QIIME2-2020.2 installation keeps solving environment.

Bing · May 7, 2020, 7:13pm

qiime2-2020.2-py36-osx-co 100%[=====================================>]   5.29K  --.-KB/s    in 0s

2020-05-07 15:06:20 (28.2 MB/s) - ‘qiime2-2020.2-py36-osx-conda.yml’ saved [5416/5416]

Jinbings-iMac:~ jinbingbai$ conda env create -n qiime2-2020.2 --file qiime2-2020.2-py36-osx-conda.yml
Solving environment: |

The installation keeps “solving environment:…” and do not move forward in my Mac. Thanks for your help.

thermokarst · May 7, 2020, 7:41pm

Hi @Bing, give it some time - sometimes this process can take a while. If you don’t see this resolve after the next hr or so, double check that there isn’t a firewall on your network that is interfering with the package download process.

Bing · May 11, 2020, 3:56am

I tried it again. It run more than 8 hours and still not responding. I am not sure what to do and please suggest.

Thanks

thermokarst · May 11, 2020, 2:21pm

Hi @Bing!

Ah, I'm sorry.

Please see my suggestion above:

Bing · May 12, 2020, 3:38am

I tried to check about it again. Actually this installation destroyed my old installation pathway of my other QIIME2 versions. i need to go back to my original version. Please let me know how can I set up my original default conda envs.

Last login: Mon May 11 23:26:39 on console

jinbingbai@Jinbings-iMac ~ % source activate qiime2-2019.10
source: no such file or directory: activate
jinbingbai@Jinbings-iMac ~ % rm qiime2-2020.2-py36-osx-conda.yml
jinbingbai@Jinbings-iMac ~ % ls
$300 Data Recovery Public
11086-file-listing 2.html Sites
11086-file-listing.html casava-18-paired-end-demultiplexed
11086-file-listing.zip heatmap-l6-Time.pdf
Applications iCloud Drive (Archive)
Bing’s Files iih.rds
BingQiime.pem.txt iih2.csv
Creative Cloud Files miniconda3
Desktop npm-debug.log
Documents private
Downloads q2-picrust2_full
DropBox 6-22-2017 cc q2studio-0.0.6
Dropbox qiime2-2020.2-py36-linux-conda.yml
HPScanner qiime2-2020.2-py36-osx-conda.yml.1
Library qiime2-2020.2-py36-osx-conda.yml.2
MY Files copy Sep 2014 qiime2-2020.2-py36-osx-conda.yml.3
Movies qiime2-2020.2-py36-osx-conda.yml.4
Music qiime2-moving-pictures-tutorial
Pictures tmp
Pictures1 xesoph.rds
jinbingbai@Jinbings-iMac ~ % rm qiime2-2020.2-py36-osx-conda.yml
rm: qiime2-2020.2-py36-osx-conda.yml: No such file or directory
jinbingbai@Jinbings-iMac ~ %

Please let me know how I can set back my default environment so that I can run QIIME2 directly. Also maybe that is the problem the new installation solving environment forever and never installed it.

Thanks,
Bing

Bing · May 12, 2020, 3:39am

Here is the complete story. I have installed several versions of QIIME2 (see codes below in my conda envs) in my computer and all work very well until i tried to install this newer version qiime2-2020.2. I tried to install qiime2-2020.2 and completed the conda update (went well), and then i moved to install qiime2-2020.2. It kept showing “solving environment |/” forever. I failed to install qiime2-2020.2. However, this process seems destroyed the path for all my other versions of qiime2 (see below).

Last login: Wed May 13 16:26:26 on ttys000
jinbingbai@Jinbings-iMac ~ % source activate qiime2-2019.10
source: no such file or directory: activate
    jinbingbai@Jinbings-iMac ~ % ls
    $300 Data Recovery			Pictures
    11086-file-listing 2.html		Pictures1
    11086-file-listing.html			Public
    11086-file-listing.zip			Sites
    Applications				casava-18-paired-end-demultiplexed
    Bing's Files				cpr
    BingQiime.pem.txt			heatmap-l6-Time.pdf
    Creative Cloud Files			iCloud Drive (Archive)
    Desktop					iih.rds
    Documents				iih2.csv
    Downloads				miniconda3
    DropBox 6-22-2017 cc			npm-debug.log
    Dropbox					private
    HPScanner				q2-picrust2_full
    Library					q2studio-0.0.6
    MY Files copy Sep 2014			qiime2-moving-pictures-tutorial
    Movies					tmp
    Music					xesoph.rds

i have to copy “activate” file from “bin” to put it in “envs” I do not think this is right as I do not need to do anything before I updated conda and tried to install this new version of qiime2. What i did before was just enter “source activate qiime2-2019.10”, it will run qiime2 for me. No additional steps at all. Here are the codes for my qiime2 installations before:

  jinbingbai@Jinbings-iMac ~ % cd miniconda3
    jinbingbai@Jinbings-iMac miniconda3 % ls
    LICENSE.txt	doc		lib		pkgs		sbin
    bin		envs		libexec		plugins		share
    conda-bld	etc		mkspecs		qml		ssl
    conda-meta	include		phrasebooks	resources	translations
    jinbingbai@Jinbings-iMac miniconda3 % source activate qiime2-2019.10
    source: no such file or directory: activate
    jinbingbai@Jinbings-iMac miniconda3 % source envs
    source: no such file or directory: envs
    jinbingbai@Jinbings-iMac miniconda3 % ls
    LICENSE.txt	doc		lib		pkgs		sbin
    bin		envs		libexec		plugins		share
    conda-bld	etc		mkspecs		qml		ssl
    conda-meta	include		phrasebooks	resources	translations
    jinbingbai@Jinbings-iMac miniconda3 % cd envs
    jinbingbai@Jinbings-iMac envs % ls 
    qiime2-2018.4	qiime2-2019.10
    qiime1		qiime2-2019.1	qiime2-2019.7
    jinbingbai@Jinbings-iMac envs % source activate qiime2-2019.10
    complete:13: command not found: compdef
    (qiime2-2019.10) jinbingbai@x86_64-apple-darwin13 envs %

The location of qiime2-2019.10 suddenly became weird too, with “@x86_64-apple-darwin13 envs” at the end, never have that before. i need your help with fixing this directory problem with miniconda first, then I need your help with qiime2-2020.2 installation.

Thanks,
Bing

thermokarst · May 15, 2020, 11:01pm

Hi @Bing - have you followed all of the miniconda installation instructions, including setting up your shell? I’m not really sure what is going on here, and I’m not certain we can help diagnose, since I don’t see anything specifically related to QIIME 2 wrong here.

Bing · May 15, 2020, 11:18pm

Yes. All the miniconda installation instructions were followed a while ago. I used QIIME2 very well without any issues. It happened suddenly when i tried to install qiime2-2020.2. As I have miniconda3 all the versions of QIIME2 in my mac already. see below:

jinbingbai@Jinbings-iMac ~ % ls
$300 Data Recovery			Pictures
11086-file-listing 2.html		Pictures1
11086-file-listing.html			Public
11086-file-listing.zip			Sites
Applications				casava-18-paired-end-demultiplexed
Bing's Files				cpr
BingQiime.pem.txt			heatmap-l6-Time.pdf
Creative Cloud Files			iCloud Drive (Archive)
Desktop					iih.rds
Documents				iih2.csv
Downloads				miniconda3
DropBox 6-22-2017 cc			npm-debug.log
Dropbox					private
HPScanner				q2-picrust2_full
Library					q2studio-0.0.6
MY Files copy Sep 2014			qiime2-moving-pictures-tutorial
Movies					tmp
Music					xesoph.rds

Do I need to reinstall the miniconda3 again? Then I can install the qiime2?

Thanks,
Bing

thermokarst · May 15, 2020, 11:20pm

Maybe?

Did you upgrade to macos catalina some time in there? That might be part of the problem...

Bing · May 16, 2020, 1:00am

Yes I updated this mac to Catalina for a while. I tried reinstall conda and it fixed some problem.

Now i installed qiime2-2020.2. Here I still have some issues:

Last login: Fri May 15 19:44:58 on ttys000
(base) jinbingbai@Jinbings-iMac ~ % source activate qiime2-2020.2
complete:13: command not found: compdef
(qiime2-2020.2) jinbingbai@x86_64-apple-darwin13 ~ % source deactivate qiime2-2020.2
source: no such file or directory: deactivate
(qiime2-2020.2) jinbingbai@x86_64-apple-darwin13 ~ %

command not found: compdef
deactivate command is not working?

Do I need to fix these problems?

Thanks,
Bing

thermokarst · May 22, 2020, 5:31pm

If you didn't perform a clean, full installation, you might need to make some adjustments to your shell in order to ensure that everything works as expected. Please see this doc from the conda team:

https://docs.conda.io/projects/conda/en/latest/user-guide/install/macos.html

Bing · May 22, 2020, 7:33pm

Thanks so much and have a good weekend!

system · June 23, 2020, 1:33am

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