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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Sorry – just noticed my typo. Lack of sleep last night.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Simon<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:
"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;
font-family:"Tahoma","sans-serif"'> bio-linux-bounces@envgen.nerc-oxford.ac.uk
[mailto:bio-linux-bounces@envgen.nerc-oxford.ac.uk] <b>On Behalf Of </b>Tiwari,
Bela<br>
<b>Sent:</b> 25 February 2010 09:21<br>
<b>To:</b> bio-linux@nebc.nox.ac.uk<br>
<b>Subject:</b> [Bio-Linux] new bio-linux-emboss and how to complete
installation<o:p></o:p></span></p>
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</div>
<p class=MsoNormal><o:p> </o:p></p>
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<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>Dear
Bio-Linux Users,<o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>The
newest version of bio-linux-emboss was released late yesterday. Many Bio-Linux
systems will have picked up this update overnight. To complete the
installation, you will need to log into your system, and run the command<o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>sudo
apt-get -f install<o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>If
your machine does not install updates automatically at night, please update
your system and then run the above command from a terminal window. <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>This
new bio-linux-emboss package changes substantially the way we have been
distributing EMBOSS and allows it to be installed on 32 or 64 bit systems. The
main changes to be aware of are listed below, in approximate order of
importance. <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>Please
feel free to write to the NEBC helpdesk (<a
href="mailto:helpdesk@nebc.nox.ac.uk">helpdesk@nebc.nox.ac.uk</a>) if you
notice any issues with the new package. <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><strong><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:black'>Overview:</span></strong><span style='font-size:10.0pt;font-family:
"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>bio-linux-emboss
is now a wrapper package. It includes the necessary indices for EMBOSS restriction
mapping programs, em_pscan for searching prints, patmatmotifs for searching
prosite, transcription factor searching using jaspscan, and programs making use
of amino acid properties such as pepwindow and pepwindowall. It also includes
Jemboss. bio-linux-emboss pulls in the base binaries, documentation and basic
data files from Ubuntu packages. The underlying version of EMBOSS on your
system is 6.0.1, and should track new versions of EMBOSS as they become
available in the Ubuntu repositories. <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><strong><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:black'>Major changes:</span></strong><span style='font-size:10.0pt;
font-family:"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>If
you have edited your emboss.default file in the past, it will be kept and saved
to /usr/share/EMBOSS/emboss.default.old. You can replace the distributed
version /usr/share/EMBOSS/emboss.default with your old version if you wish. The
emboss.default file we distribute in bio-linux-emboss supports fetching
sequences from the same databases as it has before: embl, emblcds, refseq and
uniprot (also aliased as swissprot and trembl). <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>The
pscan and cons programs distributed with the Ubuntu emboss package are called
em_pscan and em_cons. This means you will need to call these programs using
their new names, and also means that for the moment, these programs are not
available through the Jemboss interface.<o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>The
EMBASSY versions of Phylips software have changed names. They used to use the
same name as native Phylip programs, prefaced by an e (for example, eprotpars
runs the EMBASSY version of protpars). Now these programs are prefaced by an f
(so, for example, fprotpars). <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>Not
all the software available as EMBASSY packages is yet available as Ubuntu
packages. This means that the following software packages are no longer
distributed as part of bio-linux-emboss: emnu, esim4, hmmernew, mira, memenew,
signature, structure, and topo. Please note that this only refers to the
EMBASSY versions of the software. You can still install bio-linux-hmmer and
bio-linux-mira to get the native programs. If you are a user of the EMBASSY
versions of the software listed in the paragraph and are concerned about losing
these programs, please let us know by emailing <a
href="mailto:helpdesk@nebc.nox.ac.uk">helpdesk@nebc.nox.ac.uk</a> <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>The
bio-linux-emboss-kmenus package will continue to be available for Bio-Linux 5
systems (based on Ubuntu 8.04). This package provides the graphical interface
when Emboss programs are run from the main Bioinformatics menu. This will not
work on more recent Ubuntu versions due to an incompatibility with the Kaptain
software, and therefore will be removed in Bio-Linux 6. We recommend that
people consider using other ways of running the EMBOSS software. For graphical
access, we suggest Jemboss, which can be started by typing jemboss on the
command line, or by choosing the Jemboss option under the Bioinformatics menu.
Another option is to install the web-based package from Ubuntu:
emboss-explorer.<o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>regards,
<o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'>The
NEBC Team <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black'> <o:p></o:p></span></p>
<p><span style='font-size:10.0pt;color:black'><o:p> </o:p></span></p>
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<div>
<p class=MsoNormal><span style='font-size:10.0pt'>*************************<br>
NERC Environmental<br>
Bioinformatics Centre<br>
<a href="http://nebc.nox.ac.uk/">http://nebc.nox.ac.uk</a><br>
tel: 01491 69 2705<o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:10.0pt'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:10.0pt'>Centre for Ecology and
Hydrology<br>
Maclean Bldg, Benson Lane<br>
Crowmarsh Gifford<br>
Wallingford, England<br>
OX10 8BB <br>
*************************<o:p></o:p></span></p>
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<p class=MsoNormal><br>
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