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-   -   minKNOW (Linux Version) (http://seqanswers.com/forums/showthread.php?t=75136)

cement_head 03-31-2017 07:28 AM

minKNOW (Linux Version)
 
Anyone used the linux variant of the minION software? (minKNOW)?

Does it work well?

Thanks,
Andor

wdecoster 04-02-2017 08:17 AM

I installed it because the Windows version was being annoying. The problem was solved on Ubuntu16.04, but we haven't started a run yet so can't I comment on that.

gringer 04-03-2017 10:16 AM

I have a small screen, so need to shuffle the windows around to be able to click important things (e.g. the button to start a run), but otherwise it works fine.

cement_head 04-03-2017 11:43 AM

Using Ubuntu 16.04.2 LTS AMD64

Did you guys get this install error:

Setting up minknow-map (1.5.5-1~trusty) ...
insserv: Script minknow is broken: incomplete LSB comment.
insserv: missing valid name for `Provides:' please add.

The minKNOW GUI seems to load without error (even from terminal; no errors/warnings).

- Andor

wdecoster 04-04-2017 03:28 AM

No, but I should note that I still have to update our installation to the latest version.

GenoMax 04-04-2017 03:58 AM

@cement_head: Can you check the suggestion in this post? It may be completely unrelated but worth a check.

cement_head 04-04-2017 04:17 AM

I'm pretty sure that's it, I can't find the bash script to edit.

gringer 04-04-2017 04:24 AM

Yes, I got that warning. It doesn't affect the running of the program, just means that the people who prepared the package were a bit lazy with fulfilling all the deb package requirements.

cement_head 04-04-2017 05:03 AM

Quote:

Originally Posted by gringer (Post 205919)
Yes, I got that warning. It doesn't affect the running of the program, just means that the people who prepared the package were a bit lazy with fulfilling all the deb package requirements.

Okay, thanks. I cross-posted this bug/warning to the Nanopore Community Forum.

- Andor

pranalis 05-09-2018 09:35 PM

Quote:

Originally Posted by wdecoster (Post 205867)
I installed it because the Windows version was being annoying. The problem was solved on Ubuntu16.04, but we haven't started a run yet so can't I comment on that.

I have been having problems with the linux version as well. I am able to successfully install minKnow on my ubuntu machine but even though I have multiple USB 3 ports none of them are able to detect the sequencer. Did you do any additional installation for it? Is there something I am missing?

cement_head 05-10-2018 04:42 AM

Quote:

Originally Posted by pranalis (Post 217210)
I have been having problems with the linux version as well. I am able to successfully install minKnow on my ubuntu machine but even though I have multiple USB 3 ports none of them are able to detect the sequencer. Did you do any additional installation for it? Is there something I am missing?

You have to reboot after installation.

If you've done that, without starting the MinKnow software, does your computer (OS) see the sequencer?

Open a terminal and type lsusb and see if it's listed; it should show up as per the screenshot, the second <$ lsusb> command show the minION listed as the first device.


https://flic.kr/p/26X6F63

cement_head 05-10-2018 06:47 AM

For some reason I can't link a image from FLICKR to the forum.

Basically it should show up as:

$ lsusb
Bus 002 Device 001: ID 2a1d:001 <there will be no description>

pranalis 05-10-2018 06:54 AM

Well I have tried that too. The system doesn't detect the device at all

GenoMax 05-10-2018 06:56 AM

Perhaps you are using an unsupported linux distro?

cement_head 05-10-2018 06:58 AM

Quote:

Originally Posted by pranalis (Post 217229)
Well I have tried that too. The system doesn't detect the device at all

Okay, so the issue is NOT the minION, nor the minKNOW software, the issue is your machine.

Do other USB thumbdrives work?

One thing to check is at BOOT, select the BIOS menu (F2, or F7 or F12 or DEL) and make sure that the USB hub is (i) enabled and (ii) enabled for LEGACY as well. Reboot and try again.

iltisanni 05-16-2018 05:52 AM

Have you tried starting the service via terminal manually?
On our Ubuntu 18.04 the minion is not detectable (Unable to connect to the MinKNOW manager instance) until I execute the following commands:

cd /opt/ONT/MinKNOW
sudo bin/mk_manager_svc

https://community.nanoporetech.com/s...know%20service


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