[Bio-Linux] new bio-linux-emboss and how to complete installation

[Tiwari, Bela]

Dear Bio-Linux Users,



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



sudo apt-get -f install



If your machine does not install updates automatically at night, please update your system and then run the above command from a terminal window.



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.



Please feel free to write to the NEBC helpdesk (helpdesk at nebc.nox.ac.uk<mailto:helpdesk at nebc.nox.ac.uk>) if you notice any issues with the new package.



Overview:



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.



Major changes:



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).



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.



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).



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 helpdesk at nebc.nox.ac.uk<mailto:helpdesk at nebc.nox.ac.uk>



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.



regards,



The NEBC Team




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tel: 01491 69 2705

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Wallingford, England
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