Q2studio npm start error

[hesterlee]

Hi, community!
Nowdays, I wanna use q2studio in my computer, and I use ubuntu 18.04LTS. I’ve already installed qiime2-2021.2 via conda.But when I installed q2studio, everything was OK until this step:

(qtest-2102) lhr@DESKTOP-5RNK17J:~/tem_software/q2studio-2021.2.0$ npm start

q2studio@2021.2.0 start /home/lhr/tem_software/q2studio-2021.2.0
cross-env NODE_ENV=production electron -r babel-register build/main.js

npm ERR! Linux 4.4.0-19041-Microsoft
npm ERR! argv "/home/lhr/miniconda2/envs/qtest-2102/bin/node" "/home/lhr/miniconda2/envs/qtest-2102/bin/npm" "start"
npm ERR! node v6.11.2
npm ERR! npm v3.10.10
npm ERR! code ELIFECYCLE
npm ERR! q2studio@2021.2.0 start: cross-env NODE_ENV=production electron -r babel-register build/main.js
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the q2studio@2021.2.0 start script 'cross-env NODE_ENV=production electron -r babel-register build/main.js'.
npm ERR! Make sure you have the latest version of node.js and npm installed.
npm ERR! If you do, this is most likely a problem with the q2studio package,
npm ERR! not with npm itself.
npm ERR! Tell the author that this fails on your system:
npm ERR! cross-env NODE_ENV=production electron -r babel-register build/main.js
npm ERR! You can get information on how to open an issue for this project with:
npm ERR! npm bugs q2studio
npm ERR! Or if that isn't available, you can get their info via:
npm ERR! npm owner ls q2studio
npm ERR! There is likely additional logging output above.

npm ERR! Please include the following file with any support request:
npm ERR! /home/lhr/tem_software/q2studio-2021.2.0/npm-debug.log

And the content of the debug.log is shown below:

0 info it worked if it ends with ok
1 verbose cli [ '/home/lhr/miniconda2/envs/qtest-2102/bin/node',
1 verbose cli '/home/lhr/miniconda2/envs/qtest-2102/bin/npm',
1 verbose cli 'start' ]
2 info using npm@3.10.10
3 info using node@v6.11.2
4 verbose run-script [ 'prestart', 'start', 'poststart' ]
5 info lifecycle q2studio@2021.2.0~prestart: q2studio@2021.2.0
6 silly lifecycle q2studio@2021.2.0~prestart: no script for prestart, continuing
7 info lifecycle q2studio@2021.2.0~start: q2studio@2021.2.0
8 verbose lifecycle q2studio@2021.2.0~start: unsafe-perm in lifecycle true
9 verbose lifecycle q2studio@2021.2.0~start: PATH: /home/lhr/miniconda2/envs/qtest-2102/lib/node_modules/npm/bin/node-gyp-bin:/home/lhr/tem_software/q2studio-2021.2.0/node_modules/.bin:/home/lhr/miniconda2/envs/qtest-2102/bin:/home/lhr/miniconda2/condabin:/home/lhr/miniconda2/bin:/home/lhr/miniconda2/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/Program Files/WindowsApps/CanonicalGroupLimited.Ubuntu18.04onWindows_1804.2020.824.0_x64__79rhkp1fndgsc:/mnt/f/linux/bin:/mnt/c/Windows/system32:/mnt/c/Windows:/mnt/c/Windows/System32/Wbem:/mnt/c/Windows/System32/WindowsPowerShell/v1.0:/mnt/c/Windows/System32/OpenSSH:/mnt/c/Program Files (x86)/NVIDIA Corporation/PhysX/Common:/mnt/c/Users/DELL/AppData/Local/Microsoft/WindowsApps:/snap/bin
10 verbose lifecycle q2studio@2021.2.0~start: CWD: /home/lhr/tem_software/q2studio-2021.2.0
11 silly lifecycle q2studio@2021.2.0~start: Args: [ '-c',
11 silly lifecycle 'cross-env NODE_ENV=production electron -r babel-register build/main.js' ]
12 silly lifecycle q2studio@2021.2.0~start: Returned: code: 1 signal: null
13 info lifecycle q2studio@2021.2.0~start: Failed to exec start script
14 verbose stack Error: q2studio@2021.2.0 start: cross-env NODE_ENV=production electron -r babel-register build/main.js
14 verbose stack Exit status 1
14 verbose stack at EventEmitter. (/home/lhr/miniconda2/envs/qtest-2102/lib/node_modules/npm/lib/utils/lifecycle.js:255:16)
14 verbose stack at emitTwo (events.js:106:13)
14 verbose stack at EventEmitter.emit (events.js:191:7)
14 verbose stack at ChildProcess. (/home/lhr/miniconda2/envs/qtest-2102/lib/node_modules/npm/lib/utils/spawn.js:40:14)
14 verbose stack at emitTwo (events.js:106:13)
14 verbose stack at ChildProcess.emit (events.js:191:7)
14 verbose stack at maybeClose (internal/child_process.js:891:16)
14 verbose stack at Process.ChildProcess._handle.onexit (internal/child_process.js:226:5)
15 verbose pkgid q2studio@2021.2.0
16 verbose cwd /home/lhr/tem_software/q2studio-2021.2.0
17 error Linux 4.4.0-19041-Microsoft
18 error argv "/home/lhr/miniconda2/envs/qtest-2102/bin/node" "/home/lhr/miniconda2/envs/qtest-2102/bin/npm" "start"
19 error node v6.11.2
20 error npm v3.10.10
21 error code ELIFECYCLE
22 error q2studio@2021.2.0 start: cross-env NODE_ENV=production electron -r babel-register build/main.js
22 error Exit status 1
23 error Failed at the q2studio@2021.2.0 start script 'cross-env NODE_ENV=production electron -r babel-register build/main.js'.
23 error Make sure you have the latest version of node.js and npm installed.
23 error If you do, this is most likely a problem with the q2studio package,
23 error not with npm itself.
23 error Tell the author that this fails on your system:
23 error cross-env NODE_ENV=production electron -r babel-register build/main.js
23 error You can get information on how to open an issue for this project with:
23 error npm bugs q2studio
23 error Or if that isn't available, you can get their info via:
23 error npm owner ls q2studio
23 error There is likely additional logging output above.
24 verbose exit [ 1, true ]
I have none idea to deal with it.

[andrewsanchez]

Hi, @hesterlee and welcome to the forum!

The error message states:

@hesterlee

npm ERR! Make sure you have the latest version of node.js and npm installed.

It also lists the version of node you are using:

@hesterlee

npm ERR! node v6.11.2

When you follow the installation instructions here, you should get a newer version of node. If you followed those instructions (especially conda install gevent nodejs -c defaults --override-channels, which installs nodejs into your qiime 2 environment if it is activated) and you are still having a problem, then that means your computer is using a different node installation. If you activate your qiime 2 environment and then use these commands: which node and which npm, what do you see?

Your issue may be similar to the one here:

mafft does not work inside my Qiime2 environment

When it comes to the PATH variable, the order of items matters. You can see below that the mafft installation external to your qiime 2 conda environment appears before the qiime 2 environment. It's important that the qiime 2 environment comes first. Otherwise, your computer will favor programs that appear earlier in the list. PATH=/opt/local/bin/mafft:/Users/m213406/Filtlong/bin:/Users/m213406/nanotimeparse:/Users/m213406/NanoOK/bin:/opt/local/share/arb/bin:/opt/local/bin:/opt/local/sbin:/Use…

I would suggest simply creating a fresh qiime 2 enviroment and follow the q2studio installation instructions closely to see if that resolves the issue. Let me know how it works out!

[hesterlee]

Thanks for your help !
When I installed q2studio, I found 'pip install .' can't run if my conda base enviroment didn't have nodejs, even if my qiime2 environment had nodejs.Then I run

conda install gevent nodejs -c defaults --override-channels

in my base enviroment, and I can get nodejs=10.13.0.
I followed your suggestion to create a new qiime2 environment via conda, and run

conda install gevent nodejs -c defaults --override-channels

in my new environment, but it would get nodejs=6.11.2. I thought I probably ignored somthing else.

Actually, I think there may be some more important issue:my linux subsystem(Ubuntu 18.04LTS in Windows10) need some setting about visual management that is ignored by me. I tired to install q2studio in Virtual Machine(VMware, Ubuntu 20.04LTS).According to the error message, I used 'sudo apt install xxx' to install the package, and then q2studio can work normally.

[andrewsanchez]

@hesterlee

Actually, I think there may be some more important issue:my linux subsystem(Ubuntu 18.04LTS in Windows10) need some setting about visual management that is ignored by me. I tired to install q2studio in Virtual Machine(VMware, Ubuntu 20.04LTS).According to the error message, I used ‘sudo apt install xxx’ to install the package, and then q2studio can work normally.

That's good to hear! I think running q2studio in a VM is probably a safer bet rather than using WSL anyways. Side note: these kinds of issues will become less relevant as the Galaxy interface continues to be developed: QIIME 2 2021.4 is now available!