From anate25 at gmail.com  Fri Nov  4 12:32:03 2011
From: anate25 at gmail.com (Anat Eck)
Date: Fri, 4 Nov 2011 17:32:03 +0100
Subject: [Bio-Linux] Problem Calling ChimeraSlayer through Qiime installed
	on Bio-Linux 6
Message-ID: <CALH4QeqsCXJ8s9QOufUED2jGPHZ7V+gfZshDaJ5-6-DsF=xUKA@mail.gmail.com>

Dear Bio-Linux users,

I'm trying to run ChimeraSlayer using Qiime 1.3.0 on Bio-Linux.
The versions I have installed are:

dpkg -s qiime bio-linux-qiime chimeraslayer | grep ^Version
Version: 1.3.0-0ubuntu6
Version: 1:1.3.0bl-6
Version: 20101212-1ubuntu5

I have ChimeraSlayer in the PATH, but for some reason I get an error when
trying to call it using the qiime script as follows:

identify_chimeric_seqs.py -i rep_set_aligned.fna -a
Silva_108_core_aligned_seqs.fna -o chimeric_seqs.txtTraceback (most recent
call last):
  File "/usr/lib/qiime/bin/identify_chimeric_seqs.py", line 172, in <module>
    main()
  File "/usr/lib/qiime/bin/identify_chimeric_seqs.py", line 169, in main
    keep_intermediates=keep_intermediates)
  File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py",
line 148, in chimeraSlayer_identify_chimeras
    keep_intermediates=keep_intermediates):
  File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py",
line 133, in __call__
    keep_intermediates=keep_intermediates)
  File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py",
line 592, in get_chimeras_from_Nast_aligned
    app_results = app()
  File "/usr/lib/pymodules/python2.6/cogent/app/util.py", line 269, in
__call__
    result_paths=self._get_result_paths(data))
  File "/usr/lib/python2.6/dist-packages/qiime/identify_chimeric_seqs.py",
line 405, in _get_result_paths
    raise ApplicationError,"Calling ChimeraSlayer failed."
cogent.app.util.ApplicationError: Calling ChimeraSlayer failed.

I will be grateful for a hint if this kind of error had occurred to anyone
else.
I'm attaching the configuration report I get from Qiime:

root at chaysavanh-desktop:~#  qiime > print_qiime_config.py -t

System information
==================
         Platform:    linux2
   Python version:    2.6.5 (r265:79063, Apr 16 2010, 13:57:41)  [GCC 4.4.3]
Python executable:    /usr/bin/python2.6

Dependency versions
===================
                     PyCogent version:    1.5.1
                        NumPy version:    1.3.0
                   matplotlib version:    0.99.1.1
                QIIME library version:    1.3.0
                 QIIME script version:    1.3.0
        PyNAST version (if installed):    1.1
RDP Classifier version (if installed):    Not installed.

QIIME config values
===================
                     blastmat_dir:    /usr/share/ncbi/data
      topiaryexplorer_project_dir:    None
     pynast_template_alignment_fp:    None
                  cluster_jobs_fp:    None
pynast_template_alignment_blastdb:    None
                     torque_queue:    friendlyq
   template_alignment_lanemask_fp:    None
                    jobs_to_start:    1
                cloud_environment:    False
                qiime_scripts_dir:    /usr/lib/qiime/bin/
            denoiser_min_per_core:    50
                      working_dir:    .
                    python_exe_fp:    python
                         temp_dir:    /tmp
                      blastall_fp:    blastall
                 seconds_to_sleep:    60


running checks:

FastTree is in path and version is supported ... ok
INFERNAL is in path and version is supported ... ok
AmpliconNoise install looks sane. ... ok
blast is in path and version is supported ... FAIL
blastall_fp is set to a valid path ... ok
blastmat_dir is set to a valid path. ... ok
cdbtools is in path and version is supported ... ok
cd-hit is in path and version is supported ... ok
no obvious problems with ChimeraSlayer install ... ok
clearcut is in path and version is supported ... FAIL
cluster_jobs_fp is set to a valid path and is executable ... ok
denoiser aligner is ready to use ... ok
local qiime_config has no extra params ... ok
maptplotlib version is supported ... FAIL
mothur is in path and version is supported ... ERROR
muscle is in path and version is supported ... FAIL
numpy version is supported ... ok
pynast version is supported ... ok
pynast_template_alignment_blastdb, if set, is set to a valid path ... ok
pynast_template_alignment, if set, is set to a valid path ... ok
python_exe_fp is set to a working python env ... ok
python is in path and version is supported ... ok
qiime_scripts_dir, if set, is set to a valid path ... ok
raxmlHPC is in path and version is supported ... FAIL
temp_dir, if set, is set to a valid path ... ok
template_alignment_lanemask, if set, is set to a valid path ... ok
uclust is in path and version is supported ... ok
working_dir, if set, is set to a valid path ... ok

======================================================================
ERROR: mothur is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/qiime/bin/print_qiime_config.py", line 472, in
test_mothur_supported_version
    version_string = stdout.strip().split(' ')[1].strip('v.')
IndexError: list index out of range

======================================================================
FAIL: blast is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/qiime/bin/print_qiime_config.py", line 374, in
test_blast_supported_version
    % ('.'.join(map(str,acceptable_version)), version_string))
AssertionError: Unsupported blast version. 2.2.22 is required, but running
2.2.21.

======================================================================
FAIL: clearcut is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/qiime/bin/print_qiime_config.py", line 525, in
test_clearcut_supported_version
    "which components of QIIME you plan to use.")
AssertionError: clearcut not found. This may or may not be a problem
depending on which components of QIIME you plan to use.

======================================================================
FAIL: maptplotlib version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/qiime/bin/print_qiime_config.py", line 332, in
test_matplotlib_suported_version
    version_string))
AssertionError: Unsupported matplotlib version. Must be >= 0.98.5.3 and <
0.98.5.4 , but running 0.99.1.1.

======================================================================
FAIL: muscle is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/qiime/bin/print_qiime_config.py", line 458, in
test_muscle_supported_version
    % ('.'.join(map(str,acceptable_version)), version_string))
AssertionError: Unsupported muscle version. 3.6 is required, but running
3.7.

======================================================================
FAIL: raxmlHPC is in path and version is supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/qiime/bin/print_qiime_config.py", line 504, in
test_raxmlHPC_supported_version
    "which components of QIIME you plan to use.")
AssertionError: raxmlHPC not found. This may or may not be a problem
depending on which components of QIIME you plan to use.

----------------------------------------------------------------------
Ran 28 tests in 0.048s

FAILED (failures=5, errors=1)

And my PATH value:

root at chaysavanh-desktop:~# grep -i chimera ~/.bashrc
/root/.bashrc:export
PATH=:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/NX/bin:/usr/lib/qiime/bin:/usr/share/ampliconnoise/Scripts:/usr/lib/ChimeraSlayer

Thank you,
Anat

2011/11/4 Tim Booth via RT <website at nebc.nerc.ac.uk>

> Hi Anat,
>
> I think you just need to run:
>
> sudo apt-get install bio-linux-qiime
>
> This is a wrapper package that, amongst othter things, installs the
> uCLust clustering tool.  We can't put that in the main package due to
> licensing restrictions.
>
> Cheers,
>
> TIM
>
>
> --
> This message (and any attachments) is for the recipient only. NERC
> is subject to the Freedom of Information Act 2000 and the contents
> of this email and any reply you make may be disclosed by NERC unless
> it is exempt from release under the Act. Any material supplied to
> NERC may be stored in an electronic records management system.
>
>
>
>
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From djp39 at st-andrews.ac.uk  Mon Nov 14 06:45:23 2011
From: djp39 at st-andrews.ac.uk (Darren Parker)
Date: Mon, 14 Nov 2011 11:45:23 +0000
Subject: [Bio-Linux] Installing bio-linux
Message-ID: <CAOsefcVNEUeAKLTy_E4Nfgvv-HVgjC443ZHj-G0HpWUay681Ug@mail.gmail.com>

Hello

I am trying to install bio-linux onto my laptop as a duel boot from the
bio-linux memory stick.

However when I get to step 4/7 (where I want to install biolinux) I do not
have an option for installing them side by side (as it says in the
installation guide), just erase and specify partitions manually. Do you
know why this is?

Many thanks

Darren Parker

-- 

Darren J. Parker
Ph.D Student

Centre for Evolution, Genes and Genomics
School of Biology
Dyers Brae House
University of St Andrews
St Andrews, Fife
Scotland KY16 9TH

Phone: 01334 463371

http://www.genestobehaviour.co.uk/

http://biology.st-andrews.ac.uk/ritchielab/researchGroup/djp39/darrenParker.html
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From tbooth at ceh.ac.uk  Mon Nov 14 06:58:24 2011
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 14 Nov 2011 11:58:24 +0000
Subject: [Bio-Linux] Installing bio-linux
In-Reply-To: <CAOsefcVNEUeAKLTy_E4Nfgvv-HVgjC443ZHj-G0HpWUay681Ug@mail.gmail.com>
References: <CAOsefcVNEUeAKLTy_E4Nfgvv-HVgjC443ZHj-G0HpWUay681Ug@mail.gmail.com>
Message-ID: <1321271904.3992.497.camel@barsukas.nwl.ac.uk>

Hi Darren,

Off hand, I don't know what the problem might be, but there are some
things you can check.  If you boot from the USB to the live desktop,
does it recognise your existing Windows drive (under the places menu)?
Can you see the files?

Do you have anything unusual about your Windows set-up - eg. encrypted
disk, unusual partitioning setup, RAID configuration?

Cheers,

TIM

On Mon, 2011-11-14 at 11:45 +0000, Darren Parker wrote:
> Hello
> 
> 
> I am trying to install bio-linux onto my laptop as a duel boot from
> the bio-linux memory stick. 
> 
> 
> However when I get to step 4/7 (where I want to install biolinux) I do
> not have an option for installing them side by side (as it says in the
> installation guide), just erase and specify partitions manually. Do
> you know why this is?
> 
> 
> Many thanks 
> 
> 
> Darren Parker
> 
> 
> 
> -- 
> Darren J. Parker
> Ph.D Student 
> Centre for Evolution, Genes and Genomics
> School of Biology
> Dyers Brae House 
> University of St Andrews 
> St Andrews, Fife 
> Scotland KY16 9TH  
> Phone: 01334 463371
> http://www.genestobehaviour.co.uk/
> http://biology.st-andrews.ac.uk/ritchielab/researchGroup/djp39/darrenParker.html
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705

-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.



From djp39 at st-andrews.ac.uk  Mon Nov 14 07:29:26 2011
From: djp39 at st-andrews.ac.uk (Darren Parker)
Date: Mon, 14 Nov 2011 12:29:26 +0000
Subject: [Bio-Linux] Installing bio-linux
In-Reply-To: <1321271904.3992.497.camel@barsukas.nwl.ac.uk>
References: <CAOsefcVNEUeAKLTy_E4Nfgvv-HVgjC443ZHj-G0HpWUay681Ug@mail.gmail.com>
	<1321271904.3992.497.camel@barsukas.nwl.ac.uk>
Message-ID: <CAOsefcXOUN0x3exT8W1CJZDvT9cWaz8g_=CEO8nCyTKVe0DGUg@mail.gmail.com>

Hey Tim

When running live from the stick I can access all of my files.

There is no encryption or unusual partitions (I think - see attached
picture)

Any ideas?

Darren

On 14 November 2011 11:58, Tim Booth <tbooth at ceh.ac.uk> wrote:

> Hi Darren,
>
> Off hand, I don't know what the problem might be, but there are some
> things you can check.  If you boot from the USB to the live desktop,
> does it recognise your existing Windows drive (under the places menu)?
> Can you see the files?
>
> Do you have anything unusual about your Windows set-up - eg. encrypted
> disk, unusual partitioning setup, RAID configuration?
>
> Cheers,
>
> TIM
>
> On Mon, 2011-11-14 at 11:45 +0000, Darren Parker wrote:
> > Hello
> >
> >
> > I am trying to install bio-linux onto my laptop as a duel boot from
> > the bio-linux memory stick.
> >
> >
> > However when I get to step 4/7 (where I want to install biolinux) I do
> > not have an option for installing them side by side (as it says in the
> > installation guide), just erase and specify partitions manually. Do
> > you know why this is?
> >
> >
> > Many thanks
> >
> >
> > Darren Parker
> >
> >
> >
> > --
> > Darren J. Parker
> > Ph.D Student
> > Centre for Evolution, Genes and Genomics
> > School of Biology
> > Dyers Brae House
> > University of St Andrews
> > St Andrews, Fife
> > Scotland KY16 9TH
> > Phone: 01334 463371
> > http://www.genestobehaviour.co.uk/
> >
> http://biology.st-andrews.ac.uk/ritchielab/researchGroup/djp39/darrenParker.html
> >
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://nebc.nerc.ac.uk
> +44 1491 69 2705
>
> --
> This message (and any attachments) is for the recipient only. NERC
> is subject to the Freedom of Information Act 2000 and the contents
> of this email and any reply you make may be disclosed by NERC unless
> it is exempt from release under the Act. Any material supplied to
> NERC may be stored in an electronic records management system.
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>



-- 

Darren J. Parker
Ph.D Student

Centre for Evolution, Genes and Genomics
School of Biology
Dyers Brae House
University of St Andrews
St Andrews, Fife
Scotland KY16 9TH

Phone: 01334 463371

http://www.genestobehaviour.co.uk/

http://biology.st-andrews.ac.uk/ritchielab/researchGroup/djp39/darrenParker.html
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From A.J.Pemberton at bham.ac.uk  Mon Nov 14 08:59:12 2011
From: A.J.Pemberton at bham.ac.uk (Anthony Pemberton)
Date: Mon, 14 Nov 2011 13:59:12 +0000
Subject: [Bio-Linux] Installing bio-linux
In-Reply-To: <CAOsefcXOUN0x3exT8W1CJZDvT9cWaz8g_=CEO8nCyTKVe0DGUg@mail.gmail.com>
References: <CAOsefcVNEUeAKLTy_E4Nfgvv-HVgjC443ZHj-G0HpWUay681Ug@mail.gmail.com>
	<1321271904.3992.497.camel@barsukas.nwl.ac.uk>
	<CAOsefcXOUN0x3exT8W1CJZDvT9cWaz8g_=CEO8nCyTKVe0DGUg@mail.gmail.com>
Message-ID: <5FAE4EF51F20774D9C21A133494A3FE0182EE2B8E6@LESMBX1.adf.bham.ac.uk>

Darren,

You need some disk space which is currently unformatted  in order to install the Bio-linux, such as another disk. Bio-linux will not install directly in NTFS partitions. You could try installing it as a VM if you first install something like Virtualbox or Vmware and you have plenty of RAM (say 3 Gb or more),

Regards,

Tony Pemberton


From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Darren Parker
Sent: 14 November 2011 12:29
To: Bio-Linux help and discussion
Subject: Re: [Bio-Linux] Installing bio-linux

Hey Tim

When running live from the stick I can access all of my files.

There is no encryption or unusual partitions (I think - see attached picture)

Any ideas?

Darren
On 14 November 2011 11:58, Tim Booth <tbooth at ceh.ac.uk<mailto:tbooth at ceh.ac.uk>> wrote:
Hi Darren,

Off hand, I don't know what the problem might be, but there are some
things you can check.  If you boot from the USB to the live desktop,
does it recognise your existing Windows drive (under the places menu)?
Can you see the files?

Do you have anything unusual about your Windows set-up - eg. encrypted
disk, unusual partitioning setup, RAID configuration?

Cheers,

TIM

On Mon, 2011-11-14 at 11:45 +0000, Darren Parker wrote:
> Hello
>
>
> I am trying to install bio-linux onto my laptop as a duel boot from
> the bio-linux memory stick.
>
>
> However when I get to step 4/7 (where I want to install biolinux) I do
> not have an option for installing them side by side (as it says in the
> installation guide), just erase and specify partitions manually. Do
> you know why this is?
>
>
> Many thanks
>
>
> Darren Parker
>
>
>
> --
> Darren J. Parker
> Ph.D Student
> Centre for Evolution, Genes and Genomics
> School of Biology
> Dyers Brae House
> University of St Andrews
> St Andrews, Fife
> Scotland KY16 9TH
> Phone: 01334 463371
> http://www.genestobehaviour.co.uk/
> http://biology.st-andrews.ac.uk/ritchielab/researchGroup/djp39/darrenParker.html
>
--
Tim Booth <tbooth at ceh.ac.uk<mailto:tbooth at ceh.ac.uk>>
NERC Environmental Bioinformatics Centre

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB

http://nebc.nerc.ac.uk
+44 1491 69 2705

--
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.

_______________________________________________
Bio-Linux mailing list
Bio-Linux at nebclists.nerc.ac.uk<mailto:Bio-Linux at nebclists.nerc.ac.uk>
http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux



--


Darren J. Parker

Ph.D Student

Centre for Evolution, Genes and Genomics
School of Biology

Dyers Brae House

University of St Andrews

St Andrews, Fife

Scotland KY16 9TH

Phone: 01334 463371

http://www.genestobehaviour.co.uk/

http://biology.st-andrews.ac.uk/ritchielab/researchGroup/djp39/darrenParker.html

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From tbooth at ceh.ac.uk  Mon Nov 14 09:18:02 2011
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Mon, 14 Nov 2011 14:18:02 +0000
Subject: [Bio-Linux] Installing bio-linux
In-Reply-To: <5FAE4EF51F20774D9C21A133494A3FE0182EE2B8E6@LESMBX1.adf.bham.ac.uk>
References: <CAOsefcVNEUeAKLTy_E4Nfgvv-HVgjC443ZHj-G0HpWUay681Ug@mail.gmail.com>
	<1321271904.3992.497.camel@barsukas.nwl.ac.uk>
	<CAOsefcXOUN0x3exT8W1CJZDvT9cWaz8g_=CEO8nCyTKVe0DGUg@mail.gmail.com>
	<5FAE4EF51F20774D9C21A133494A3FE0182EE2B8E6@LESMBX1.adf.bham.ac.uk>
Message-ID: <1321280282.3992.675.camel@barsukas.nwl.ac.uk>

Hi,

The installer is definitely able to resize Windows in basic situations,
but maybe your partition layout has stumped it.  I think Tony is right
and you need to do the partitioning manually and leave space for Ubuntu
to install to.  One way I've done this before is to boot from the latest
Ubuntu system rescue CD.

https://help.ubuntu.com/community/DualBoot/Windows#Using_QtParted_from_the_System_Rescue_CD

It's a bit of a faff but it gives you full control and you can resize
NTFS in-place.

It should go without saying: Before repartitioning your Windows drive,
assume you are likely to hose it, and do a full backup.

Cheers,

TIM

-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.



From a.travis at abdn.ac.uk  Mon Nov 14 09:47:58 2011
From: a.travis at abdn.ac.uk (Tony Travis)
Date: Mon, 14 Nov 2011 14:47:58 +0000
Subject: [Bio-Linux] Installing bio-linux
In-Reply-To: <1321280282.3992.675.camel@barsukas.nwl.ac.uk>
References: <CAOsefcVNEUeAKLTy_E4Nfgvv-HVgjC443ZHj-G0HpWUay681Ug@mail.gmail.com>	<1321271904.3992.497.camel@barsukas.nwl.ac.uk>	<CAOsefcXOUN0x3exT8W1CJZDvT9cWaz8g_=CEO8nCyTKVe0DGUg@mail.gmail.com>	<5FAE4EF51F20774D9C21A133494A3FE0182EE2B8E6@LESMBX1.adf.bham.ac.uk>
	<1321280282.3992.675.camel@barsukas.nwl.ac.uk>
Message-ID: <4EC12A1E.4090500@abdn.ac.uk>

On 14/11/11 14:18, Tim Booth wrote:
> Hi,
>
> The installer is definitely able to resize Windows in basic situations,
> but maybe your partition layout has stumped it.  I think Tony is right
> and you need to do the partitioning manually and leave space for Ubuntu
> to install to.  One way I've done this before is to boot from the latest
> Ubuntu system rescue CD.

Hi, Tim.

As far as I can tell from the image that Darren posted the problem is 
that there are already four primary partitions, which is the maximum for 
a DOS partition table. If you want more, you need to make one of these 
four an 'extended' partition. Just shrinking the windows C: partition 
will not solve his problem. However, Darren could use WUBI to create a 
'container' file in the Windows C: NTFS filesystem, and dual-boot from 
that leaving his Windows partitions as they are now.

HTH,

   Tony.

> https://help.ubuntu.com/community/DualBoot/Windows#Using_QtParted_from_the_System_Rescue_CD
>
> It's a bit of a faff but it gives you full control and you can resize
> NTFS in-place.
>
> It should go without saying: Before repartitioning your Windows drive,
> assume you are likely to hose it, and do a full backup.
>
> Cheers,
>
> TIM
>


-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk


From agjennings at gmail.com  Mon Nov 14 14:31:50 2011
From: agjennings at gmail.com (Adam Jennings)
Date: Mon, 14 Nov 2011 14:31:50 -0500
Subject: [Bio-Linux] Installing bio-linux
Message-ID: <CALFa43Cz8gXufSaTGW0zY0XgGnh873Vp8KMeRwMge4--DYnjBw@mail.gmail.com>

Is your windows already taking up all 4 primary partitions?

Read this link on the ubuntu forums:
http://ubuntuforums.org/showthread.php?t=1752582

Adam


Message: 1
> Date: Mon, 14 Nov 2011 11:45:23 +0000
> From: Darren Parker <djp39 at st-andrews.ac.uk>
> Subject: [Bio-Linux] Installing bio-linux
> To: bio-linux at nebclists.nerc.ac.uk
> Message-ID:
>        <CAOsefcVNEUeAKLTy_E4Nfgvv-HVgjC443ZHj-G0HpWUay681Ug at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello
>
> I am trying to install bio-linux onto my laptop as a duel boot from the
> bio-linux memory stick.
>
> However when I get to step 4/7 (where I want to install biolinux) I do not
> have an option for installing them side by side (as it says in the
> installation guide), just erase and specify partitions manually. Do you
> know why this is?
>
> Many thanks
>
> Darren Parker
>
> --
>
> Darren J. Parker
> Ph.D Student
>
> Centre for Evolution, Genes and Genomics
> School of Biology
> Dyers Brae House
> University of St Andrews
> St Andrews, Fife
> Scotland KY16 9TH
>
> Phone: 01334 463371
>
> http://www.genestobehaviour.co.uk/
>
>
> http://biology.st-andrews.ac.uk/ritchielab/researchGroup/djp39/darrenParker.html
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From djp39 at st-andrews.ac.uk  Mon Nov 14 14:55:25 2011
From: djp39 at st-andrews.ac.uk (Darren Parker)
Date: Mon, 14 Nov 2011 19:55:25 +0000
Subject: [Bio-Linux] Installing bio-linux
In-Reply-To: <CALFa43Cz8gXufSaTGW0zY0XgGnh873Vp8KMeRwMge4--DYnjBw@mail.gmail.com>
References: <CALFa43Cz8gXufSaTGW0zY0XgGnh873Vp8KMeRwMge4--DYnjBw@mail.gmail.com>
Message-ID: <CAOsefcVtk=0Eo_Mzez2pi6=PWYzVMztt1Pt07r+AvhKxFbF06g@mail.gmail.com>

Hello

Many thanks for all the help!

Turned out that windows was taking up 4 partitions - which I managed to
sort out using the ubuntu forums and then the install from the stick was
easy (option for installing them side by side was there).

Many thanks to all of you!

Darren

On 14 November 2011 19:31, Adam Jennings <agjennings at gmail.com> wrote:

> Is your windows already taking up all 4 primary partitions?
>
> Read this link on the ubuntu forums:
> http://ubuntuforums.org/showthread.php?t=1752582
>
> Adam
>
>
> Message: 1
>> Date: Mon, 14 Nov 2011 11:45:23 +0000
>> From: Darren Parker <djp39 at st-andrews.ac.uk>
>> Subject: [Bio-Linux] Installing bio-linux
>> To: bio-linux at nebclists.nerc.ac.uk
>> Message-ID:
>>        <
>> CAOsefcVNEUeAKLTy_E4Nfgvv-HVgjC443ZHj-G0HpWUay681Ug at mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>>
>> Hello
>>
>> I am trying to install bio-linux onto my laptop as a duel boot from the
>> bio-linux memory stick.
>>
>> However when I get to step 4/7 (where I want to install biolinux) I do not
>> have an option for installing them side by side (as it says in the
>> installation guide), just erase and specify partitions manually. Do you
>> know why this is?
>>
>> Many thanks
>>
>> Darren Parker
>>
>> --
>>
>> Darren J. Parker
>> Ph.D Student
>>
>> Centre for Evolution, Genes and Genomics
>> School of Biology
>> Dyers Brae House
>> University of St Andrews
>> St Andrews, Fife
>> Scotland KY16 9TH
>>
>> Phone: 01334 463371
>>
>> http://www.genestobehaviour.co.uk/
>>
>>
>> http://biology.st-andrews.ac.uk/ritchielab/researchGroup/djp39/darrenParker.html
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: <
>> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20111114/dbe12639/attachment.html
>> >
>>
>
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>
>


-- 

Darren J. Parker
Ph.D Student

Centre for Evolution, Genes and Genomics
School of Biology
Dyers Brae House
University of St Andrews
St Andrews, Fife
Scotland KY16 9TH

Phone: 01334 463371

http://www.genestobehaviour.co.uk/

http://biology.st-andrews.ac.uk/ritchielab/researchGroup/djp39/darrenParker.html
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