minKNOW (Linux Version)

cement_head · 03-31-2017, 08:28 AM

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

Does it work well?

Thanks,
Andor

wdecoster · 04-02-2017, 09:17 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, 11:16 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, 12:43 PM

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, 04:28 AM

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

GenoMax · 04-04-2017, 04:58 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, 05:17 AM

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

gringer · 04-04-2017, 05:24 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, 06:03 AM

Quote:

Originally Posted by gringer

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, 10:35 PM

Quote:

Originally Posted by wdecoster

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, 05:42 AM

Quote:

Originally Posted by pranalis

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.

cement_head · 05-10-2018, 07:47 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, 07:54 AM

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

GenoMax · 05-10-2018, 07:56 AM

Perhaps you are using an unsupported linux distro?

cement_head · 05-10-2018, 07:58 AM

Quote:

Originally Posted by pranalis

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, 06:52 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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03-31-2017, 08:28 AM	#1
cement_head Senior Member Location: Oxford, Ohio Join Date: Mar 2012 Posts: 253	minKNOW (Linux Version) Anyone used the linux variant of the minION software? (minKNOW)? Does it work well? Thanks, Andor

04-03-2017, 12:43 PM	#4
cement_head Senior Member Location: Oxford, Ohio Join Date: Mar 2012 Posts: 253	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 Last edited by cement_head; 04-03-2017 at 12:49 PM.

05-10-2018, 07:47 AM	#12
cement_head Senior Member Location: Oxford, Ohio Join Date: Mar 2012 Posts: 253	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> Last edited by cement_head; 05-10-2018 at 07:51 AM.

05-16-2018, 06:52 AM	#16
iltisanni Member Location: Mainz, Germany Join Date: Mar 2017 Posts: 21	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 Last edited by iltisanni; 05-16-2018 at 07:01 AM.

04-02-2017, 09:17 AM	#2
wdecoster Member Location: Antwerp, Belgium Join Date: Oct 2015 Posts: 97	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.

04-03-2017, 11:16 AM	#3
gringer David Eccles (gringer) Location: Wellington, New Zealand Join Date: May 2011 Posts: 838	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.

04-04-2017, 04:28 AM	#5
wdecoster Member Location: Antwerp, Belgium Join Date: Oct 2015 Posts: 97	No, but I should note that I still have to update our installation to the latest version.

04-04-2017, 04:58 AM	#6
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	@cement_head: Can you check the suggestion in this post? It may be completely unrelated but worth a check.

04-04-2017, 05:17 AM	#7
cement_head Senior Member Location: Oxford, Ohio Join Date: Mar 2012 Posts: 253	I'm pretty sure that's it, I can't find the bash script to edit.

04-04-2017, 05:24 AM	#8
gringer David Eccles (gringer) Location: Wellington, New Zealand Join Date: May 2011 Posts: 838	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.

05-10-2018, 07:54 AM	#13
pranalis Junior Member Location: bangalore Join Date: May 2018 Posts: 2	Well I have tried that too. The system doesn't detect the device at all

05-10-2018, 07:56 AM	#14
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Perhaps you are using an unsupported linux distro?