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.
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.
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
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
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
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.
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
Maybe?
Did you upgrade to macos catalina some time in there? That might be part of the problem...
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 ~ %
Do I need to fix these problems?
Thanks,
Bing
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
Thanks so much and have a good weekend!
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