instaling quiime 2 studio - error

I am trying to install quite 2 studio on my Mac, and following the steps in: QIIME 2 Studio (q2studio) — QIIME 2 2021.4.0 documentation

All steps complete successfully, However, at the 'run build' step, I am getting an 'unable to resolve dependency' error. My full oupput is below (please scroll to the end for errors). Thank you!

(base) FVFCW3NGP3Y0:~ natalia_palacios$ wget \

-O "q2studio-2021.4.0.zip"
"https://codeload.github.com/qiime2/q2studio/zip/2021.4.0"
--2021-06-15 09:27:02-- https://codeload.github.com/qiime2/q2studio/zip/2021.4.0
Resolving codeload.github.com... 140.82.112.9
Connecting to codeload.github.com|140.82.112.9|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: unspecified [application/zip]
Saving to: 'q2studio-2021.4.0.zip'

q2studio-2021.4.0.zip [ <=> ] 287.23K --.-KB/s in 0.1s

2021-06-15 09:27:03 (2.01 MB/s) - 'q2studio-2021.4.0.zip' saved [294126]

(base) FVFCW3NGP3Y0:~ natalia_palacios$ conda activate qiime2-2021.4
(qiime2-2021.4) FVFCW3NGP3Y0:~ natalia_palacios$ unzip q2studio-2021.4.0.zip && rm q2studio-2021.4.0.zip
Archive: q2studio-2021.4.0.zip
3c2b5572bdfb47ca53c60b2941e66b995c205f6a
creating: q2studio-2021.4.0/
creating: q2studio-2021.4.0/.github/
inflating: q2studio-2021.4.0/.github/CONTRIBUTING.md
creating: q2studio-2021.4.0/.github/ISSUE_TEMPLATE/
inflating: q2studio-2021.4.0/.github/ISSUE_TEMPLATE/1-user-need-help.md
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inflating: q2studio-2021.4.0/.github/ISSUE_TEMPLATE/4-make-better.md
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creating: q2studio-2021.4.0/app/
creating: q2studio-2021.4.0/app/css/
inflating: q2studio-2021.4.0/app/css/JobHistory.css
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inflating: q2studio-2021.4.0/app/js/components/JobRunning.jsx
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creating: q2studio-2021.4.0/app/js/components/pages/
inflating: q2studio-2021.4.0/app/js/components/pages/App.jsx
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creating: q2studio-2021.4.0/config/
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creating: q2studio-2021.4.0/q2studio/
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creating: q2studio-2021.4.0/q2studio/api/
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creating: q2studio-2021.4.0/test/
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(qiime2-2021.4) FVFCW3NGP3Y0:~ natalia_palacios$ cd q2studio-2021.4.0
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ unzip q2studio-2021.4.0.zip && rm q2studio-2021.4.0.zip
unzip: cannot find or open q2studio-2021.4.0.zip, q2studio-2021.4.0.zip.zip or q2studio-2021.4.0.zip.ZIP.
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ ls
LICENSE Makefile README.md app config package.json q2studio setup.py test
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ pwd
/Users/natalia_palacios/q2studio-2021.4.0
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ cd q2studio-2021.4.0
-bash: cd: q2studio-2021.4.0: No such file or directory
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ owd
-bash: owd: command not found
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ pwd
/Users/natalia_palacios/q2studio-2021.4.0
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ conda install gevent nodejs -c defaults --override-channels
Collecting package metadata (current_repodata.json): done
Solving environment: done

All requested packages already installed.

(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ pip install .
Processing /Users/natalia_palacios/q2studio-2021.4.0
Requirement already satisfied: click in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from q2studio==2021.4.0) (7.1.2)
Requirement already satisfied: flask in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from q2studio==2021.4.0) (2.0.1)
Requirement already satisfied: gevent in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from q2studio==2021.4.0) (21.1.2)
Requirement already satisfied: qiime2==2021.4.* in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from q2studio==2021.4.0) (2021.4.0)
Requirement already satisfied: Werkzeug>=2.0 in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from flask->q2studio==2021.4.0) (2.0.1)
Requirement already satisfied: Jinja2>=3.0 in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from flask->q2studio==2021.4.0) (3.0.1)
Requirement already satisfied: itsdangerous>=2.0 in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from flask->q2studio==2021.4.0) (2.0.1)
Requirement already satisfied: MarkupSafe>=2.0 in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from Jinja2>=3.0->flask->q2studio==2021.4.0) (2.0.1)
Requirement already satisfied: zope.interface in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from gevent->q2studio==2021.4.0) (5.3.0)
Requirement already satisfied: greenlet<2.0,>=0.4.17 in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from gevent->q2studio==2021.4.0) (1.1.0)
Requirement already satisfied: setuptools in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from gevent->q2studio==2021.4.0) (49.6.0.post20210108)
Requirement already satisfied: zope.event in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from gevent->q2studio==2021.4.0) (4.5.0)
Building wheels for collected packages: q2studio
Building wheel for q2studio (setup.py) ... done
Created wheel for q2studio: filename=q2studio-2021.4.0-py3-none-any.whl size=13540 sha256=87ede8c15f604e3eee2fdf9157ef3337023c92e7f003f58b6181879a75b6a157
Stored in directory: /Users/natalia_palacios/Library/Caches/pip/wheels/dd/d7/7c/1e25ced34bc370f961207425ea60c3a9d1ff0e03852293ecc1
Successfully built q2studio
Installing collected packages: q2studio
Attempting uninstall: q2studio
Found existing installation: q2studio 2021.4.0
Uninstalling q2studio-2021.4.0:
Successfully uninstalled q2studio-2021.4.0
Successfully installed q2studio-2021.4.0
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ npm install && npm run build
npm notice
npm notice New minor version of npm available! 7.7.6 -> 7.17.0
npm notice Changelog: Release v7.17.0 · npm/cli · GitHub
npm notice Run npm install -g [email protected] to update!
npm notice
npm ERR! code ERESOLVE
npm ERR! ERESOLVE unable to resolve dependency tree
npm ERR!
npm ERR! While resolving: [email protected]
npm ERR! Found: [email protected]
npm ERR! node_modules/react
npm ERR! [email protected]"^15.0.1" from the root project
npm ERR!
npm ERR! Could not resolve dependency:
npm ERR! peer [email protected]"^16.3.0" from [email protected]
npm ERR! node_modules/redux-devtools-dock-monitor
npm ERR! [email protected]"^1.1.1" from the root project
npm ERR!
npm ERR! Fix the upstream dependency conflict, or retry
npm ERR! this command with --force, or --legacy-peer-deps
npm ERR! to accept an incorrect (and potentially broken) dependency resolution.
npm ERR!
npm ERR! See /Users/natalia_palacios/.npm/eresolve-report.txt for a full report.

npm ERR! A complete log of this run can be found in:
npm ERR! /Users/natalia_palacios/.npm/_logs/2021-06-15T13_44_38_737Z-debug.log

I am getting an error when trying to install qqiime 2 studio(below). I would really appreciate your help!
(base) FVFCW3NGP3Y0:~ natalia_palacios$ wget \

-O “q2studio-2021.4.0.zip”
https://codeload.github.com/qiime2/q2studio/zip/2021.4.0
–2021-06-15 09:27:02-- https://codeload.github.com/qiime2/q2studio/zip/2021.4.0
Resolving codeload.github.com… 140.82.112.9
Connecting to codeload.github.com|140.82.112.9|:443… connected.
HTTP request sent, awaiting response… 200 OK
Length: unspecified [application/zip]
Saving to: ‘q2studio-2021.4.0.zip’

q2studio-2021.4.0.zip [ <=> ] 287.23K --.-KB/s in 0.1s

2021-06-15 09:27:03 (2.01 MB/s) - ‘q2studio-2021.4.0.zip’ saved [294126]

(base) FVFCW3NGP3Y0:~ natalia_palacios$ conda activate qiime2-2021.4
(qiime2-2021.4) FVFCW3NGP3Y0:~ natalia_palacios$ unzip q2studio-2021.4.0.zip && rm q2studio-2021.4.0.zip
Archive: q2studio-2021.4.0.zip
3c2b5572bdfb47ca53c60b2941e66b995c205f6a
creating: q2studio-2021.4.0/
creating: q2studio-2021.4.0/.github/
inflating: q2studio-2021.4.0/.github/CONTRIBUTING.md
creating: q2studio-2021.4.0/.github/ISSUE_TEMPLATE/
inflating: q2studio-2021.4.0/.github/ISSUE_TEMPLATE/1-user-need-help.md
inflating: q2studio-2021.4.0/.github/ISSUE_TEMPLATE/2-dev-need-help.md
inflating: q2studio-2021.4.0/.github/ISSUE_TEMPLATE/3-found-bug.md
inflating: q2studio-2021.4.0/.github/ISSUE_TEMPLATE/4-make-better.md
inflating: q2studio-2021.4.0/.github/ISSUE_TEMPLATE/5-make-new.md
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creating: q2studio-2021.4.0/config/
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(qiime2-2021.4) FVFCW3NGP3Y0:~ natalia_palacios$ cd q2studio-2021.4.0
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ unzip q2studio-2021.4.0.zip && rm q2studio-2021.4.0.zip
unzip: cannot find or open q2studio-2021.4.0.zip, q2studio-2021.4.0.zip.zip or q2studio-2021.4.0.zip.ZIP.
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ ls
LICENSE Makefile README.md app config package.json q2studio setup.py test
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ pwd
/Users/natalia_palacios/q2studio-2021.4.0
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ cd q2studio-2021.4.0
-bash: cd: q2studio-2021.4.0: No such file or directory
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ owd
-bash: owd: command not found
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ pwd
/Users/natalia_palacios/q2studio-2021.4.0
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ conda install gevent nodejs -c defaults --override-channels
Collecting package metadata (current_repodata.json): done
Solving environment: done

All requested packages already installed.

(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ pip install .
Processing /Users/natalia_palacios/q2studio-2021.4.0
Requirement already satisfied: click in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from q2studio==2021.4.0) (7.1.2)
Requirement already satisfied: flask in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from q2studio==2021.4.0) (2.0.1)
Requirement already satisfied: gevent in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from q2studio==2021.4.0) (21.1.2)
Requirement already satisfied: qiime2==2021.4.* in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from q2studio==2021.4.0) (2021.4.0)
Requirement already satisfied: Werkzeug>=2.0 in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from flask->q2studio==2021.4.0) (2.0.1)
Requirement already satisfied: Jinja2>=3.0 in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from flask->q2studio==2021.4.0) (3.0.1)
Requirement already satisfied: itsdangerous>=2.0 in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from flask->q2studio==2021.4.0) (2.0.1)
Requirement already satisfied: MarkupSafe>=2.0 in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from Jinja2>=3.0->flask->q2studio==2021.4.0) (2.0.1)
Requirement already satisfied: zope.interface in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from gevent->q2studio==2021.4.0) (5.3.0)
Requirement already satisfied: greenlet<2.0,>=0.4.17 in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from gevent->q2studio==2021.4.0) (1.1.0)
Requirement already satisfied: setuptools in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from gevent->q2studio==2021.4.0) (49.6.0.post20210108)
Requirement already satisfied: zope.event in /Users/natalia_palacios/opt/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages (from gevent->q2studio==2021.4.0) (4.5.0)
Building wheels for collected packages: q2studio
Building wheel for q2studio (setup.py) … done
Created wheel for q2studio: filename=q2studio-2021.4.0-py3-none-any.whl size=13540 sha256=87ede8c15f604e3eee2fdf9157ef3337023c92e7f003f58b6181879a75b6a157
Stored in directory: /Users/natalia_palacios/Library/Caches/pip/wheels/dd/d7/7c/1e25ced34bc370f961207425ea60c3a9d1ff0e03852293ecc1
Successfully built q2studio
Installing collected packages: q2studio
Attempting uninstall: q2studio
Found existing installation: q2studio 2021.4.0
Uninstalling q2studio-2021.4.0:
Successfully uninstalled q2studio-2021.4.0
Successfully installed q2studio-2021.4.0
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ npm install && npm run build
npm notice
npm notice New minor version of npm available! 7.7.6 → 7.17.0
npm notice Changelog: Release v7.17.0 · npm/cli · GitHub
npm notice Run npm install -g [email protected] to update!
npm notice
npm ERR! code ERESOLVE
npm ERR! ERESOLVE unable to resolve dependency tree
npm ERR!
npm ERR! While resolving: [email protected]
npm ERR! Found: [email protected]
npm ERR! node_modules/react
npm ERR! [email protected]"^15.0.1" from the root project
npm ERR!
npm ERR! Could not resolve dependency:
npm ERR! peer [email protected]"^16.3.0" from [email protected]
npm ERR! node_modules/redux-devtools-dock-monitor
npm ERR! [email protected]"^1.1.1" from the root project
npm ERR!
npm ERR! Fix the upstream dependency conflict, or retry
npm ERR! this command with --force, or --legacy-peer-deps
npm ERR! to accept an incorrect (and potentially broken) dependency resolution.
npm ERR!
npm ERR! See /Users/natalia_palacios/.npm/eresolve-report.txt for a full report.

npm ERR! A complete log of this run can be found in:
npm ERR! /Users/natalia_palacios/.npm/_logs/2021-06-15T13_44_38_737Z-debug.log
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ ls
LICENSE Makefile README.md app config package.json q2studio setup.py test
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ pwd
/Users/natalia_palacios/q2studio-2021.4.0
(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$

Hi Natasha,

Thanks for reaching out! Can you take a look at @ebolyen’s suggestion from this similar forum post and see if that resolves the issue?

Thank you! I looked into this and I don’t have a /node_modules folder in my q2studio folder, so this link is not helpful…below are the contents of the folder…thank you!

(qiime2-2021.4) FVFCW3NGP3Y0:q2studio-2021.4.0 natalia_palacios$ ls
LICENSE Makefile README.md app config package.json q2studio setup.py test

Hi Natasha,

Thanks for trying that! I'm going to take a closer look at your output and see what I can find. I'll follow up with you shortly with next steps!

After reviewing your logs, I think I found the source of the error. It looks like you have some conflicting dependencies for the packages that are being installed. See below:

npm ERR! While resolving: [email protected]
npm ERR! Found: [email protected]
npm ERR! node_modules/react
npm ERR! [email protected]"^15.0.1" from the root project

.......

npm ERR! peer [email protected]"^16.3.0" from [email protected]
npm ERR! node_modules/redux-devtools-dock-monitor
npm ERR! [email protected]"^1.1.1" from the root project

I recommend attempting to change the versions of react and redux-devtools-dock-monitor to match those of the root project (react 15.0.1 and redux-devtools-dock-monitor 1.1.1 respectively).

You can do so using the following command:

npm install <package>@<version>

Please try using this to install the specified versions of those two packages, and let me know if you are successful!

Hey Natasha,

I went ahead and ran the installation on my laptop just to double check that I was able to successfully install q2-studio using our newest version of QIIME 2 (2021.4) and I am actually getting the same dependency errors that you listed above (which means this isn't an issue local to your machine). We'll need to take a closer look at this on our end to resolve the issue. I'll circle back with you once we are able to determine the source of the issue on our end and get this resolved. Thanks for your patience and understanding here!

Hey @Natasha_Palacios,

Thanks for your patience! I think I've found a resolution for this error, but I'd like you to try and re-install q2studio with the following modifications to our installation instructions to confirm that it works for you as well.

Go ahead and delete the q2studio files from your machine, if you haven't already done so. The easiest way to do this is just to navigate to the directory that these files are housed under and manually delete them (just using your machine's finder/file explorer).

Once that's complete, I'll go through the installation instructions and what will change:

  1. Activate your conda environment:
    conda activate qiime2-2021.4

  2. Download the source code for q2studio using one of the following options:

  • Web Browser:
    Download URL: https://codeload.github.com/qiime2/q2studio/zip/2021.4.0
    Save as: q2studio-2021.4.0.zip

  • wget:
    wget \
    -O "q2studio-2021.4.0.zip" \
    "https://codeload.github.com/qiime2/q2studio/zip/2021.4.0"

  • curl:
    curl -sL \
    "https://codeload.github.com/qiime2/q2studio/zip/2021.4.0" > \
    "q2studio-2021.4.0.zip"

  1. Next you'll unzip and navigate to the q2studio directory:
    unzip q2studio-2021.4.0.zip && rm q2studio-2021.4.0.zip
    cd q2studio-2021.4.0

  2. This is where the installation steps will be slightly modified - installing q2studio as a Python and NodeJS package:
    conda install gevent nodejs -c defaults --override-channels
    pip install .
    npm install --legacy-peer-deps && npm run build

The --legacy-peer-deps flag has been added here, which resolved the dependency conflicts on my machine when I tested this out - please let me know if this works for you as well!

  1. Pending a successful install, you should be able to run the following command and successfully launch q2studio:
    npm start

Please let me know if you are successful, or if you are still running into any installation errors - fingers crossed this will work for you!

1 Like

Hi Liz,
Thanks. Problem resolved. :slight_smile:
MF