Installing Qiime2 Studio using Ubuntu

Hi,
I have been trying to install Qiime 2 studio on my Windows 10 computer using Ubuntu. On the final step trying to launch the Interface using nmp start this Message was recieved.

(qiime2-2019.1) [email protected]:~/q2studio-2019.1.0$ npm start

[email protected] start /home/charlottenilsen/q2studio-2019.1.0
cross-env NODE_ENV=production electron -r babel-register build/main.js

/home/charlottenilsen/q2studio-2019.1.0/node_modules/electron/dist/electron: error while loading shared libraries: libgtk-x11-2.0.so.0: cannot open shared object file: No such file or directory
npm ERR! file sh
npm ERR! code ELIFECYCLE
npm ERR! errno ENOENT
npm ERR! syscall spawn
npm ERR! [email protected] start: cross-env NODE_ENV=production electron -r babel-register build/main.js
npm ERR! spawn ENOENT
npm ERR!
npm ERR! Failed at the [email protected] start script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.

npm ERR! A complete log of this run can be found in:
npm ERR! /home/charlottenilsen/.npm/_logs/2019-02-12T09_43_40_409Z-debug.log

I have tried reinstalling, do you have any other suggestions?

Charlotte

Hey there @charlotte.nilsen! Are you using Ubuntu 18.04 on the Windows Subsystem for Linux (WSL)? I just recently upgrading our Virtualbox images from Ubuntu 16.04 to 18.04 and learned that there were a few dependencies that Ubuntu used to ship with, but doesn’t as of 18.04:

apt-get install -y nodejs npm build-essential libgtk2.0-0 libgconf2-4

That did it for me, but, your mileage may vary. Keep us posted!

Thank you!
I am using Ubuntu 18.04.
The code you provided solved the first error, now this remains:

(qiime2-2019.1) [email protected]:~/q2studio-2019.1.0$ npm start

[email protected] start /home/charlottenilsen/q2studio-2019.1.0
cross-env NODE_ENV=production electron -r babel-register build/main.js

npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! [email protected] 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 [email protected] start script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.

npm ERR! A complete log of this run can be found in:
npm ERR! /home/charlottenilsen/.npm/_logs/2019-02-13T13_27_12_964Z-debug.log

Hi @charlotte.nilsen.

Just checking, did you remember to rebuild (via npm run build) after you installed those dependencies?

What does this file contain?

1 Like

Hi,

Yes I did npm run build.
The file contains:

(qiime2-2019.1) [email protected]:~/q2studio-2019.1.0$ cat /home/charlottenilsen/.npm/_logs/2019-02-14T08_59_37_755Z-debug.log
0 info it worked if it ends with ok
1 verbose cli [ ‘/usr/bin/node’, ‘/usr/bin/npm’, ‘start’ ]
2 info using [email protected]
3 info using [email protected]
4 verbose run-script [ ‘prestart’, ‘start’, ‘poststart’ ]
5 info lifecycle [email protected]~prestart: [email protected]
6 info lifecycle [email protected]~start: [email protected]
7 verbose lifecycle [email protected]~start: unsafe-perm in lifecycle true
8 verbose lifecycle [email protected]~start: PATH: /usr/lib/node_modules/npm/node_modules/npm-lifecycle/node-gyp-bin:/home/charlottenilsen/q2studio-2019.1.0/node_modules/.bin:/home/charlottenilsen/miniconda2/envs/qiime2-2019.1/bin:/home/charlottenilsen/miniconda2/condabin:/home/charlottenilsen/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.UbuntuonWindows_1804.2018.817.0_x64__79rhkp1fndgsc:/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/Applied Biosystems/SeqScanner/bin:/snap/bin
9 verbose lifecycle [email protected]~start: CWD: /home/charlottenilsen/q2studio-2019.1.0
10 silly lifecycle [email protected]~start: Args: [ ‘-c’,
10 silly lifecycle ‘cross-env NODE_ENV=production electron -r babel-register build/main.js’ ]
11 silly lifecycle [email protected]~start: Returned: code: 1 signal: null
12 info lifecycle [email protected]~start: Failed to exec start script
13 verbose stack Error: [email protected] start: cross-env NODE_ENV=production electron -r babel-register build/main.js
13 verbose stack Exit status 1
13 verbose stack at EventEmitter. (/usr/lib/node_modules/npm/node_modules/npm-lifecycle/index.js:301:16)
13 verbose stack at EventEmitter.emit (events.js:189:13)
13 verbose stack at ChildProcess. (/usr/lib/node_modules/npm/node_modules/npm-lifecycle/lib/spawn.js:55:14)
13 verbose stack at ChildProcess.emit (events.js:189:13)
13 verbose stack at maybeClose (internal/child_process.js:970:16)
13 verbose stack at Process.ChildProcess._handle.onexit (internal/child_process.js:259:5)
14 verbose pkgid [email protected]
15 verbose cwd /home/charlottenilsen/q2studio-2019.1.0
16 verbose Linux 4.4.0-17763-Microsoft
17 verbose argv “/usr/bin/node” “/usr/bin/npm” “start”
18 verbose node v10.15.1
19 verbose npm v6.4.1
20 error code ELIFECYCLE
21 error errno 1
22 error [email protected] start: cross-env NODE_ENV=production electron -r babel-register build/main.js
22 error Exit status 1
23 error Failed at the [email protected] start script.
23 error This is probably not a problem with npm. There is likely additional logging output above.
24 verbose exit [ 1, true ]

Hi,
tried to start q2studio today, but the error message has changed:

(qiime2-2019.1) [email protected]:~/q2studio-2019.1.0$ sudo npm start
[sudo] password for charlottenilsen:

[email protected] start /home/charlottenilsen/q2studio-2019.1.0
cross-env NODE_ENV=production electron -r babel-register build/main.js

npm ERR! Linux 4.4.0-17763-Microsoft
npm ERR! argv “/usr/bin/node” “/usr/bin/npm” “start”
npm ERR! node v8.10.0
npm ERR! npm v3.5.2
npm ERR! code ELIFECYCLE
npm ERR! [email protected] 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 [email protected] 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/charlottenilsen/q2studio-2019.1.0/npm-debug.log

Any solutions to this: 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

Here is the debug log:
(qiime2-2019.1) [email protected]:~/q2studio-2019.1.0$ cat /home/charlottenilsen/q2studio-2019.1.0/npm-debug.log
0 info it worked if it ends with ok
1 verbose cli [ ‘/usr/bin/node’, ‘/usr/bin/npm’, ‘start’ ]
2 info using [email protected]
3 info using [email protected]
4 verbose run-script [ ‘prestart’, ‘start’, ‘poststart’ ]
5 info lifecycle [email protected]~prestart: [email protected]
6 silly lifecycle [email protected]~prestart: no script for prestart, continuing
7 info lifecycle [email protected]~start: [email protected]
8 verbose lifecycle [email protected]~start: unsafe-perm in lifecycle true
9 verbose lifecycle [email protected]~start: PATH: /usr/share/npm/bin/node-gyp-bin:/home/charlottenilsen/q2studio-2019.1.0/node_modules/.bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin
10 verbose lifecycle [email protected]~start: CWD: /home/charlottenilsen/q2studio-2019.1.0
11 silly lifecycle [email protected]~start: Args: [ ‘-c’,
11 silly lifecycle ‘cross-env NODE_ENV=production electron -r babel-register build/main.js’ ]
12 silly lifecycle [email protected]~start: Returned: code: 1 signal: null
13 info lifecycle [email protected]~start: Failed to exec start script
14 verbose stack Error: [email protected] start: cross-env NODE_ENV=production electron -r babel-register build/main.js
14 verbose stack Exit status 1
14 verbose stack at EventEmitter. (/usr/share/npm/lib/utils/lifecycle.js:232:16)
14 verbose stack at emitTwo (events.js:126:13)
14 verbose stack at EventEmitter.emit (events.js:214:7)
14 verbose stack at ChildProcess. (/usr/share/npm/lib/utils/spawn.js:24:14)
14 verbose stack at emitTwo (events.js:126:13)
14 verbose stack at ChildProcess.emit (events.js:214:7)
14 verbose stack at maybeClose (internal/child_process.js:925:16)
14 verbose stack at Process.ChildProcess._handle.onexit (internal/child_process.js:209:5)
15 verbose pkgid [email protected]
16 verbose cwd /home/charlottenilsen/q2studio-2019.1.0
17 error Linux 4.4.0-17763-Microsoft
18 error argv “/usr/bin/node” “/usr/bin/npm” “start”
19 error node v8.10.0
20 error npm v3.5.2
21 error code ELIFECYCLE
22 error [email protected] start: cross-env NODE_ENV=production electron -r babel-register build/main.js
22 error Exit status 1
23 error Failed at the [email protected] 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 ]

Node.js and npm Version:
(qiime2-2019.1) [email protected]:~/q2studio-2019.1.0$ nodejs -v
v8.10.0
(qiime2-2019.1) [email protected]:~/q2studio-2019.1.0$ npm -v
6.8.0

Charlotte

Hi @charlotte.nilsen,

Sorry I didn't pick up on this in the initial post.

q2studio will not be able to start because there is not a corresponding X server for it to communicate with (this is how graphics show up on Linux typically). WSL is essentially a "headless" environment, which will work fine for almost anything as long as you don't attempt to draw a graphical UI.

This guide suggests it may be possible to run GUIs on WSL after some tinkering:

But I don't know how well that will work as I haven't tried it myself.

Are you familiar with X-forwarding or is this all new? It would be a good learning oppurtunity, however don't get discouraged if it doesn't seem to be working as X servers and forwarding X sessions is a really complicated thing that even a lot of programmers are unfamiliar with.

Another option would include using VirtualBox (which conflicts with the Hyper V system that WSL uses, so you could only use one or the other between system restarts).

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