From tony.travis at minke-informatics.co.uk  Thu Mar  2 04:44:52 2017
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Thu, 2 Mar 2017 09:44:52 +0000
Subject: [Bio-linux-list] FW: bio-linux manager password
In-Reply-To: <VI1PR0601MB2494DA328D4F71062A457F25E5280@VI1PR0601MB2494.eurprd06.prod.outlook.com>
References: <CA+w3U6hma3ejw1zZ3KoV1Z-VOoD=tkECPK=gFd_WBhdizZz==Q@mail.gmail.com>
	<VI1PR0601MB2494DA328D4F71062A457F25E5280@VI1PR0601MB2494.eurprd06.prod.outlook.com>
Message-ID: <84614fb2-b1fc-6c61-183e-94160b00a3d4@minke-informatics.co.uk>

On 02/03/17 08:52, Timms-Wilson, Tracey wrote:
>  
> 
>  
> 
> *From:*disheng liu [mailto:liumengjiadis at gmail.com]
> *Sent:* 02 March 2017 01:41
> *To:* Timms-Wilson, Tracey <tmt at ceh.ac.uk>
> *Subject:* bio-linux manager password
> 
>  
> 
> hi,
> 
>   I have just downloaded the bio-linux-8-latest.ova from your website, I
> imported the ova file into the VMware, now I have a question, I don't
> know the password of the manager(root) .
> 
>   I have read many documents again and again, but my English is limited
> and I can find the default password. so I wish u can reply me the letter
> and told me the password. 

Hi, Mengjia.

Tracey forwarded your message to me and I've CC'ed my reply to the
Bio-Linux mailing list in case anyone else has the same problem.

The default password for the "manager" account on the Bio-Linux .ova is
"manager". This information is given on the Bio-Linux web-page at:

> http://environmentalomics.org/bio-linux-installation/

Instructions for importing the .ova into "Virtualbox" are:

> Setup for VirtualBox:
> 
>     Ensure you have at least 40GB free disk space.
>     Download and install the appropriate version of VirtualBox from the link above.
>     Download the OVA file.
>     Start VirtualBox and select Import Appliance from the File menu and import the .ova file (don?t worry that it says you need an OVF file).
>     When importing the appliance, select the option to reinitialize the MAC addresses of network cards.
>     Start the VM and if you see a log-in screen, log in as user manager with password also manager.
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>     Once this is working, you can delete the .ova file to save space.
>     See the VirtualBox docs for more details including how to share folders and hardware.  You will also want to adjust hardware settings such as CPU, RAM and video acceleration settings to suit your hardware.

You can import the .ova into VMware in a similar way and use the same
"manager" account with password "manager".

PLEASE NOTE: You should change the "manager" password to something more
secure if you connect your Bio-Linux VM instance to the Internet!

HTH,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk

From dr.tony.travis at gmail.com  Mon Mar 20 05:55:48 2017
From: dr.tony.travis at gmail.com (Tony Travis)
Date: Mon, 20 Mar 2017 09:55:48 +0000
Subject: [Bio-linux-list] FW: account password of Bio-Linux
In-Reply-To: <HE1PR0601MB2490D506BB3D5B5A32D57612E53A0@HE1PR0601MB2490.eurprd06.prod.outlook.com>
References: <201703171859304585034@foxmail.com>
	<HE1PR0601MB2490D506BB3D5B5A32D57612E53A0@HE1PR0601MB2490.eurprd06.prod.outlook.com>
Message-ID: <5e2b3375-a4db-55a7-29ab-dcd750125e02@minke-informatics.co.uk>

On 20/03/17 08:44, Timms-Wilson, Tracey wrote:
>  
> 
>  
> 
> *From:*gw.lee at foxmail.com [mailto:gw.lee at foxmail.com]
> *Sent:* 17 March 2017 11:00
> *To:* Timms-Wilson, Tracey <tmt at ceh.ac.uk>
> *Subject:* account password of Bio-Linux
> 
>  
> 
> Dear Tracey,
> 
>     I'm very grateful that you offer us the Bio-Linux. That's a
> wonderful system for biologist. 
> 
>     But I still have a little requirement, i was wondering if you could
> tell me the password of "System Manager"? Cuz we deeply need
>  authentication when we are working.

Hi, Guowei.

Tracey forwarded your question to me and I've CC'ed it to the Bio-Linux
mailing list for anyone else who has the same problem. The password for
the "manager" account on the VM is "manager" as described here:

> http://environmentalomics.org/bio-linux-installation/

Note: Please change the password if your VM is connected to a network.

Let me know how you get on using the Bio-Linux VM,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk

From dr.tony.travis at gmail.com  Mon Mar 20 10:52:37 2017
From: dr.tony.travis at gmail.com (Tony Travis)
Date: Mon, 20 Mar 2017 14:52:37 +0000
Subject: [Bio-linux-list] FW: GROMACS in Bio-Linux
In-Reply-To: <HE1PR0601MB24906FE6579AE6D8BCEDA0DAE53A0@HE1PR0601MB2490.eurprd06.prod.outlook.com>
References: <CACvwHkE=5GVQ68XfJ2vMy8-RenyMak7XMSWANQW2DNkZy=rxvw@mail.gmail.com>
	<HE1PR0601MB24906FE6579AE6D8BCEDA0DAE53A0@HE1PR0601MB2490.eurprd06.prod.outlook.com>
Message-ID: <fcd3a879-abe8-630f-8bec-f0f494f95527@minke-informatics.co.uk>

On 20/03/17 08:48, Timms-Wilson, Tracey wrote:
>  
> 
>  
> 
> *From:*Bishwajit Das [mailto:das.bishwajit at gmail.com]
> *Sent:* 18 March 2017 10:18
> *To:* Timms-Wilson, Tracey <tmt at ceh.ac.uk>
> *Subject:* GROMACS in Bio-Linux
> 
>  
> 
> Dear Prof. Tracey Timms-Wilson
> 
> I want to calculate free energy (MM-PBSA/MM-GBSA) in GROMACS, but I
> couldn't find GROMACS in your software list. So Please let me know
> whether GROMACS is available in Bio-Linux ? If no, then Please let me
> know the procedure to install GROMACS in Bio-Linux.

Hi, Bishwat.

Tracey forwarded your email to me and I'm copying my reply to the list
in case anyone else has the same problem. In fact, "GROMACS" is not part
of Bio-Linux - It's available in the standard Ubuntu repositories and
can be installed under Bio-Linux 8 (based on Ubuntu 14.04 LTS):

> rwt017 at wildcat:~$ lsb_release -d
> Description:	Ubuntu 14.04.5 LTS
> rwt017 at wildcat:~$ apt-cache policy gromacs
> gromacs:
>   Installed: 4.6.5-1build1
>   Candidate: 4.6.5-1build1
>   Version table:
>  *** 4.6.5-1build1 0
>         500 http://gb.archive.ubuntu.com/ubuntu/ trusty/universe amd64 Packages
>         100 /var/lib/dpkg/status
>      4.5.5-1 0
>         500 http://archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages

HTH,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk

From mkmodi at aau.ac.in  Mon Mar 20 11:47:20 2017
From: mkmodi at aau.ac.in (Mahendra Modi)
Date: Mon, 20 Mar 2017 21:17:20 +0530
Subject: [Bio-linux-list] FW: GROMACS in Bio-Linux
In-Reply-To: <fcd3a879-abe8-630f-8bec-f0f494f95527@minke-informatics.co.uk>
References: <CACvwHkE=5GVQ68XfJ2vMy8-RenyMak7XMSWANQW2DNkZy=rxvw@mail.gmail.com>
	<HE1PR0601MB24906FE6579AE6D8BCEDA0DAE53A0@HE1PR0601MB2490.eurprd06.prod.outlook.com>
	<fcd3a879-abe8-630f-8bec-f0f494f95527@minke-informatics.co.uk>
Message-ID: <CAPUhUGxQGRSfMRZy6RK0Gic7V4RRVVmX=cKCKK4dsdNKG6WkLQ@mail.gmail.com>

Hi all,

Tony described the easiest way to install Gromacs on biolinux. However,
using simple consumer Nvidia GPU cards like GTX 1050Ti, ($150) one can
speed up Gromacs considerably. In this case it is better to install Gromacs
5 current stable version following the quick & dirty installation guide
available on Gromacs website. It doesn't break any other bio-linux package.

Mahendra K Modi

On Mar 20, 2017 20:22, "Tony Travis" <dr.tony.travis at gmail.com> wrote:

> On 20/03/17 08:48, Timms-Wilson, Tracey wrote:
> >
> >
> >
> >
> > *From:*Bishwajit Das [mailto:das.bishwajit at gmail.com]
> > *Sent:* 18 March 2017 10:18
> > *To:* Timms-Wilson, Tracey <tmt at ceh.ac.uk>
> > *Subject:* GROMACS in Bio-Linux
> >
> >
> >
> > Dear Prof. Tracey Timms-Wilson
> >
> > I want to calculate free energy (MM-PBSA/MM-GBSA) in GROMACS, but I
> > couldn't find GROMACS in your software list. So Please let me know
> > whether GROMACS is available in Bio-Linux ? If no, then Please let me
> > know the procedure to install GROMACS in Bio-Linux.
>
> Hi, Bishwat.
>
> Tracey forwarded your email to me and I'm copying my reply to the list
> in case anyone else has the same problem. In fact, "GROMACS" is not part
> of Bio-Linux - It's available in the standard Ubuntu repositories and
> can be installed under Bio-Linux 8 (based on Ubuntu 14.04 LTS):
>
> > rwt017 at wildcat:~$ lsb_release -d
> > Description:  Ubuntu 14.04.5 LTS
> > rwt017 at wildcat:~$ apt-cache policy gromacs
> > gromacs:
> >   Installed: 4.6.5-1build1
> >   Candidate: 4.6.5-1build1
> >   Version table:
> >  *** 4.6.5-1build1 0
> >         500 http://gb.archive.ubuntu.com/ubuntu/ trusty/universe amd64
> Packages
> >         100 /var/lib/dpkg/status
> >      4.5.5-1 0
> >         500 http://archive.ubuntu.com/ubuntu/ precise/universe amd64
> Packages
>
> HTH,
>
>   Tony.
>
> --
> Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> tel. +44(0)19755 63548                    http://minke-informatics.co.uk
> mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk
> _______________________________________________
> Bio-Linux-list mailing list
> Bio-Linux-list at bioinformatics.org
> http://www.bioinformatics.org/mm/listinfo/bio-linux-list
>
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From dr.tony.travis at gmail.com  Wed Mar 29 05:42:50 2017
From: dr.tony.travis at gmail.com (Tony Travis)
Date: Wed, 29 Mar 2017 10:42:50 +0100
Subject: [Bio-linux-list] How to expand the storage capacity of Bio-Linux
In-Reply-To: <tencent_213566F444866D95343EB65F@qq.com>
References: <201703171859304585034@foxmail.com>
	<HE1PR0601MB2490D506BB3D5B5A32D57612E53A0@HE1PR0601MB2490.eurprd06.prod.outlook.com>
	<5e2b3375-a4db-55a7-29ab-dcd750125e02@minke-informatics.co.uk>
	<tencent_213566F444866D95343EB65F@qq.com>
Message-ID: <5b2106ee-7784-cd46-7981-79914a47ffcf@minke-informatics.co.uk>

On 29/03/17 09:00, ??? wrote:
> Dear Tony,
> 
> I think I have got another problem right now. The default harddrive
> storage capacity is about 100 GB for the Bio-Linux vmdk, I want to know
> how to expand it out of my work needed.
> Thanks for all the hard work you have done!

Hi, Guowei.

There isn't a simple way to expand the size of a virtual disk image,
because you also have to resize the filesystem it contains. However,
these links might help:

> https://mariusvw.com/2017/03/01/how-to-resizegrow-a-vmware-or-virtualbox-disk/
> https://kb.vmware.com/selfservice/microsites/search.do?language=en_US&cmd=displayKC&externalId=1004047

A simpler option is to create a new virtual disk and mount it as e.g.

  /work

This is what I do :-)

HTH,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk

From gawbul at gmail.com  Wed Mar 29 06:22:21 2017
From: gawbul at gmail.com (Steve Moss)
Date: Wed, 29 Mar 2017 11:22:21 +0100
Subject: [Bio-linux-list] How to expand the storage capacity of Bio-Linux
In-Reply-To: <5b2106ee-7784-cd46-7981-79914a47ffcf@minke-informatics.co.uk>
References: <201703171859304585034@foxmail.com>
	<HE1PR0601MB2490D506BB3D5B5A32D57612E53A0@HE1PR0601MB2490.eurprd06.prod.outlook.com>
	<5e2b3375-a4db-55a7-29ab-dcd750125e02@minke-informatics.co.uk>
	<tencent_213566F444866D95343EB65F@qq.com>
	<5b2106ee-7784-cd46-7981-79914a47ffcf@minke-informatics.co.uk>
Message-ID: <CALKAsdp3Kp=vbJpXHnoMzDV28aYuC9W70TCy8qsLBnqGQYjRww@mail.gmail.com>

I also like this link re. resizing - it has more screen dumps, though is
specific to VirtualBox -
http://www.tomordonez.com/virtualbox-resize-disk-vmdk-vdi/.

---
*Dr. Stephen Moss*
e: gawbul at gmail.com
www: https://www.gawbul.io

On 29 March 2017 at 10:42, Tony Travis <dr.tony.travis at gmail.com> wrote:

> On 29/03/17 09:00, ??? wrote:
> > Dear Tony,
> >
> > I think I have got another problem right now. The default harddrive
> > storage capacity is about 100 GB for the Bio-Linux vmdk, I want to know
> > how to expand it out of my work needed.
> > Thanks for all the hard work you have done!
>
> Hi, Guowei.
>
> There isn't a simple way to expand the size of a virtual disk image,
> because you also have to resize the filesystem it contains. However,
> these links might help:
>
> > https://mariusvw.com/2017/03/01/how-to-resizegrow-a-vmware-
> or-virtualbox-disk/
> > https://kb.vmware.com/selfservice/microsites/search.
> do?language=en_US&cmd=displayKC&externalId=1004047
>
> A simpler option is to create a new virtual disk and mount it as e.g.
>
>   /work
>
> This is what I do :-)
>
> HTH,
>
>   Tony.
>
> --
> Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> tel. +44(0)19755 63548                    http://minke-informatics.co.uk
> mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk
> _______________________________________________
> Bio-Linux-list mailing list
> Bio-Linux-list at bioinformatics.org
> http://www.bioinformatics.org/mm/listinfo/bio-linux-list
>
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