From william.spooner at eaglegenomics.com  Wed Dec  5 17:56:30 2012
From: william.spooner at eaglegenomics.com (William Spooner)
Date: Wed, 5 Dec 2012 22:56:30 +0000
Subject: [Bio-linux-dev] tophat2
In-Reply-To: <1352904538.3383.163.camel@balisaur>
References: <59C02DE0-7837-49E3-89C3-6BC38FA0083A@eaglegenomics.com>
	<1352825891.3383.133.camel@balisaur>
	<35EBB6CF-1F06-4B3A-B44F-E98366F6A0A8@eaglegenomics.com>
	<1352904538.3383.163.camel@balisaur>
Message-ID: <99D40500-87CD-4E9D-A674-D2BDD965F611@eaglegenomics.com>

Hi Tim,

Many thanks for taking care of this.

I've finally got around to trying it out. tophat seems to be the at version 2 (as is cufflinks);
http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/t/tophat/

bowtie, however, is languishing on version 0;
http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/b/bowtie/

Is this as expected?

Thanks,

Will


On 14 Nov 2012, at 14:48, Tim Booth wrote:

> Hi,
> 
> I've pushed the updates to all these and Velvet, so everything should be
> current now.
> 
> Cheers,
> 
> TIM
> 
> On Tue, 2012-11-13 at 17:32 +0000, William Spooner wrote:
>> Many thanks Tim,
>> 
>> We'll test that tomorrow. I presume it's the complete bowtie2/tophat2/cufflinks2 stack?
>> 
>> Will
>> 
>> On 13 Nov 2012, at 16:58, Tim Booth wrote:
>> 
>>> Hi Will,
>>> 
>>> The TopHat package maintained by Debian Med is up-to-date and seems to
>>> build fine on Ubuntu, so I've pushed a newer version to the Bio-Linux
>>> PPA.  Anyone who already upgraded to BL7 will get the update
>>> automatically.
>>> 
>>> Cheers,
>>> 
>>> TIM
>>> 
>>> On Tue, 2012-11-13 at 09:58 +0000, William Spooner wrote:
>>>> One for Tim, Brad,
>>>> 
>>>> What is the status of tophat2 packaging for BL? Google suggests that Brad is working on something. Anything we can do to help?
>>>> 
>>>> Thanks,
>>>> 
>>>> Will
>>>> 
>>>> ---
>>>> William Spooner                          http://eaglegenomics.com
>>>> Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/
>>>> 
>>>> _______________________________________________
>>>> Bio-Linux-dev mailing list
>>>> Bio-Linux-dev at nebclists.nerc.ac.uk
>>>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>>> 
>>> -- 
>>> 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-dev mailing list
>>> Bio-Linux-dev at nebclists.nerc.ac.uk
>>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>> 
>> ---
>> William Spooner                          http://eaglegenomics.com
>> Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/
>> 
>> _______________________________________________
>> Bio-Linux-dev mailing list
>> Bio-Linux-dev at nebclists.nerc.ac.uk
>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> 
> -- 
> 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
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev

---
William Spooner                          http://eaglegenomics.com
Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/



From tony.travis at ed.ac.uk  Thu Dec  6 07:44:50 2012
From: tony.travis at ed.ac.uk (Tony Travis)
Date: Thu, 06 Dec 2012 12:44:50 +0000
Subject: [Bio-linux-dev] Fwd: Bio-Linux 7 package versions
In-Reply-To: <50C09305.4020107@ed.ac.uk>
References: <50C09305.4020107@ed.ac.uk>
Message-ID: <50C09342.1000500@ed.ac.uk>

Hi, Tim.

I upgraded my laptop "beluga" from Bio-Linux 6 -> 7 using your script
and everything seems to be working, but there are problems with some deb
package versions. In particular, you seem to have omitted the 'epoch'
for some new packages, making them look older than they are:

> root at beluga:~# apt-show-versions | grep -v uptodate
> bio-linux-emboss 1:1bl1-1 newer than version in archive
> bio-linux-estscan 2.1-12 newer than version in archive
> bio-linux-mothur 2bl-5 newer than version in archive
> bio-linux-paml 1:1bl1 newer than version in archive
> bio-linux-prank 1:1bl1-1 newer than version in archive
> bio-linux-rdp-classifier 2:1bl1-1 newer than version in archive
> bio-linux-seaview 1:1bl1-1 newer than version in archive
> bio-linux-transterm-hp 1:1bl1-1 newer than version in archive
> bio-linux-trnascan 1:1bl1-1 newer than version in archive
> bio-linux-wise2 1:1bl1-1 newer than version in archive

This is because the default 'epoch' is 0, and you put "1:" in the old
Bio-Linux 6 deb version, but have omitted the 'epoch' in the newer
Bio-Linux 7 version. For example:

> root at beluga:~# apt-cache policy bio-linux-emboss
> bio-linux-emboss:
>   Installed: 1:1bl1-1
>   Candidate: 1:1bl1-1
>   Version table:
>  *** 1:1bl1-1 0
>         100 /var/lib/dpkg/status
>      6.3bl1-8 0
>         500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages

This can, of course, be resolved by forcing the correct version, but
automatic upgrades will keep the 'newest' (i.e. epoch = 1:) version and
not install the 'older' (default epoch = 0) version. I think this might
expalin some of the problems with QIIME...

HTH,

   Tony.





From tbooth at ceh.ac.uk  Thu Dec  6 08:06:20 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 6 Dec 2012 13:06:20 +0000
Subject: [Bio-linux-dev] Fwd: Bio-Linux 7 package versions
In-Reply-To: <50C09342.1000500@ed.ac.uk>
References: <50C09305.4020107@ed.ac.uk> <50C09342.1000500@ed.ac.uk>
Message-ID: <1354799180.3061.83.camel@balisaur>

Hi Tony,

This isn't a mistake.  These package versions are correct.  The ones in
the archive really are older.  I've held off putting this new stuff in
the archive because as soon as I do (which will be very soon), Bio-Linux
6 users will start getting warnings that they can't upgrade these
packages due to dependency issues.  I could re-structure the archive to
avoid this but that entails extra work I don't want to do.

I've closed all the QIIME bugs I know about, and run some basic
regression tests which all passed.  If you have any more bugs please do
report them via Launchpad.  I should probably run a full regression test
using the official data but I've not got around to it yet.

Cheers,

TIM

On Thu, 2012-12-06 at 12:44 +0000, Tony Travis wrote:
> Hi, Tim.
> 
> I upgraded my laptop "beluga" from Bio-Linux 6 -> 7 using your script
> and everything seems to be working, but there are problems with some deb
> package versions. In particular, you seem to have omitted the 'epoch'
> for some new packages, making them look older than they are:
> 
> > root at beluga:~# apt-show-versions | grep -v uptodate
> > bio-linux-emboss 1:1bl1-1 newer than version in archive
> > bio-linux-estscan 2.1-12 newer than version in archive
> > bio-linux-mothur 2bl-5 newer than version in archive
> > bio-linux-paml 1:1bl1 newer than version in archive
> > bio-linux-prank 1:1bl1-1 newer than version in archive
> > bio-linux-rdp-classifier 2:1bl1-1 newer than version in archive
> > bio-linux-seaview 1:1bl1-1 newer than version in archive
> > bio-linux-transterm-hp 1:1bl1-1 newer than version in archive
> > bio-linux-trnascan 1:1bl1-1 newer than version in archive
> > bio-linux-wise2 1:1bl1-1 newer than version in archive
> 
> This is because the default 'epoch' is 0, and you put "1:" in the old
> Bio-Linux 6 deb version, but have omitted the 'epoch' in the newer
> Bio-Linux 7 version. For example:
> 
> > root at beluga:~# apt-cache policy bio-linux-emboss
> > bio-linux-emboss:
> >   Installed: 1:1bl1-1
> >   Candidate: 1:1bl1-1
> >   Version table:
> >  *** 1:1bl1-1 0
> >         100 /var/lib/dpkg/status
> >      6.3bl1-8 0
> >         500 http://nebc.nerc.ac.uk/bio-linux/ unstable/bio-linux amd64 Packages
> 
> This can, of course, be resolved by forcing the correct version, but
> automatic upgrades will keep the 'newest' (i.e. epoch = 1:) version and
> not install the 'older' (default epoch = 0) version. I think this might
> expalin some of the problems with QIIME...
> 
> HTH,
> 
>    Tony.
> 
> 
> 
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev

-- 
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


From tony.travis at ed.ac.uk  Thu Dec  6 09:26:04 2012
From: tony.travis at ed.ac.uk (Tony Travis)
Date: Thu, 06 Dec 2012 14:26:04 +0000
Subject: [Bio-linux-dev] Fwd: Bio-Linux 7 package versions
In-Reply-To: <1354799180.3061.83.camel@balisaur>
References: <50C09305.4020107@ed.ac.uk> <50C09342.1000500@ed.ac.uk>
	<1354799180.3061.83.camel@balisaur>
Message-ID: <50C0AAFC.2040008@ed.ac.uk>

On 06/12/12 13:06, Tim Booth wrote:
> Hi Tony,
>
> This isn't a mistake.  These package versions are correct.  The ones in
> the archive really are older.

Hi, Tim.

I don't understand your package versions:

bio-linux-emboss 1:1bl1-1 means	epoch = 1, upstream = 1bl1, deb = 1
bio-linux-emboss 6.3bl1-8 means	epoch = 0, upstream = 6.3bl1, deb = 8

I posted to the list because that looks like upstream 6.3bl1 is newer 
than upstream 1bl1 to me. Have I got that wrong?

> I've held off putting this new stuff in
> the archive because as soon as I do (which will be very soon), Bio-Linux
> 6 users will start getting warnings that they can't upgrade these
> packages due to dependency issues.  I could re-structure the archive to
> avoid this but that entails extra work I don't want to do.

Drat, that means all our NBX's are going to be broken: Well, maybe it's 
time to upgrade them to Bio-Linux 7 anyway :-)

> I've closed all the QIIME bugs I know about, and run some basic
> regression tests which all passed.  If you have any more bugs please do
> report them via Launchpad.  I should probably run a full regression test
> using the official data but I've not got around to it yet.

OK, I'll report anything I find + I'll take a look at Wubi too.

Bye,

   Tony.


From tbooth at ceh.ac.uk  Thu Dec  6 10:28:06 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 6 Dec 2012 15:28:06 +0000
Subject: [Bio-linux-dev] Fwd: Bio-Linux 7 package versions
In-Reply-To: <50C0AAFC.2040008@ed.ac.uk>
References: <50C09305.4020107@ed.ac.uk> <50C09342.1000500@ed.ac.uk>
	<1354799180.3061.83.camel@balisaur> <50C0AAFC.2040008@ed.ac.uk>
Message-ID: <1354807686.3061.99.camel@balisaur>

Hi Tony,

You're right, except that there is no upstream for these packages as
they are not built from the source packages at all...

My reasoning is that these packages have been converted from ones that
contain the actual application to wrappers that depend on the native
Debian packages (either from upstream or from the PPA).  So
bio-linux-emboss 1:1bl1-1 is actually wrapper package v1 that pulls in
the real EMBOSS version whatever.  I've deliberately taken the EMBOSS
version out of there as the wrapper wraps emboss+jemboss+embassy and
these all have different versions, and I don't want to have to manually
update the wrapper version every time I update EMBOSS.

The proper Debian packages within the PPA all have proper versions that
match the upstream, so if you see anything like '1bl1' in the version
you need to check out the real package it wraps.

I know that the -1 extension indicates a non-native package but I
started calling them bl1, bl2 etc. until I realised that bl10 sorts
before bl2.  At that point I just gave up and went with bl1-1.

Clear as mud?

On Wubi, I've made a decision that I don't have time to look at it
myself but I know many users would be grateful to have it running if you
are able to take it on.

Cheers,

TIM

> I don't understand your package versions:
> 
> bio-linux-emboss 1:1bl1-1 means	epoch = 1, upstream = 1bl1, deb = 1
> bio-linux-emboss 6.3bl1-8 means	epoch = 0, upstream = 6.3bl1, deb = 8
> 
> I posted to the list because that looks like upstream 6.3bl1 is newer 
> than upstream 1bl1 to me. Have I got that wrong?
> 
> > I've held off putting this new stuff in
> > the archive because as soon as I do (which will be very soon), Bio-Linux
> > 6 users will start getting warnings that they can't upgrade these
> > packages due to dependency issues.  I could re-structure the archive to
> > avoid this but that entails extra work I don't want to do.
> 
> Drat, that means all our NBX's are going to be broken: Well, maybe it's 
> time to upgrade them to Bio-Linux 7 anyway :-)
> 
> > I've closed all the QIIME bugs I know about, and run some basic
> > regression tests which all passed.  If you have any more bugs please do
> > report them via Launchpad.  I should probably run a full regression test
> > using the official data but I've not got around to it yet.
> 
> OK, I'll report anything I find + I'll take a look at Wubi too.
> 
> Bye,
> 
>    Tony.
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev

-- 
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


From tbooth at ceh.ac.uk  Thu Dec  6 13:34:05 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 6 Dec 2012 18:34:05 +0000
Subject: [Bio-linux-dev] tophat2
In-Reply-To: <99D40500-87CD-4E9D-A674-D2BDD965F611@eaglegenomics.com>
References: <59C02DE0-7837-49E3-89C3-6BC38FA0083A@eaglegenomics.com>
	<1352825891.3383.133.camel@balisaur>
	<35EBB6CF-1F06-4B3A-B44F-E98366F6A0A8@eaglegenomics.com>
	<1352904538.3383.163.camel@balisaur>
	<99D40500-87CD-4E9D-A674-D2BDD965F611@eaglegenomics.com>
Message-ID: <1354818845.3061.125.camel@balisaur>

Hi Will,

Hmmm - they've renamed it from bowtie to bowtie2 so uscan didn't see
that the new version was available.  I wonder if there's any reason you
might want both at once?

I'll have a try rebuilding it now.

Cheers,

TIM

On Wed, 2012-12-05 at 22:56 +0000, William Spooner wrote:
> Hi Tim,
> 
> Many thanks for taking care of this.
> 
> I've finally got around to trying it out. tophat seems to be the at version 2 (as is cufflinks);
> http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/t/tophat/
> 
> bowtie, however, is languishing on version 0;
> http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/b/bowtie/
> 
> Is this as expected?
> 
> Thanks,
> 
> Will
> 
> 
> On 14 Nov 2012, at 14:48, Tim Booth wrote:
> 
> > Hi,
> > 
> > I've pushed the updates to all these and Velvet, so everything should be
> > current now.
> > 
> > Cheers,
> > 
> > TIM
> > 
> > On Tue, 2012-11-13 at 17:32 +0000, William Spooner wrote:
> >> Many thanks Tim,
> >> 
> >> We'll test that tomorrow. I presume it's the complete bowtie2/tophat2/cufflinks2 stack?
> >> 
> >> Will
> >> 
> >> On 13 Nov 2012, at 16:58, Tim Booth wrote:
> >> 
> >>> Hi Will,
> >>> 
> >>> The TopHat package maintained by Debian Med is up-to-date and seems to
> >>> build fine on Ubuntu, so I've pushed a newer version to the Bio-Linux
> >>> PPA.  Anyone who already upgraded to BL7 will get the update
> >>> automatically.
> >>> 
> >>> Cheers,
> >>> 
> >>> TIM
> >>> 
> >>> On Tue, 2012-11-13 at 09:58 +0000, William Spooner wrote:
> >>>> One for Tim, Brad,
> >>>> 
> >>>> What is the status of tophat2 packaging for BL? Google suggests that Brad is working on something. Anything we can do to help?
> >>>> 
> >>>> Thanks,
> >>>> 
> >>>> Will
> >>>> 
> >>>> ---
> >>>> William Spooner                          http://eaglegenomics.com
> >>>> Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/
> >>>> 
> >>>> _______________________________________________
> >>>> Bio-Linux-dev mailing list
> >>>> Bio-Linux-dev at nebclists.nerc.ac.uk
> >>>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> >>> 
> >>> -- 
> >>> 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-dev mailing list
> >>> Bio-Linux-dev at nebclists.nerc.ac.uk
> >>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> >> 
> >> ---
> >> William Spooner                          http://eaglegenomics.com
> >> Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/
> >> 
> >> _______________________________________________
> >> Bio-Linux-dev mailing list
> >> Bio-Linux-dev at nebclists.nerc.ac.uk
> >> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> > 
> > -- 
> > 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
> > _______________________________________________
> > Bio-Linux-dev mailing list
> > Bio-Linux-dev at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> 
> ---
> William Spooner                          http://eaglegenomics.com
> Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/
> 
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev

-- 
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


From william.spooner at eaglegenomics.com  Thu Dec  6 16:32:08 2012
From: william.spooner at eaglegenomics.com (William Spooner)
Date: Thu, 6 Dec 2012 21:32:08 +0000
Subject: [Bio-linux-dev] tophat2
In-Reply-To: <1354818845.3061.125.camel@balisaur>
References: <59C02DE0-7837-49E3-89C3-6BC38FA0083A@eaglegenomics.com>
	<1352825891.3383.133.camel@balisaur>
	<35EBB6CF-1F06-4B3A-B44F-E98366F6A0A8@eaglegenomics.com>
	<1352904538.3383.163.camel@balisaur>
	<99D40500-87CD-4E9D-A674-D2BDD965F611@eaglegenomics.com>
	<1354818845.3061.125.camel@balisaur>
Message-ID: <3513CEF5-D4EA-4C24-BF4A-8B803250CBFA@eaglegenomics.com>

Thanks Tim,

Actually, there is; bowtie2 is a big update and there are still people who want to use the 'original' bowtie in established workflows. I've found bowtie2 has a different memory profile which can cause problems, but I expect it's worth it for the extra sensitivity.

Will

On 6 Dec 2012, at 18:34, Tim Booth wrote:

> Hi Will,
> 
> Hmmm - they've renamed it from bowtie to bowtie2 so uscan didn't see
> that the new version was available.  I wonder if there's any reason you
> might want both at once?
> 
> I'll have a try rebuilding it now.
> 
> Cheers,
> 
> TIM
> 
> On Wed, 2012-12-05 at 22:56 +0000, William Spooner wrote:
>> Hi Tim,
>> 
>> Many thanks for taking care of this.
>> 
>> I've finally got around to trying it out. tophat seems to be the at version 2 (as is cufflinks);
>> http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/t/tophat/
>> 
>> bowtie, however, is languishing on version 0;
>> http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/b/bowtie/
>> 
>> Is this as expected?
>> 
>> Thanks,
>> 
>> Will
>> 
>> 
>> On 14 Nov 2012, at 14:48, Tim Booth wrote:
>> 
>>> Hi,
>>> 
>>> I've pushed the updates to all these and Velvet, so everything should be
>>> current now.
>>> 
>>> Cheers,
>>> 
>>> TIM
>>> 
>>> On Tue, 2012-11-13 at 17:32 +0000, William Spooner wrote:
>>>> Many thanks Tim,
>>>> 
>>>> We'll test that tomorrow. I presume it's the complete bowtie2/tophat2/cufflinks2 stack?
>>>> 
>>>> Will
>>>> 
>>>> On 13 Nov 2012, at 16:58, Tim Booth wrote:
>>>> 
>>>>> Hi Will,
>>>>> 
>>>>> The TopHat package maintained by Debian Med is up-to-date and seems to
>>>>> build fine on Ubuntu, so I've pushed a newer version to the Bio-Linux
>>>>> PPA.  Anyone who already upgraded to BL7 will get the update
>>>>> automatically.
>>>>> 
>>>>> Cheers,
>>>>> 
>>>>> TIM
>>>>> 
>>>>> On Tue, 2012-11-13 at 09:58 +0000, William Spooner wrote:
>>>>>> One for Tim, Brad,
>>>>>> 
>>>>>> What is the status of tophat2 packaging for BL? Google suggests that Brad is working on something. Anything we can do to help?
>>>>>> 
>>>>>> Thanks,
>>>>>> 
>>>>>> Will
>>>>>> 
>>>>>> ---
>>>>>> William Spooner                          http://eaglegenomics.com
>>>>>> Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/
>>>>>> 
>>>>>> _______________________________________________
>>>>>> Bio-Linux-dev mailing list
>>>>>> Bio-Linux-dev at nebclists.nerc.ac.uk
>>>>>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>>>>> 
>>>>> -- 
>>>>> 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-dev mailing list
>>>>> Bio-Linux-dev at nebclists.nerc.ac.uk
>>>>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>>>> 
>>>> ---
>>>> William Spooner                          http://eaglegenomics.com
>>>> Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/
>>>> 
>>>> _______________________________________________
>>>> Bio-Linux-dev mailing list
>>>> Bio-Linux-dev at nebclists.nerc.ac.uk
>>>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>>> 
>>> -- 
>>> 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
>>> _______________________________________________
>>> Bio-Linux-dev mailing list
>>> Bio-Linux-dev at nebclists.nerc.ac.uk
>>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>> 
>> ---
>> William Spooner                          http://eaglegenomics.com
>> Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/
>> 
>> _______________________________________________
>> Bio-Linux-dev mailing list
>> Bio-Linux-dev at nebclists.nerc.ac.uk
>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> 
> -- 
> 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
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev

---
William Spooner                          http://eaglegenomics.com
Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/



From Simon.Wagstaff at liverpool.ac.uk  Thu Dec  6 17:23:46 2012
From: Simon.Wagstaff at liverpool.ac.uk (Wagstaff, Simon)
Date: Thu, 6 Dec 2012 22:23:46 +0000
Subject: [Bio-linux-dev] tophat2
In-Reply-To: <3513CEF5-D4EA-4C24-BF4A-8B803250CBFA@eaglegenomics.com>
References: <59C02DE0-7837-49E3-89C3-6BC38FA0083A@eaglegenomics.com>
	<1352825891.3383.133.camel@balisaur>
	<35EBB6CF-1F06-4B3A-B44F-E98366F6A0A8@eaglegenomics.com>
	<1352904538.3383.163.camel@balisaur>
	<99D40500-87CD-4E9D-A674-D2BDD965F611@eaglegenomics.com>
	<1354818845.3061.125.camel@balisaur>
	<3513CEF5-D4EA-4C24-BF4A-8B803250CBFA@eaglegenomics.com>
Message-ID: <834710117A5F2048B9EC075D397DDB1B241FC849@CHEXMBX1.livad.liv.ac.uk>

Hi Tim,
I second Will's comments. Although there are improvements with speed and memory footprint of Bowtie2 over Bowtie, there are also important differences in the way Bowtie and Bowtie2 actually process the reads - see http://bowtie-bio.sourceforge.net/index.shtml. There are plenty of reasons why you might want to have both versions available for different analytical workflows. In essence they should be considered as different but related programs, rather than versions. Substituting Bowtie2 for Bowtie in established workflows may not necessarily give you what you expect.

Am enjoying Biolinux 7 immensely.

Cheers,

Simon
_________________________________

Simon Wagstaff
Tel: +44-(0)151-705-3164
Fax: +44-(0)151-705-3371
email: simonw at liv.ac.uk<mailto:simonw at liv.ac.uk>




On 6 Dec 2012, at 21:32, William Spooner wrote:

Thanks Tim,

Actually, there is; bowtie2 is a big update and there are still people who want to use the 'original' bowtie in established workflows. I've found bowtie2 has a different memory profile which can cause problems, but I expect it's worth it for the extra sensitivity.

Will

On 6 Dec 2012, at 18:34, Tim Booth wrote:

Hi Will,

Hmmm - they've renamed it from bowtie to bowtie2 so uscan didn't see
that the new version was available.  I wonder if there's any reason you
might want both at once?

I'll have a try rebuilding it now.

Cheers,

TIM

On Wed, 2012-12-05 at 22:56 +0000, William Spooner wrote:
Hi Tim,

Many thanks for taking care of this.

I've finally got around to trying it out. tophat seems to be the at version 2 (as is cufflinks);
http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/t/tophat/

bowtie, however, is languishing on version 0;
http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/b/bowtie/

Is this as expected?

Thanks,

Will


On 14 Nov 2012, at 14:48, Tim Booth wrote:

Hi,

I've pushed the updates to all these and Velvet, so everything should be
current now.

Cheers,

TIM

On Tue, 2012-11-13 at 17:32 +0000, William Spooner wrote:
Many thanks Tim,

We'll test that tomorrow. I presume it's the complete bowtie2/tophat2/cufflinks2 stack?

Will

On 13 Nov 2012, at 16:58, Tim Booth wrote:

Hi Will,

The TopHat package maintained by Debian Med is up-to-date and seems to
build fine on Ubuntu, so I've pushed a newer version to the Bio-Linux
PPA.  Anyone who already upgraded to BL7 will get the update
automatically.

Cheers,

TIM

On Tue, 2012-11-13 at 09:58 +0000, William Spooner wrote:
One for Tim, Brad,

What is the status of tophat2 packaging for BL? Google suggests that Brad is working on something. Anything we can do to help?

Thanks,

Will

---
William Spooner                          http://eaglegenomics.com
Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/

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

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

---
William Spooner                          http://eaglegenomics.com
Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/

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

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

---
William Spooner                          http://eaglegenomics.com
Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/

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

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

---
William Spooner                          http://eaglegenomics.com
Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/

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

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From tbooth at ceh.ac.uk  Fri Dec  7 04:27:34 2012
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Fri, 7 Dec 2012 09:27:34 +0000
Subject: [Bio-linux-dev] tophat2
In-Reply-To: <834710117A5F2048B9EC075D397DDB1B241FC849@CHEXMBX1.livad.liv.ac.uk>
References: <59C02DE0-7837-49E3-89C3-6BC38FA0083A@eaglegenomics.com>
	<1352825891.3383.133.camel@balisaur>
	<35EBB6CF-1F06-4B3A-B44F-E98366F6A0A8@eaglegenomics.com>
	<1352904538.3383.163.camel@balisaur>
	<99D40500-87CD-4E9D-A674-D2BDD965F611@eaglegenomics.com>
	<1354818845.3061.125.camel@balisaur>
	<3513CEF5-D4EA-4C24-BF4A-8B803250CBFA@eaglegenomics.com>
	<834710117A5F2048B9EC075D397DDB1B241FC849@CHEXMBX1.livad.liv.ac.uk>
Message-ID: <1354872454.3061.127.camel@balisaur>

I hear you.  Am packaging bowtie2 as "bowtie2" and will let you know
when it's ready to install.

Cheers,

TIM

On Thu, 2012-12-06 at 22:23 +0000, Wagstaff, Simon wrote:
> Hi Tim, 
> I second Will's comments. Although there are improvements with speed
> and memory footprint of Bowtie2 over Bowtie, there are also important
> differences in the way Bowtie and Bowtie2 actually process the reads -
> see http://bowtie-bio.sourceforge.net/index.shtml. There are plenty of
> reasons why you might want to have both versions available for
> different analytical workflows. In essence they should be considered
> as different but related programs, rather than versions. Substituting
> Bowtie2 for Bowtie in established workflows may not necessarily give
> you what you expect.
> 
> 
> Am enjoying Biolinux 7 immensely.
> 
> 
> Cheers,
> 
> 
> Simon
> _________________________________
> 
> 
> Simon Wagstaff
> Tel: +44-(0)151-705-3164
> Fax: +44-(0)151-705-3371
> email: simonw at liv.ac.uk
> 
> 
> 
> 
> 
> On 6 Dec 2012, at 21:32, William Spooner wrote:
> 
> > Thanks Tim,
> > 
> > Actually, there is; bowtie2 is a big update and there are still
> > people who want to use the 'original' bowtie in established
> > workflows. I've found bowtie2 has a different memory profile which
> > can cause problems, but I expect it's worth it for the extra
> > sensitivity.
> > 
> > Will
> > 
> > On 6 Dec 2012, at 18:34, Tim Booth wrote:
> > 
> > > Hi Will,
> > > 
> > > Hmmm - they've renamed it from bowtie to bowtie2 so uscan didn't
> > > see
> > > that the new version was available.  I wonder if there's any
> > > reason you
> > > might want both at once?
> > > 
> > > I'll have a try rebuilding it now.
> > > 
> > > Cheers,
> > > 
> > > TIM
> > > 
> > > On Wed, 2012-12-05 at 22:56 +0000, William Spooner wrote:
> > > > Hi Tim,
> > > > 
> > > > Many thanks for taking care of this.
> > > > 
> > > > I've finally got around to trying it out. tophat seems to be the
> > > > at version 2 (as is cufflinks);
> > > > http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/t/tophat/
> > > > 
> > > > bowtie, however, is languishing on version 0;
> > > > http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/b/bowtie/
> > > > 
> > > > Is this as expected?
> > > > 
> > > > Thanks,
> > > > 
> > > > Will
> > > > 
> > > > 
> > > > On 14 Nov 2012, at 14:48, Tim Booth wrote:
> > > > 
> > > > > Hi,
> > > > > 
> > > > > I've pushed the updates to all these and Velvet, so everything
> > > > > should be
> > > > > current now.
> > > > > 
> > > > > Cheers,
> > > > > 
> > > > > TIM
> > > > > 
> > > > > On Tue, 2012-11-13 at 17:32 +0000, William Spooner wrote:
> > > > > > Many thanks Tim,
> > > > > > 
> > > > > > We'll test that tomorrow. I presume it's the complete
> > > > > > bowtie2/tophat2/cufflinks2 stack?
> > > > > > 
> > > > > > Will
> > > > > > 
> > > > > > On 13 Nov 2012, at 16:58, Tim Booth wrote:
> > > > > > 
> > > > > > > Hi Will,
> > > > > > > 
> > > > > > > The TopHat package maintained by Debian Med is up-to-date
> > > > > > > and seems to
> > > > > > > build fine on Ubuntu, so I've pushed a newer version to
> > > > > > > the Bio-Linux
> > > > > > > PPA.  Anyone who already upgraded to BL7 will get the
> > > > > > > update
> > > > > > > automatically.
> > > > > > > 
> > > > > > > Cheers,
> > > > > > > 
> > > > > > > TIM
> > > > > > > 
> > > > > > > On Tue, 2012-11-13 at 09:58 +0000, William Spooner wrote:
> > > > > > > > One for Tim, Brad,
> > > > > > > > 
> > > > > > > > What is the status of tophat2 packaging for BL? Google
> > > > > > > > suggests that Brad is working on something. Anything we
> > > > > > > > can do to help?
> > > > > > > > 
> > > > > > > > Thanks,
> > > > > > > > 
> > > > > > > > Will
> > > > > > > > 
> > > > > > > > ---
> > > > > > > > William Spooner
> > > > > > > >                          http://eaglegenomics.com
> > > > > > > > Disclaimer:
> > > > > > > > http://www.eaglegenomics.com/about/privacy-statement/
> > > > > > > > 
> > > > > > > > _______________________________________________
> > > > > > > > Bio-Linux-dev mailing list
> > > > > > > > Bio-Linux-dev at nebclists.nerc.ac.uk
> > > > > > > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> > > > > > > 
> > > > > > > -- 
> > > > > > > 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-dev mailing list
> > > > > > > Bio-Linux-dev at nebclists.nerc.ac.uk
> > > > > > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> > > > > > 
> > > > > > ---
> > > > > > William Spooner
> > > > > >                          http://eaglegenomics.com
> > > > > > Disclaimer:
> > > > > > http://www.eaglegenomics.com/about/privacy-statement/
> > > > > > 
> > > > > > _______________________________________________
> > > > > > Bio-Linux-dev mailing list
> > > > > > Bio-Linux-dev at nebclists.nerc.ac.uk
> > > > > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> > > > > 
> > > > > -- 
> > > > > 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
> > > > > _______________________________________________
> > > > > Bio-Linux-dev mailing list
> > > > > Bio-Linux-dev at nebclists.nerc.ac.uk
> > > > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> > > > 
> > > > ---
> > > > William Spooner
> > > >                          http://eaglegenomics.com
> > > > Disclaimer:
> > > > http://www.eaglegenomics.com/about/privacy-statement/
> > > > 
> > > > _______________________________________________
> > > > Bio-Linux-dev mailing list
> > > > Bio-Linux-dev at nebclists.nerc.ac.uk
> > > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> > > 
> > > -- 
> > > 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
> > > _______________________________________________
> > > Bio-Linux-dev mailing list
> > > Bio-Linux-dev at nebclists.nerc.ac.uk
> > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> > 
> > ---
> > William Spooner                          http://eaglegenomics.com
> > Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/
> > 
> > _______________________________________________
> > Bio-Linux-dev mailing list
> > Bio-Linux-dev at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
> > 
> 
> 

-- 
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


From william.spooner at eaglegenomics.com  Fri Dec  7 04:28:33 2012
From: william.spooner at eaglegenomics.com (William Spooner)
Date: Fri, 7 Dec 2012 09:28:33 +0000
Subject: [Bio-linux-dev] tophat2
In-Reply-To: <1354872454.3061.127.camel@balisaur>
References: <59C02DE0-7837-49E3-89C3-6BC38FA0083A@eaglegenomics.com>
	<1352825891.3383.133.camel@balisaur>
	<35EBB6CF-1F06-4B3A-B44F-E98366F6A0A8@eaglegenomics.com>
	<1352904538.3383.163.camel@balisaur>
	<99D40500-87CD-4E9D-A674-D2BDD965F611@eaglegenomics.com>
	<1354818845.3061.125.camel@balisaur>
	<3513CEF5-D4EA-4C24-BF4A-8B803250CBFA@eaglegenomics.com>
	<834710117A5F2048B9EC075D397DDB1B241FC849@CHEXMBX1.livad.liv.ac.uk>
	<1354872454.3061.127.camel@balisaur>
Message-ID: <C714B578-51DD-432F-96D7-F806F0A6B45C@eaglegenomics.com>

Thanks Tim,

Much appreciated, as always!

Will

On 7 Dec 2012, at 09:27, Tim Booth wrote:

> I hear you.  Am packaging bowtie2 as "bowtie2" and will let you know
> when it's ready to install.
> 
> Cheers,
> 
> TIM
> 
> On Thu, 2012-12-06 at 22:23 +0000, Wagstaff, Simon wrote:
>> Hi Tim, 
>> I second Will's comments. Although there are improvements with speed
>> and memory footprint of Bowtie2 over Bowtie, there are also important
>> differences in the way Bowtie and Bowtie2 actually process the reads -
>> see http://bowtie-bio.sourceforge.net/index.shtml. There are plenty of
>> reasons why you might want to have both versions available for
>> different analytical workflows. In essence they should be considered
>> as different but related programs, rather than versions. Substituting
>> Bowtie2 for Bowtie in established workflows may not necessarily give
>> you what you expect.
>> 
>> 
>> Am enjoying Biolinux 7 immensely.
>> 
>> 
>> Cheers,
>> 
>> 
>> Simon
>> _________________________________
>> 
>> 
>> Simon Wagstaff
>> Tel: +44-(0)151-705-3164
>> Fax: +44-(0)151-705-3371
>> email: simonw at liv.ac.uk
>> 
>> 
>> 
>> 
>> 
>> On 6 Dec 2012, at 21:32, William Spooner wrote:
>> 
>>> Thanks Tim,
>>> 
>>> Actually, there is; bowtie2 is a big update and there are still
>>> people who want to use the 'original' bowtie in established
>>> workflows. I've found bowtie2 has a different memory profile which
>>> can cause problems, but I expect it's worth it for the extra
>>> sensitivity.
>>> 
>>> Will
>>> 
>>> On 6 Dec 2012, at 18:34, Tim Booth wrote:
>>> 
>>>> Hi Will,
>>>> 
>>>> Hmmm - they've renamed it from bowtie to bowtie2 so uscan didn't
>>>> see
>>>> that the new version was available.  I wonder if there's any
>>>> reason you
>>>> might want both at once?
>>>> 
>>>> I'll have a try rebuilding it now.
>>>> 
>>>> Cheers,
>>>> 
>>>> TIM
>>>> 
>>>> On Wed, 2012-12-05 at 22:56 +0000, William Spooner wrote:
>>>>> Hi Tim,
>>>>> 
>>>>> Many thanks for taking care of this.
>>>>> 
>>>>> I've finally got around to trying it out. tophat seems to be the
>>>>> at version 2 (as is cufflinks);
>>>>> http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/t/tophat/
>>>>> 
>>>>> bowtie, however, is languishing on version 0;
>>>>> http://ppa.launchpad.net/nebc/bio-linux/ubuntu/pool/main/b/bowtie/
>>>>> 
>>>>> Is this as expected?
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Will
>>>>> 
>>>>> 
>>>>> On 14 Nov 2012, at 14:48, Tim Booth wrote:
>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I've pushed the updates to all these and Velvet, so everything
>>>>>> should be
>>>>>> current now.
>>>>>> 
>>>>>> Cheers,
>>>>>> 
>>>>>> TIM
>>>>>> 
>>>>>> On Tue, 2012-11-13 at 17:32 +0000, William Spooner wrote:
>>>>>>> Many thanks Tim,
>>>>>>> 
>>>>>>> We'll test that tomorrow. I presume it's the complete
>>>>>>> bowtie2/tophat2/cufflinks2 stack?
>>>>>>> 
>>>>>>> Will
>>>>>>> 
>>>>>>> On 13 Nov 2012, at 16:58, Tim Booth wrote:
>>>>>>> 
>>>>>>>> Hi Will,
>>>>>>>> 
>>>>>>>> The TopHat package maintained by Debian Med is up-to-date
>>>>>>>> and seems to
>>>>>>>> build fine on Ubuntu, so I've pushed a newer version to
>>>>>>>> the Bio-Linux
>>>>>>>> PPA.  Anyone who already upgraded to BL7 will get the
>>>>>>>> update
>>>>>>>> automatically.
>>>>>>>> 
>>>>>>>> Cheers,
>>>>>>>> 
>>>>>>>> TIM
>>>>>>>> 
>>>>>>>> On Tue, 2012-11-13 at 09:58 +0000, William Spooner wrote:
>>>>>>>>> One for Tim, Brad,
>>>>>>>>> 
>>>>>>>>> What is the status of tophat2 packaging for BL? Google
>>>>>>>>> suggests that Brad is working on something. Anything we
>>>>>>>>> can do to help?
>>>>>>>>> 
>>>>>>>>> Thanks,
>>>>>>>>> 
>>>>>>>>> Will
>>>>>>>>> 
>>>>>>>>> ---
>>>>>>>>> William Spooner
>>>>>>>>>                         http://eaglegenomics.com
>>>>>>>>> Disclaimer:
>>>>>>>>> http://www.eaglegenomics.com/about/privacy-statement/
>>>>>>>>> 
>>>>>>>>> _______________________________________________
>>>>>>>>> Bio-Linux-dev mailing list
>>>>>>>>> Bio-Linux-dev at nebclists.nerc.ac.uk
>>>>>>>>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>>>>>>>> 
>>>>>>>> -- 
>>>>>>>> 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-dev mailing list
>>>>>>>> Bio-Linux-dev at nebclists.nerc.ac.uk
>>>>>>>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>>>>>>> 
>>>>>>> ---
>>>>>>> William Spooner
>>>>>>>                         http://eaglegenomics.com
>>>>>>> Disclaimer:
>>>>>>> http://www.eaglegenomics.com/about/privacy-statement/
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> Bio-Linux-dev mailing list
>>>>>>> Bio-Linux-dev at nebclists.nerc.ac.uk
>>>>>>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>>>>>> 
>>>>>> -- 
>>>>>> 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
>>>>>> _______________________________________________
>>>>>> Bio-Linux-dev mailing list
>>>>>> Bio-Linux-dev at nebclists.nerc.ac.uk
>>>>>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>>>>> 
>>>>> ---
>>>>> William Spooner
>>>>>                         http://eaglegenomics.com
>>>>> Disclaimer:
>>>>> http://www.eaglegenomics.com/about/privacy-statement/
>>>>> 
>>>>> _______________________________________________
>>>>> Bio-Linux-dev mailing list
>>>>> Bio-Linux-dev at nebclists.nerc.ac.uk
>>>>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>>>> 
>>>> -- 
>>>> 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
>>>> _______________________________________________
>>>> Bio-Linux-dev mailing list
>>>> Bio-Linux-dev at nebclists.nerc.ac.uk
>>>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>>> 
>>> ---
>>> William Spooner                          http://eaglegenomics.com
>>> Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/
>>> 
>>> _______________________________________________
>>> Bio-Linux-dev mailing list
>>> Bio-Linux-dev at nebclists.nerc.ac.uk
>>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev
>>> 
>> 
>> 
> 
> -- 
> 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
> _______________________________________________
> Bio-Linux-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev

---
William Spooner                          http://eaglegenomics.com
Disclaimer: http://www.eaglegenomics.com/about/privacy-statement/