pro:~ godric$ conda list

packages in environment at /Users/godric/miniconda3:

Name Version Build Channel

asn1crypto 0.24.0 py37_0
bzip2 1.0.8 h1de35cc_0
ca-certificates 2019.5.15 1
certifi 2019.6.16 py37_1
cffi 1.12.3 py37hb5b8e2f_0
chardet 3.0.4 py37_1003
conda 4.7.11 py37_0
conda-package-handling 1.3.11 py37_0
cryptography 2.7 py37ha12b0ac_0
idna 2.8 py37_0
libarchive 3.3.3 h786848e_5
libcxx 4.0.1 hcfea43d_1
libcxxabi 4.0.1 hcfea43d_1
libedit 3.1.20181209 hb402a30_0
libffi 3.2.1 h475c297_4
libiconv 1.15 hdd342a3_7
libxml2 2.9.9 hf6e021a_1
lz4-c 1.8.1.2 h1de35cc_0
lzo 2.10 h362108e_2
ncurses 6.1 h0a44026_1
openssl 1.1.1c h1de35cc_1
pip 19.2.2 py37_0
pycosat 0.6.3 py37h1de35cc_0
pycparser 2.19 py37_0
pyopenssl 19.0.0 py37_0
pysocks 1.7.0 py37_0
python 3.7.3 h359304d_0
python-libarchive-c 2.8 py37_13
readline 7.0 h1de35cc_5
requests 2.22.0 py37_0
ruamel_yaml 0.15.46 py37h1de35cc_0
setuptools 41.0.1 py37_0
six 1.12.0 py37_0
sqlite 3.29.0 ha441bb4_0
tk 8.6.8 ha441bb4_0
tqdm 4.32.1 py_0
urllib3 1.24.2 py37_0
wget 1.20.1 h051b688_0
wheel 0.33.4 py37_0
xz 5.2.4 h1de35cc_4
yaml 0.1.7 hc338f04_2
zlib 1.2.11 h1de35cc_3
zstd 1.3.7 h5bba6e5_0
(base) Godrics-MacBook-Pro:~ godric$ activate qiime2-2019.7
(base) Godrics-MacBook-Pro:~ godric$ qiime --help
-bash: qiime: command not found
(base) Godrics-MacBook-Pro:~ godric$ conda update conda
Collecting package metadata (current_repodata.json): done
Solving environment: done

All requested packages already installed.

(base) Godrics-MacBook-Pro:~ godric$ conda install wget
Collecting package metadata (current_repodata.json): done
Solving environment: done

All requested packages already installed.

(base) Godrics-MacBook-Pro:~ godric$ wget https://data.qiime2.org/distro/core/qiime2-2019.7-py36-osx-conda.yml
–2019-09-06 07:57:48-- https://data.qiime2.org/distro/core/qiime2-2019.7-py36-osx-conda.yml
Resolving data.qiime2.org… 52.35.38.247
Connecting to data.qiime2.org|52.35.38.247|:443… connected.
HTTP request sent, awaiting response… 302 FOUND
Location: https://raw.githubusercontent.com/qiime2/environment-files/master/2019.7/release/qiime2-2019.7-py36-osx-conda.yml [following]
–2019-09-06 07:57:48-- https://raw.githubusercontent.com/qiime2/environment-files/master/2019.7/release/qiime2-2019.7-py36-osx-conda.yml
Resolving raw.githubusercontent.com… 151.101.80.133
Connecting to raw.githubusercontent.com|151.101.80.133|:443… connected.
HTTP request sent, awaiting response… 200 OK
Length: 5879 (5.7K) [text/plain]
Saving to: ‘qiime2-2019.7-py36-osx-conda.yml.1’

qiime2-2019.7-py36-osx-conda.yml.1 100%[================================================================================================================>] 5.74K --.-KB/s in 0s

2019-09-06 07:57:49 (13.7 MB/s) - ‘qiime2-2019.7-py36-osx-conda.yml.1’ saved [5879/5879]

(base) Godrics-MacBook-Pro:~ godric$ conda env create -n qiime2-2019.7 --file qiime2-2019.7-py36-osx-conda.yml

CondaValueError: prefix already exists: /Users/godric/miniconda3/envs/qiime2-2019.7

(base) Godrics-MacBook-Pro:~ godric$ cd /Users/godric/miniconda3/

(base) Godrics-MacBook-Pro:miniconda3 godric$ acivate qiime2-2019.7

-bash: acivate: command not found

(base) Godrics-MacBook-Pro:miniconda3 godric$ activate qiime2-2019.7

(base) Godrics-MacBook-Pro:miniconda3 godric$ qiime --help

-bash: qiime: command not found

Hi @Godric_Wang,

You’re missing your activation step.

You can tell the environment isn’t on yet because you have the (base) preceding your name.

Try activating with

conda activate qiime2-2019.7

(And if that doesn’t work because your conda installation is old, try

source activate qiime2-2019.7

If you’re unfamiliar with conda, I the conda documentation is excellent. Conda in and of itself is a super powerful tool that QIIME uses.

Best,
Justine

Hi Justine,

Thank you. I nailed it.

I did activate the qiime2, but what I typed is “activate qiime2-2019.7”. And nothing happened, i thought it is successful.

I forgot to type “conda/source” in front of the “activate”. Thank you so much for correcting me!

Godric

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