From karel at javeriana.edu.co Thu Feb 12 07:02:19 2004 From: karel at javeriana.edu.co (=?ISO-8859-1?Q?Carlos_Manuel_Est=E9vez-Bret=F3n?=) Date: Thu, 12 Feb 2004 07:02:19 -0500 Subject: [Bio-linux-list] (no subject) Message-ID: <4EE296B2-5D53-11D8-ACD2-0030656749CC@javeriana.edu.co> Hi everybody, Does someone has think about in make a Live CD distro for bio-linux? We are developing a Linux Distribution called SciLix (http://www.javeriana.edu.co/ciencias/u_sistemas/proyectos/csilix.htm), but it is more Science general theme alike. The question is that the base for it is Morphix (http://morphix.sourceforge.net) that maybe some of you know. It is a debian base distro that allows to make modules of any kind. There is actually a bioinformatics LiveCD distro called DNALinux (http://www.danalinux.com) maked in Argentina Universidad Nacional de Quilmes. It is based on Slackware GNU Linux _______________________________ Carlos Manuel Est?vez-Bret?n R. Coordinador Unidad Sistemas Facultad de Ciencias Pontificia Universidad Javeriana Tel.(571) 320 8320 Ext.4033/32/75 From dswan at ceh.ac.uk Mon Feb 2 09:02:00 2004 From: dswan at ceh.ac.uk (Dan Swan) Date: Mon, 02 Feb 2004 14:02:00 +0000 Subject: [Bio-Linux] Note to Bio-Linux 3.0 beta testers Message-ID: <401E5858.9070000@ceh.ac.uk> Hi All, This is just a quick note that those of you with installs of Bio-Linux dating to mid December 2003 (beta testing period) should probably think about syncing against the latest image. The latest Bio-Linux image is : bio-linux_3.0_650_NVIDIA_30012004 If you need instructions on using updateclient to update to the latest image, please contact the helpdesk : helpdesk at envgen.nox.ac.uk regards, Dan -- Dr Dan Swan - Bio-Linux Developer | RHCE EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR Tel: 01865 281 658 Fax: 01865 281 696 http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk From al.anthony at ed.ac.uk Mon Feb 2 10:44:27 2004 From: al.anthony at ed.ac.uk (Alasdair Anthony) Date: 02 Feb 2004 15:44:27 +0000 Subject: [Bio-Linux] trace2dbest version 2.0.1 available Message-ID: <1075736667.2460.307.camel@toxocara.cap.ed.ac.uk> Hi All, This email is to inform you of the release of trace2dbest version 2.0.1, the EST trace processing software provided by the EGTDC. If you use trace2dbest, we reccommend that you upgrade to this latest version. It includes several small cosmetic changes and some bug fixes. More details can be found on the trace2dbest changelog page: http://envgen.nox.ac.uk/envgen/software/archives/000354.html trace2dbest version 2.0.1 is packaged as an rpm, so it is very easy to install: 1- download the rpm from the egtdc web site: http://envgen.nox.ac.uk/envgen/software/egtdc_dev/trace2dbest2.0rpm/ right click on the trace2dbest-2.0.1-1.i386.rpm file to save it. 2- Install the rpm. As manager type: sudo rpm -ivh trace2dbest-2.0.1-1.i386.rpm 3- Check softlinks. The rpm will create a softlink /usr/software/trace2dbest/trace2dbest to the install directory (trace2dbest2.0.1). If you have not already done so, create a softlink to the executable in this directory in /usr/software/exec: ln -s /usr/software/trace2dbest/trace2dbest/trace2dbest.pl /usr/software/exec/trace2dbest.pl [all on one line] 4 - If you have saved Pub, Lib or Cont records then just copy the Pubfile.db, Libfile.db and Contfile.db files from /usr/software/trace2dbest/trace2dbest2.0 to /usr/software/trace2dbest/trace2dbest2.0.1 If you have any problems then please email the helpdesk (helpdesk at envgen.nox.ac.uk). regards, Alasdair Anthony EST software developer EGTDC - Edinburgh From dswan at ceh.ac.uk Mon Feb 9 04:21:34 2004 From: dswan at ceh.ac.uk (Dan Swan) Date: Mon, 09 Feb 2004 09:21:34 +0000 Subject: [Bio-Linux] Acrobat Reader and Nautilus Message-ID: <4027511E.60808@ceh.ac.uk> Hi All, This tip comes from Rob Anderson at Imperial College. There are issues using Adobe Acrobat Reader under Bio-Linux (this is installed as: /usr/local/Acrobat5/bin/acroread Nautilus, the Bio-Linux file browser does not automagically launch this application if you double click a pdf. Here is Rob's solution: ********** You obviously spotted that the LANG environment variable needed to be set in order to make Acrobat reader work, but she still couldn?t get it to launch from Nautilus. I?ve fixed it. Here?s what I did (from the console): 1) Made a script called acroread in her bin directory, containing #!/bin/zsh export LANG=C /usr/local/acrobat/bin/acroread $1 2)Made it executable 3)Opened a PDF file with a command such as ~/bin/acroread my_pdf_file.pdf Now Nautilus has Acrobat Reader on the list of applications when you right-click the file and do Open With?, and it is the default, and it works when you double-click it. The link refers to the acroread in ~/bin because if you rename the script, the menu item disappears. Obviously if you want to put a similar change in for all users, you?d want to relocate the script. You might also want to adjust to use $* instead of $1, so that more than one parameter is passed. (I just bashed something together quickly for testing.) Rob. ************* Cheers Rob, we'll have a fix in the image today. regards, Dan -- Dr Dan Swan - Bio-Linux Developer | RHCE EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR Tel: 01865 281 658 Fax: 01865 281 696 http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk From dswan at ceh.ac.uk Mon Feb 9 06:35:19 2004 From: dswan at ceh.ac.uk (Dan Swan) Date: Mon, 09 Feb 2004 11:35:19 +0000 Subject: [Bio-Linux] Jemboss on Bio-Linux Message-ID: <40277077.8060607@ceh.ac.uk> Hi all, It has been reported that Jemboss under EMBOSS 2.8.0 has not been correctly configured on Bio-Linux yet. If you need to run Jemboss you might want to consider using the version in 2.7.1 In order to run Jemboss you need to do the following: cd /usr/software/EMBOSS/EMBOSS-2.7.1/emboss/share/EMBOSS/jemboss ./runJemboss.csh We are looking into why this is not working in version 2.8.0 regards, Dan -- Dr Dan Swan - Bio-Linux Developer | RHCE EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR Tel: 01865 281 658 Fax: 01865 281 696 http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk From dswan at ceh.ac.uk Wed Feb 18 06:46:31 2004 From: dswan at ceh.ac.uk (Dan Swan) Date: Wed, 18 Feb 2004 11:46:31 +0000 Subject: [Bio-Linux] Bio-Linux future strategy Message-ID: <40335097.1090700@ceh.ac.uk> Dear all - here is a consultation document on the future of Bio-Linux - comments appreciated either on list or off list. For a breakdown on how we comnpared the distributions the delightfully coloured Excel spreadsheet can be downloaded from: http://genomics.nox.ac.uk/~dswan/Linux_comparisons.xls Bio-Linux future directions ? OS selection. ------------------------------------------- Bio-Linux 3.0 and earlier versions were based on the popular Red Hat Linux distribution. Red Hat will be dropping support for the freely available and distributable version of the Linux operating system (OS) in April 2004. This has prompted the need to review the Linux distributions currently available and to make a decision based on this review as to the best choice for the base of future Bio-Linux development. Issues of key importance to our decision include: Compatibility with the hardware provided to Environmental Genomics Thematic Programme Awardee Labs Level of difference in administration, interface and overall feel of the system compared to the current Bio-Linux Overall level of user (and administrator)-friendliness Release schedule, automatic updating systems, versions of base system components Licensing issues for redistribution Documentation availability In addition, we will take into account the mechanism by which the OS can be distributed as distribution via hard media rather than the current situation, using SystemImager software, would free a significant amount of time for EGTDC staff providing user support, and allow distribution of the Bio-Linux system to a wider audience with no significant support cost to the EGTDC. Associated with the distribution system, some OS versions provide an easy mechanism to produce ?Live CD?s? which would allow Bio-Linux to be demonstrated easily, for example at conferences, thus raising its profile. A live CD version would also enable people to run a cut down version of Bio-Linux on machines without dedicating the machine to a Linux installation. Our testing is made up of several stages: from all the Linux distributions, choose those to be tested from those chosen, make choices for further testing based on obvious issues such as hardware incompatibility test a number of distributions further and choose two that will be tested by a larger group on the basis of all the above, decide on the OS on which to base the future development Distributions chosen for testing There are many Linux distributions available. On the basis of our requirements, some distributions were immediately excluded from consideration: Gentoo was considered to be inappropriate for the remit of Bio-Linux as the installation process allows such fine grained control an install can take upwards of a day and you must be extremely competent with Linux already. Debian was excluded on the basis that its install was too complex for people not familiar with Linux. Slackware was excluded as it lacks an integral modern system of package management (deb or rpm). Mandrake was excluded from initial consideration as it was close to receivership last year and there were worries about its long term future. The distributions reviewed include: Knoppix (a Live-CD distribution of Debian) Fedora SuSE DNALinux (a Slackware based Live-CD with some bioinformatics applications bundled) BioBrew Morphix (a ?modular? Knoppix derivative ) Mandrake MandrakeMove BioKnoppix Results of testing 2 distributions failed to boot on our test hardware due to the inability to deal with 2 CPU machines and were immediately excluded from further consideration: DNALinux Morphix These bugs were reported to the development teams responsible. 1 distribution was excluded on the basis that the Live-CD format had no option to install to disk: MandrakeMove. The remaining distributions were tested further: Knoppix Fedora SuSE BioBrew BioKnoppix A brief overview of these distributions is given here, followed by the testing results: Knoppix Knoppix is probably the oldest and best known Live-CD distribution and has a long history of customisation for various purposes (see ?Related Projects? at http://www.knopper.net/knoppix-links/index-en.html). Knoppix is of interest as it could be not only used as a Bio-Linux demo system at conferences, but could also be used in a teaching environment and most importantly of all can be installed onto the hard disk of a machine to give a Debian install without the pain of a traditional Debian install. It has excellent hardware detection routines. Fedora The Fedora Project is a Red-Hat-sponsored and community-supported open source project. It is also a proving ground for new technology that may eventually make its way into Red Hat products. It is not a supported product of Red Hat, Inc. Fedora Core 1 is effectively Red Hat 10. Fedora is of interest to us as this will most resemble the system Bio-Linux 3.0 and earlier are based upon. The configuration tools are largely unchanged from Red Hat 9.0. Whilst we can not make a Live-CD for Fedora we would be able to create a distribution based on it. SuSE SuSE is a German, but internationalised, distribution very much in Red Hat's image. They have a heavy focus on enterprise solutions like Red Hat and have recently been acquired by Novell as a platform for the next generation or Novell products. SuSE has a highly integrated configuration GUI, much more advanced than Red Hat's. BioBrew BioBrew is a cluster focused Linux distribution which comes with some bioinformatics software preinstalled. For the most part, the programs included form a subset of those available on Bio-Linux. BioBrew is based on NCAPI/Rocks Linux, a derivative of Red Hat Advanced Server. Bio-Brew has the look and feel of a default Red Hat 7.3 install. Bio-Knoppix A derivative of Knoppix (see above). It includes some bioinformatics tools and is in early beta development (version 0.2 currently, version 0.3 was recalled due to mastering problems); essentially it is Knoppix with a new splashscreen and KDE menus for some bioinformatics software (not all of which work). If Bio-Linux 4.0 was to be derived from Knoppix we would be using a clean Knoppix base rather than a derived system such as Bio-Knoppix. Summary of some positive and negative aspects of the different distributions Knoppix Positive: 1)Once installed it never has to be upgraded with CD's 2)Exceedingly stable code base 3)Very long release cycle 4)Can be used to make a Live-CD 5)Strong remastering community 6)Can be made to track stable releases, or testing releases when appropriate 7)Installs a perfectly configured Debian system to disk. 8)Excellent hardware detection and configuration Negative: 1)Not as advanced GUI for systems administration 2)Debian package management system ? will be unfamiliar to RPM users Fedora Positive: 1)It's the closest distribution to Bio-Linux 2)Has reasonably advanced GUI configurations 3)Have most in house administration experience on the related RedHat platform 4)Will be familiar to the Environmental Genomics user community 5)Exceedingly easy to install Negative: 1)Very new project, despite established base 2)Focus on cutting edge -i.e. FC2 is 2.6 Kernel, 2.6 Gnome and we do not know how this will impact the software included on Bio-Linux 3)Rapid release schedule: 2-3 releases a year to keep up with and remaster 4)Releases not always out on date initially scheduled 5)Cannot be made into a Live CD SuSE Positive: 1)Exceedingly easy to install 2)Centralised administration through yast2 3)RPM based, therefore familiar to awardees 4)Likely to be guaranteed to work with Novell products in the future. Negative: 1)Licensing terms for redistribution are unclear 2)There are no SuSE-derived releases on the market hence: 3)There are no instructions for remastering SuSE 4)Cannot be made into a Live-CD 5)There is the possibility of it ?pulling a Red Hat? and focusing on Enterprise exclusively 6)Will be remastering at least once a year (SuSE are slowing release dates for stability) BioBrew Positive: 1)Based on Red Hat and so would be familiar to Bio-Linux users and administrators 2)Large installed base 3)Ready to cluster 4)Already has some bioinformatics applications installed Negative: 1)Cannot be made into a Live-CD 2)Based on outdated version of RHAS 3)Text mode install 4)Not at all focused on desktop usage Bio-Knoppix This distribution has the same base list of positive and negative attributes as Knoppix, but also includes: Positive: 1)Has some bioinformatics software preinstalled 2)Some EMBOSS customisation has been done 3)Menu customisations have been already implemented for bioinformatics software Negative: 1)Current version is at 0.2 and is clearly labeled beta 2)Not all menus work 3)All added software, bioinformatics and non-bioinformatics, has been installed into /usr/local 4)Even if we used it as a base, we'd end up ripping out everything they've done and remastering it. Linux distributions chosen for further testing On the basis of the above results, two distributions were chosen at the Bio-Linux Development strategy meeting on February 13, 2004 for further testing as potential base systems for Bio-Linux: Fedora Core 1 Knoppix Testing strategy: Two machines will be set up, one for each of the above distributions. Over the next two weeks, EGTDC staff will dedicate time to work on both systems. A final decision for the distribution to be used for further Bio-Linux development will be made on February 27, 2004 on the basis of this testing. For those wishing to read up on what is happening in the Linux world there is an excellent article here on the relative market share of the top Linux variants: http://www.internetnews.com/ent-news/article.php/3313211 -- Dr Dan Swan - Bio-Linux Developer | RHCE EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR Tel: 01865 281 658 Fax: 01865 281 696 http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk From biotechinfobytes at yahoo.com Thu Feb 19 06:53:36 2004 From: biotechinfobytes at yahoo.com (M.S YATNATTI) Date: Thu, 19 Feb 2004 03:53:36 -0800 (PST) Subject: [Bio-Linux] Re: Bio-Linux future versions In-Reply-To: <200402181201.i1IC11318865@ivsun01.nerc-oxford.ac.uk> Message-ID: <20040219115336.3936.qmail@web60303.mail.yahoo.com> Dear All, Thanks for the efforts taken by Centre For Ecology and Hydrology In our view, the direction in which center for ecology and Hydrology lead by Dan Swan for future Bio-linux version is throught provoking. We have following suggestions to make; 1. It is suggested that the Bio-Linux version can continue on Redhat 9 or Fedora 1 as in our view it does not make much difference for open source community whether Redhat goes commercial and support Fedora project. THe Redhat 9 will continue in the name of Fedora 1 (Instead of Redhat 10), The linux community is mature and strong enough to support its continuity worldwide. 2. The Bio-Linux Future versions should contain OSCAR, GLOBUS, CONDOR, OPEN MOSIX, Sun Grid Engine(All must be included) user should have choice to use whatever he needs in whatever contest. 3. Bio-Linux should contain almost all Biotechnology, Bioinformatics, Medical informatics, Chem-informatics, proteomics, Bio-chemistry, chemistry, inlcuding visualization, modelling, graphic multi-media utilities and applications.All applications either they are RPM or tar. files can be installed in the system instead of converting all applications into rpm and making a installable distribution of Bio-Linux in CDs. As this will take still some time to take to convert all scientific application to RPM format. We are building up Bio-Linux in this direction. 4. All databases available opensource should be included in the Local server. 5. With regard to districution of this type of Bio-linux system can be made in CDs or hard-discs by cloning the entire system on the hard disc or on CDs. Linux has many such utilities. SYstem Imager is very much fine when the installation is done at a Local LAN to 100s of nodes to build a cluster. But with regard with the internet installation it will have still bandwidth problem. 6. We request Dan Swan to send atleast Bio-Linux 3 cloning on CDs by using Linux utilities for Backup or system recovery or cloning the hard-discs by using free linux softwares. With regards, Mr.M.S.Yatnatti, CEO, Biotechinfobytes, Super Computer Aided Biotechnology center (SUCAB Center) University of Agricultural Sciences, Hebbal Campus, Bangalore - 560 024. (India) bio-linux-request at ivsun01.nerc-oxford.ac.uk wrote: Send Bio-Linux mailing list submissions to bio-linux at bioinf.ceh.ac.uk To subscribe or unsubscribe via the World Wide Web, visit http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux or, via email, send a message with subject or body 'help' to bio-linux-request at bioinf.ceh.ac.uk You can reach the person managing the list at bio-linux-admin at bioinf.ceh.ac.uk When replying, please edit your Subject line so it is more specific than "Re: Contents of Bio-Linux digest..." Today's Topics: 1. Bio-Linux future strategy (Dan Swan) --__--__-- Message: 1 Date: Wed, 18 Feb 2004 11:46:31 +0000 From: Dan Swan Reply-To: dswan at ceh.ac.uk Organization: Centre For Ecology and Hydrology To: bio-linux at ivsun01.nerc-oxford.ac.uk Subject: [Bio-Linux] Bio-Linux future strategy Dear all - here is a consultation document on the future of Bio-Linux - comments appreciated either on list or off list. For a breakdown on how we comnpared the distributions the delightfully coloured Excel spreadsheet can be downloaded from: http://genomics.nox.ac.uk/~dswan/Linux_comparisons.xls Bio-Linux future directions ? OS selection. ------------------------------------------- Bio-Linux 3.0 and earlier versions were based on the popular Red Hat Linux distribution. Red Hat will be dropping support for the freely available and distributable version of the Linux operating system (OS) in April 2004. This has prompted the need to review the Linux distributions currently available and to make a decision based on this review as to the best choice for the base of future Bio-Linux development. Issues of key importance to our decision include: Compatibility with the hardware provided to Environmental Genomics Thematic Programme Awardee Labs Level of difference in administration, interface and overall feel of the system compared to the current Bio-Linux Overall level of user (and administrator)-friendliness Release schedule, automatic updating systems, versions of base system components Licensing issues for redistribution Documentation availability In addition, we will take into account the mechanism by which the OS can be distributed as distribution via hard media rather than the current situation, using SystemImager software, would free a significant amount of time for EGTDC staff providing user support, and allow distribution of the Bio-Linux system to a wider audience with no significant support cost to the EGTDC. Associated with the distribution system, some OS versions provide an easy mechanism to produce ?Live CD?s? which would allow Bio-Linux to be demonstrated easily, for example at conferences, thus raising its profile. A live CD version would also enable people to run a cut down version of Bio-Linux on machines without dedicating the machine to a Linux installation. Our testing is made up of several stages: from all the Linux distributions, choose those to be tested from those chosen, make choices for further testing based on obvious issues such as hardware incompatibility test a number of distributions further and choose two that will be tested by a larger group on the basis of all the above, decide on the OS on which to base the future development Distributions chosen for testing There are many Linux distributions available. On the basis of our requirements, some distributions were immediately excluded from consideration: Gentoo was considered to be inappropriate for the remit of Bio-Linux as the installation process allows such fine grained control an install can take upwards of a day and you must be extremely competent with Linux already. Debian was excluded on the basis that its install was too complex for people not familiar with Linux. Slackware was excluded as it lacks an integral modern system of package management (deb or rpm). Mandrake was excluded from initial consideration as it was close to receivership last year and there were worries about its long term future. The distributions reviewed include: Knoppix (a Live-CD distribution of Debian) Fedora SuSE DNALinux (a Slackware based Live-CD with some bioinformatics applications bundled) BioBrew Morphix (a ?modular? Knoppix derivative ) Mandrake MandrakeMove BioKnoppix Results of testing 2 distributions failed to boot on our test hardware due to the inability to deal with 2 CPU machines and were immediately excluded from further consideration: DNALinux Morphix These bugs were reported to the development teams responsible. 1 distribution was excluded on the basis that the Live-CD format had no option to install to disk: MandrakeMove. The remaining distributions were tested further: Knoppix Fedora SuSE BioBrew BioKnoppix A brief overview of these distributions is given here, followed by the testing results: Knoppix Knoppix is probably the oldest and best known Live-CD distribution and has a long history of customisation for various purposes (see ?Related Projects? at http://www.knopper.net/knoppix-links/index-en.html). Knoppix is of interest as it could be not only used as a Bio-Linux demo system at conferences, but could also be used in a teaching environment and most importantly of all can be installed onto the hard disk of a machine to give a Debian install without the pain of a traditional Debian install. It has excellent hardware detection routines. Fedora The Fedora Project is a Red-Hat-sponsored and community-supported open source project. It is also a proving ground for new technology that may eventually make its way into Red Hat products. It is not a supported product of Red Hat, Inc. Fedora Core 1 is effectively Red Hat 10. Fedora is of interest to us as this will most resemble the system Bio-Linux 3.0 and earlier are based upon. The configuration tools are largely unchanged from Red Hat 9.0. Whilst we can not make a Live-CD for Fedora we would be able to create a distribution based on it. SuSE SuSE is a German, but internationalised, distribution very much in Red Hat's image. They have a heavy focus on enterprise solutions like Red Hat and have recently been acquired by Novell as a platform for the next generation or Novell products. SuSE has a highly integrated configuration GUI, much more advanced than Red Hat's. BioBrew BioBrew is a cluster focused Linux distribution which comes with some bioinformatics software preinstalled. For the most part, the programs included form a subset of those available on Bio-Linux. BioBrew is based on NCAPI/Rocks Linux, a derivative of Red Hat Advanced Server. Bio-Brew has the look and feel of a default Red Hat 7.3 install. Bio-Knoppix A derivative of Knoppix (see above). It includes some bioinformatics tools and is in early beta development (version 0.2 currently, version 0.3 was recalled due to mastering problems); essentially it is Knoppix with a new splashscreen and KDE menus for some bioinformatics software (not all of which work). If Bio-Linux 4.0 was to be derived from Knoppix we would be using a clean Knoppix base rather than a derived system such as Bio-Knoppix. Summary of some positive and negative aspects of the different distributions Knoppix Positive: 1)Once installed it never has to be upgraded with CD's 2)Exceedingly stable code base 3)Very long release cycle 4)Can be used to make a Live-CD 5)Strong remastering community 6)Can be made to track stable releases, or testing releases when appropriate 7)Installs a perfectly configured Debian system to disk. 8)Excellent hardware detection and configuration Negative: 1)Not as advanced GUI for systems administration 2)Debian package management system ? will be unfamiliar to RPM users Fedora Positive: 1)It's the closest distribution to Bio-Linux 2)Has reasonably advanced GUI configurations 3)Have most in house administration experience on the related RedHat platform 4)Will be familiar to the Environmental Genomics user community 5)Exceedingly easy to install Negative: 1)Very new project, despite established base 2)Focus on cutting edge -i.e. FC2 is 2.6 Kernel, 2.6 Gnome and we do not know how this will impact the software included on Bio-Linux 3)Rapid release schedule: 2-3 releases a year to keep up with and remaster 4)Releases not always out on date initially scheduled 5)Cannot be made into a Live CD SuSE Positive: 1)Exceedingly easy to install 2)Centralised administration through yast2 3)RPM based, therefore familiar to awardees 4)Likely to be guaranteed to work with Novell products in the future. Negative: 1)Licensing terms for redistribution are unclear 2)There are no SuSE-derived releases on the market hence: 3)There are no instructions for remastering SuSE 4)Cannot be made into a Live-CD 5)There is the possibility of it ?pulling a Red Hat? and focusing on Enterprise exclusively 6)Will be remastering at least once a year (SuSE are slowing release dates for stability) BioBrew Positive: 1)Based on Red Hat and so would be familiar to Bio-Linux users and administrators 2)Large installed base 3)Ready to cluster 4)Already has some bioinformatics applications installed Negative: 1)Cannot be made into a Live-CD 2)Based on outdated version of RHAS 3)Text mode install 4)Not at all focused on desktop usage Bio-Knoppix This distribution has the same base list of positive and negative attributes as Knoppix, but also includes: Positive: 1)Has some bioinformatics software preinstalled 2)Some EMBOSS customisation has been done 3)Menu customisations have been already implemented for bioinformatics software Negative: 1)Current version is at 0.2 and is clearly labeled beta 2)Not all menus work 3)All added software, bioinformatics and non-bioinformatics, has been installed into /usr/local 4)Even if we used it as a base, we'd end up ripping out everything they've done and remastering it. Linux distributions chosen for further testing On the basis of the above results, two distributions were chosen at the Bio-Linux Development strategy meeting on February 13, 2004 for further testing as potential base systems for Bio-Linux: Fedora Core 1 Knoppix Testing strategy: Two machines will be set up, one for each of the above distributions. Over the next two weeks, EGTDC staff will dedicate time to work on both systems. A final decision for the distribution to be used for further Bio-Linux development will be made on February 27, 2004 on the basis of this testing. For those wishing to read up on what is happening in the Linux world there is an excellent article here on the relative market share of the top Linux variants: http://www.internetnews.com/ent-news/article.php/3313211 -- Dr Dan Swan - Bio-Linux Developer | RHCE EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR Tel: 01865 281 658 Fax: 01865 281 696 http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk --__--__-- _______________________________________________ Bio-Linux mailing list Bio-Linux at bioinf.ceh.ac.uk http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux End of Bio-Linux Digest --------------------------------- Do you Yahoo!? Yahoo! Mail SpamGuard - Read only the mail you want. -------------- next part -------------- An HTML attachment was scrubbed... URL: From robert.anderson at imperial.ac.uk Thu Feb 19 07:30:00 2004 From: robert.anderson at imperial.ac.uk (Anderson, Rob A) Date: Thu, 19 Feb 2004 12:30:00 -0000 Subject: [Bio-Linux] Re: Bio-Linux future versions Message-ID: <972A5A4D5DCE4B4989643A8BF329AD7E07F533@icex34.cc.ic.ac.uk> It seems that you are asking for a lot of something that is being given away for free. Remember that EGTDC have to install, test and support every package that they include in BioLinux and that takes resources. Would your organization contribute the necessary resources for EGTDC to be able to include and support all the packages you request (and any interaction between them)? From a support point of view it is much simpler to include a core set of applications that cover most of the tasks people using a BioLinux box are likely to use, and then allow them to install and support their own specific packages on top of that. There is nothing to stop you installing your own extra applications on top of the BioLinux 3 distribution. Rob Anderson Computing Support Officer Centre for Population Biology Imperial College -----Original Message----- From: bio-linux-admin at ivsun01.nerc-oxford.ac.uk [mailto:bio-linux-admin at ivsun01.nerc-oxford.ac.uk] On Behalf Of M.S YATNATTI Sent: 19 February 2004 11:54 To: bio-linux at ivsun01.nerc-oxford.ac.uk Subject: [Bio-Linux] Re: Bio-Linux future versions Dear All, Thanks for the efforts taken by Centre For Ecology and Hydrology In our view, the direction in which center for ecology and Hydrology lead by Dan Swan for future Bio-linux version is throught provoking. We have following suggestions to make; 1. It is suggested that the Bio-Linux version can continue on Redhat 9 or Fedora 1 as in our view it does not make much difference for open source community whether Redhat goes commercial and support Fedora project. THe Redhat 9 will continue in the name of Fedora 1 (Instead of Redhat 10), The linux community is mature and strong enough to support its continuity worldwide. 2. The Bio-Linux Future versions should contain OSCAR, GLOBUS, CONDOR, OPEN MOSIX, Sun Grid Engine(All must be included) user should have choice to use whatever he needs in whatever contest. 3. Bio-Linux should contain almost all Biotechnology, Bioinformatics, Medical informatics, Chem-informatics, proteomics, Bio-chemistry, chemistry, inlcuding visualization, modelling, graphic multi-media utilities and applications.All applications either they are RPM or tar. files can be installed in the system instead of converting all applications into rpm and making a installable distribution of Bio-Linux in CDs. As this will take still some time to take to convert all scientific application to RPM format. We are building up Bio-Linux in this direction. 4. All databases available opensource should be included in the Local server. 5. With regard to districution of this type of Bio-linux system can be made in CDs or hard-discs by cloning the entire system on the hard disc or on CDs. Linux has many such utilities. SYstem Imager is very much fine when the installation is done at a Local LAN to 100s of nodes to build a cluster. But with regard with the internet installation it will have still bandwidth problem. 6. We request Dan Swan to send atleast Bio-Linux 3 cloning on CDs by using Linux utilities for Backup or system recovery or cloning the hard-discs by using free linux softwares. With regards, Mr.M.S.Yatnatti, CEO, Biotechinfobytes, Super Computer Aided Biotechnology center (SUCAB Center) University of Agricultural Sciences, Hebbal Campus, Bangalore - 560 024. (India) bio-linux-request at ivsun01.nerc-oxford.ac.uk wrote: Send Bio-Linux mailing list submissions to bio-linux at bioinf.ceh.ac.uk To subscribe or unsubscribe via the World Wide Web, visit http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux or, via email, send a message with subject or body 'help' to bio-linux-request at bioinf.ceh.ac.uk You can reach the person managing the list at bio-linux-admin at bioinf.ceh.ac.uk When replying, please edit your Subject line so it is more specific than "Re: Contents of Bio-Linux digest..." Today's Topics: 1. Bio-Linux future strategy (Dan Swan) --__--__-- Message: 1 Date: Wed, 18 Feb 2004 11:46:31 +0000 From: Dan Swan Reply-To: dswan at ceh.ac.uk Organization: Centre For Ecology and Hydrology To: bio-linux at ivsun01.nerc-oxford.ac.uk Subject: [Bio-Linux] Bio-Linux future strategy Dear all - here is a consultation document on the future of Bio-Linux - comments appreciated either on list or off list. For a breakdown on how we comnpared the distributions the delightfully coloured Excel spreadsheet can be downloaded from: http://genomics.nox.ac.uk/~dswan/Linux_comparisons.xls Bio-Linux future directions - OS selection. ------------------------------------------- Bio-Linux 3.0 and earlier versions were based on the popular Red Hat Liinux distribution. Red Hat will be dropping support for the freely available and distributable version of the Linux operating system (OS) in April 2004. This has prompted the need to review the Linux distributions currently available and to make a decision based on this review as to the best choice for the base of future Bio-Linux development. Issues of key importance to our decision include: Compatibility with the hardware provided to Environmental Genomics Thematic Programme Awardee Labs Level of difference in administration, interface and overall feel of the system compared to the current Bio-Linux Overall level of user (and administrator)-friendliness Release schedule, automatic updating systems, versions of base system components Licensing issues for redistribution Documentation availability In addition, we will take into account the mechanism by which the OS can be distributed as distribution via hard media rather than the current situation, using SystemImager software, would free a significant amount of time for EGTDC staff providing user support, and allow distribution of the Bio-Linux system to a wider audience with no significant support cost to the EGTDC. Associated with the distribution system, some OS versions provide an easy mechanism to produce "Live CD's" which would allow Bio-Linux to be demonstrated easily, for example at conferences, thus raising its profile. A live CD version would also enable people to run a cut down version of Bio-Linux on machines without dedicating the machine to a Linux installation. Our testing is made up of several stages: from all the Linux distributions, choose those to be tested from those chosen, make choices for further testing based on obvious issues such as hardware incompatibility test a number of distributions further and choose two that will be tested by a larger group on the basis of all the above, decide on the OS on which to base the future development Distributions chosen for testing There are many Linux distributions available. On the basis of our requirements, some distributions were immediately excluded from consideration: Gentoo was considered to be inappropriate for the remit of Bio-Linux as the installation process allows such fine grained control an install can take upwards of a day and you must be extremely competent with Linux already. Debian was excluded on the basis that its install was too complex for people not familiar with Linux. Slackware was excluded as it lacks an integral modern system of package management (deb or rpm). Mandrake was excluded from initial consideration as it was close to receivership last year and there were worries about its long term future. The distributions reviewed include: Knoppix (a Live-CD distribution of Debian) Fedora SuSE DNALinux (a Slackware based Live-CD with some bioinformatics applications bundled) BioBrew Morphix (a "modular" Knoppix derivative ) Mandrake MandrakeMove BioKnoppix Results of testing 2 distributions failed to boot on our test hardware due to the inability to deal with 2 CPU machines and were immediately excluded from further consideration: DNALinux Morphix These bugs were reported to the development teams responsible. 1 distribution was excluded on the basis that the Live-CD format had no option to install to disk: MandrakeMove. The remaining distributions were tested further: Knoppix Fedora SuSE BioBrew BioKnoppix A brief overview of these distributions is given here, followed by the testing results: Knoppix Knoppix is probably the oldest and best known Live-CD distribution and has a long history of customisation for various purposes (see "Related Projects" at http://www.knopper.net/knoppix-links/index-en.html). Knoppix is of interest as it could be not only used as a Bio-Linux demo system at conferences, but could also be used in a teaching environment and most importantly of all can be installed onto the hard disk of a machine to give a Debian install without the pain of a traditional Debian install. It has excellent hardware detection routines. Fedora The Fedora Project is a Red-Hat-sponsored and community-supported open source project. It is also a proving ground for new technology that may eventually make its way into Red Hat products. It is not a supported product of Red Hat, Inc. Fedora Core 1 is effectively Red Hat 10. Fedora is of interest to us as this will most resemble the system Bio-Linux 3.0 and earlier are based upon. The configuration tools are largely unchanged from Red Hat 9.0. Whilst we can not make a Live-CD for Fedora we would be able to create a distribution based on it. SuSE SuSE is a German, but internationalised, distribution very much in Red Hat's image. They have a heavy focus on enterprise solutions like Red Hat and have recently been acquired by Novell as a platform for the next generation or Novell products. SuSE has a highly integrated configuration GUI, much more advanced than Red Hat's. BioBrew BioBrew is a cluster focused Linux distribution which comes with some bioinformatics software preinstalled. For the most part, the programs included form a subset of those available on Bio-Linux. BioBrew is based on NCAPI/Rocks Linux, a derivative of Red Hat Advanced Server. Bio-Brew has the look and feel of a default Red Hat 7.3 install. Bio-Knoppix A derivative of Knoppix (see above). It includes some bioinformatics tools and is in early beta development (version 0.2 currently, version 0.3 was recalled due to mastering problems); essentially it is Knoppix with a new splashscreen and KDE menus for some bioinformatics software (not all of which work). If Bio-Linux 4.0 was to be derived from Knoppix we would be using a clean Knoppix base rather than a derived system such as Bio-Knoppix. Summary of some positive and negative aspects of the different distributions Knoppix Positive: 1)Once installed it never has to be upgraded with CD's 2)Exceedingly stable code base 3)Very long release cycle 4)Can be used to make a Live-CD 5)Strong remastering community 6)Can be made to track stable releases, or testing releases when appropriate 7)Installs a perfectly configured Debian system to disk. 8)Excellent hardware detection and configuration Negative: 1)Not as advanced GUI for systems administration 2)Debian package management system - will be unfamiliar to RPM users Fedora Positive: 1)It's the closest distribution to Bio-Linux 2)Has reasonably advanced GUI configurations 3)Have most in house administration experience on the related RedHat platform 4)Will be familiar to the Environmental Genomics user community 5)Exceedingly easy to install Negative: 1)Very new project, despite established base 2)Focus on cutting edge -i.e. FC2 is 2.6 Kernel, 2.6 Gnome and we do not know how this will impact the software included on Bio-Linux 3)Rapid release schedule: 2-3 releases a year to keep up with and remaster 4)Releases not always out on date initially scheduled 5)Cannot be made into a Live CD SuSE Positive: 1)Exceedingly easy to install 2)Centralised administration through yast2 3)RPM based, therefore familiar to awardees 4)Likely to be guaranteed to work with Novell products in the future. Negative: 1)Licensing terms for redistribution are unclear 2)There are no SuSE-derived releases on the market hence: 3)There are no instructions for remastering SuSE 4)Cannot be made into a Live-CD 5)There is the possibility of it "pulling a Red Hat" and focusing on Enterprise exclusively 6)Will be remastering at least once a year (SuSE are slowing release dates for stability) BioBrew Positive: 1)Based on Red Hat and so would be familiar to Bio-Linux users and administrators 2)Large installed base 3)Ready to cluster 4)Already has some bioinformatics applications installed Negative: 1)Cannot be made into a Live-CD 2)Based on outdated version of RHAS 3)Text mode install 4)Not at all focused on desktop usage Bio-Knoppix This distribution has the same base list of positive and negative attributes as Knoppix, but also includes: Positive: 1)Has some bioinformatics software preinstalled 2)Some EMBOSS customisation has been done 3)Menu customisations have been already implemented for bioinformatics software Negative: 1)Current version is at 0.2 and is clearly labeled beta 2)Not all menus work 3)All added software, bioinformatics and non-bioinformatics, has been installed into /usr/local 4)Even if we used it as a base, we'd end up ripping out everything they've done and remastering it. Linux distributions chosen for further testing On the basis of the above results, two distributions were chosen at the Bio-Linux Development strategy meeting on February 13, 2004 for further testing as potential base systems for Bio-Linux: Fedora Core 1 Knoppix Testing strategy: Two machines will be set up, one for each of the above distributions. Over the next two weeks, EGTDC staff will dedicate time to work on both systems. A final decision for the distribution to be used for further Bio-Linux development will be made on February 27, 2004 on the basis of this testing. For those wishing to read up on what is happening in the Linux world there is an excellent article here on the relative market share of the top Linux variants: http://www.internetnews.com/ent-news/article.php/3313211 -- Dr Dan Swan - Bio-Linux Developer | RHCE EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR Tel: 01865 281 658 Fax: 018665 281 696 http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk --__--__-- _______________________________________________ Bio-Linux mailing list Bio-Linux at bioinf.ceh.ac.uk http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux End of Bio-Linux Digest _____ Do you Yahoo!? Yahoo! Mail SpamGuard - Read only the mail you want. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dswan at ceh.ac.uk Thu Feb 19 08:28:53 2004 From: dswan at ceh.ac.uk (Dan Swan) Date: Thu, 19 Feb 2004 13:28:53 +0000 Subject: [Bio-Linux] Re: Bio-Linux future versions In-Reply-To: <20040219115336.3936.qmail@web60303.mail.yahoo.com> References: <20040219115336.3936.qmail@web60303.mail.yahoo.com> Message-ID: <4034BA15.3040304@ceh.ac.uk> Hi, I'd just like to offer the following comments. > 1. It is suggested that the Bio-Linux version can continue on Redhat 9 > or Fedora 1 as in our view it does not make much difference for open > source community whether Redhat goes commercial and support Fedora > project. THe Redhat 9 will continue in the name of Fedora 1 (Instead of > Redhat 10), The linux community is mature and strong enough to support > its continuity worldwide. The issue is not so much that of Red Hat's move away from non-enterprise support, but the fact that the Bio-Linux is having to move away from its traditional deployment system due to an increase of interest from external researchers. What we are interested in is the amnout of time it would take to remaster various distributions. I am the sole developer on this project, and I am lucky that other members of my group contribute time to the development of Bio-Linux and support, but if we are to advance Bio-Linux then time constraints have to be balanced with making a great product. > 2. The Bio-Linux Future versions should contain OSCAR, GLOBUS, CONDOR, > OPEN MOSIX, Sun Grid Engine(All must be included) user should have > choice to use whatever he needs in whatever contest. We are committed to Condor, as this is part of the UK Grid Consortium plan - along with Globus. Whilst it may be possible to include SGE at a later date, this is not a priority. If you are focused on cluster development the Bio-Linux team recommend you use BioBew (http://biobrew.org). BioBrew is cluster focused, the focus for Bio-Linux is as a scientific workstation - allowing the 2 projects to comfortably co-exist. Bio-Linux 3.0 comes with Condor preinstalled. > 3. Bio-Linux should contain almost all Biotechnology, Bioinformatics, > Medical informatics, Chem-informatics, proteomics, Bio-chemistry, > chemistry, inlcuding visualization, modelling, graphic multi-media > utilities and applications.All applications either they are RPM or tar. > files can be installed in the system instead of converting all > applications into rpm and making a installable distribution of Bio-Linux > in CDs. As this will take still some time to take to convert all > scientific application to RPM format. We are building up Bio-Linux in > this direction. Unfortunately this simply isn't possible - we do not have the experience (for instance) to ascertain what is important in Medical Informatics. We support genomic and proteomic research teams and Bio-Linux will have to support these foci as a primary goal. We always accept suggestions for other packages to be included, but at the very least we try to provide a broad base of research tools that most bench biologists will be able to find a use for. Bio-Linux 4.0 should have a properly package managed set of Bioinformatics software, whether this is deb or rpm. We will not be including .tgz packages as this is just too hard to version control. Building the deb/rpm's is going to be a major part of the next version of Bio-Linux and of course we will make these available to the wider scientific community as appropriate. > 4. All databases available opensource should be included in the Local > server. Bio-Linux already includes MySQL and PostgreSQL, and will continue to do so. > 5. With regard to districution of this type of Bio-linux system can be > made in CDs or hard-discs by cloning the entire system on the hard disc > or on CDs. Linux has many such utilities. SYstem Imager is very much > fine when the installation is done at a Local LAN to 100s of nodes to > build a cluster. But with regard with the internet installation it will > have still bandwidth problem. We have to move away from Systemimager for external researchers - the bandwidth constraints are too much for installs outside the UK. > 6. We request Dan Swan to send atleast Bio-Linux 3 cloning on CDs by > using Linux utilities for Backup or system recovery or cloning the > hard-discs by using free linux softwares. We have already been through this :) I know that it is technically feasible to send you a set of bootable CD's with the HD image, but I do NOT know how this will deal with different hardware. With the Systemimager installation we at least have a degree of control over the installation (eg partitioning, SCSI hardware etc). Until Bio-Linux 4.0 comes as a distribution we can only offer installs through the Systemimager suite. I am aware this is not ideal, but it is the best I can do for now. I'd just like to add that it is outside my job description, and even the remit of our funding to open Bio-Linux up outside the NERC/EG community. I'm really pushing for this because I believe of the bioinformatics centred Linux distributions, Bio-Linux is streets ahead of the competition and I don't want to limit the work we do just to the people we are contractually obliged support. This is why when Bio-Linux 4.0 is released, we hope to have a lot more community input - and community support and the project can take on a life of its own. All the best, Dan -- Dr Dan Swan - Bio-Linux Developer | RHCE EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR Tel: 01865 281 658 Fax: 01865 281 696 http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk From biotechinfobytes at yahoo.com Fri Feb 20 00:25:48 2004 From: biotechinfobytes at yahoo.com (M.S YATNATTI) Date: Thu, 19 Feb 2004 21:25:48 -0800 (PST) Subject: [Bio-Linux] Bio-Linux future versions In-Reply-To: <200402191233.i1JCX0301793@ivsun01.nerc-oxford.ac.uk> Message-ID: <20040220052548.26235.qmail@web60303.mail.yahoo.com> Dear Sir It seems that you are mixing the two issues which are very seprate, one is you provide under GPL and other is support at cost. General user will never ask the support from you Because you provide Bio-Linux 3 Under GPL. After that what user does is his risk. Ours was general responce to future versions of Bio-Linux.It is upto you to consider or reject in the intrest of Linux community under GPL. With regards, Mr.M.S.Yatnatti, CEO, Biotechinfobytes, Super Computer Aided Biotechnology center (SUCAB Center) University of Agricultural Sciences, Hebbal Campus, Bangalore - 560 024. (India) bio-linux-request at ivsun01.nerc-oxford.ac.uk wrote: Send Bio-Linux mailing list submissions to bio-linux at bioinf.ceh.ac.uk To subscribe or unsubscribe via the World Wide Web, visit http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux or, via email, send a message with subject or body 'help' to bio-linux-request at bioinf.ceh.ac.uk You can reach the person managing the list at bio-linux-admin at bioinf.ceh.ac.uk When replying, please edit your Subject line so it is more specific than "Re: Contents of Bio-Linux digest..." Today's Topics: 1. RE: Re: Bio-Linux future versions (Anderson, Rob A) --__--__-- Message: 1 Subject: RE: [Bio-Linux] Re: Bio-Linux future versions Date: Thu, 19 Feb 2004 12:30:00 -0000 From: "Anderson, Rob A" To: This is a multi-part message in MIME format. ------_=_NextPart_001_01C3F6E4.17A29E89 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable It seems that you are asking for a lot of something that is being given away for free. Remember that EGTDC have to install, test and support every package that they include in BioLinux and that takes resources. Would your organization contribute the necessary resources for EGTDC to be able to include and support all the packages you request (and any interaction between them)? From a support point of view it is much simpler to include a core set of applications that cover most of the tasks people using a BioLinux box are likely to use, and then allow them to install and support their own specific packages on top of that. There is nothing to stop you installing your own extra applications on top of the BioLinux 3 distribution. =20 Rob Anderson Computing Support Officer Centre for Population Biology Imperial College -----Original Message----- From: bio-linux-admin at ivsun01.nerc-oxford.ac.uk [mailto:bio-linux-admin at ivsun01.nerc-oxford.ac.uk] On Behalf Of M.S YATNATTI Sent: 19 February 2004 11:54 To: bio-linux at ivsun01.nerc-oxford.ac.uk Subject: [Bio-Linux] Re: Bio-Linux future versions =20 Dear All,=20 Thanks for the efforts taken by Centre For Ecology and Hydrology In our view, the direction in which center for ecology and Hydrology lead by Dan Swan for future Bio-linux version is throught provoking. We have following suggestions to make; 1. It is suggested that the Bio-Linux version can continue on Redhat 9 or Fedora 1 as in our view it does not make much difference for open source community whether Redhat goes commercial and support Fedora project. THe Redhat 9 will continue in the name of Fedora 1 (Instead of Redhat 10), The linux community is mature and strong enough to support its continuity worldwide. 2. The Bio-Linux Future versions should contain OSCAR, GLOBUS, CONDOR, OPEN MOSIX, Sun Grid Engine(All must be included) user should have choice to use whatever he needs in whatever contest. 3. Bio-Linux should contain almost all Biotechnology, Bioinformatics, Medical informatics, Chem-informatics, proteomics, Bio-chemistry, chemistry, inlcuding visualization, modelling, graphic multi-media utilities and applications.All applications either they are RPM or tar. files can be installed in the system instead of converting all applications into rpm and making a installable distribution of Bio-Linux in CDs. As this will take still some time to take to convert all scientific application to RPM format. We are building up Bio-Linux in this direction. 4. All databases available opensource should be included in the Local server. 5. With regard to districution of this type of Bio-linux system can be made in CDs or hard-discs by cloning the entire system on the hard disc or on CDs. Linux has many such utilities. SYstem Imager is very much fine when the installation is done at a Local LAN to 100s of nodes to build a cluster. But with regard with the internet installation it will have still bandwidth problem. 6. We request Dan Swan to send atleast Bio-Linux 3 cloning on CDs by using Linux utilities for Backup or system recovery or cloning the hard-discs by using free linux softwares. With regards, Mr.M.S.Yatnatti, CEO, Biotechinfobytes, Super Computer Aided Biotechnology center (SUCAB Center) University of Agricultural Sciences, Hebbal Campus, Bangalore - 560 024. (India) bio-linux-request at ivsun01.nerc-oxford.ac.uk wrote: Send Bio-Linux mailing list submissions to bio-linux at bioinf.ceh.ac.uk =09 To subscribe or unsubscribe via the World Wide Web, visit http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux or, via email, send a message with subject or body 'help' to bio-linux-request at bioinf.ceh.ac.uk =09 You can reach the person managing the list at bio-linux-admin at bioinf.ceh.ac.uk =09 When replying, please edit your Subject line so it is more specific than "Re: Contents of Bio-Linux digest..." =09 =09 Today's Topics: =09 1. Bio-Linux future strategy (Dan Swan) =09 -- __--__-- =09 Message: 1 Date: Wed, 18 Feb 2004 11:46:31 +0000 From: Dan Swan=20 Reply-To: dswan at ceh.ac.uk Organization: Centre For Ecology and Hydrology To: bio-linux at ivsun01.nerc-oxford.ac.uk Subject: [Bio-Linux] Bio-Linux future strategy =09 Dear all - here is a consultation document on the future of Bio-Linux -=20 comments appreciated either on list or off list. =09 For a breakdown on how we comnpared the distributions the delightfully=20 coloured Excel spreadsheet can be downloaded from: =09 http://genomics.nox.ac.uk/~dswan/Linux_comparisons.xls =09 Bio-Linux future directions - OS selection. ------------------------------------------- =09 Bio-Linux 3.0 and earlier versions were based on the popular Red Hat=20 Liinux distribution. Red Hat will be dropping support for the freely=20 available and distributable version of the Linux operating system (OS)=20 in April 2004. This has prompted the need to review the Linux=20 distributions currently available and to make a decision based on this=20 review as to the best choice for the base of future Bio-Linux development. =09 Issues of key importance to our decision include: =09 Compatibility with the hardware provided to Environmental Genomics=20 Thematic Programme Awardee Labs =09 Level of difference in administration, interface and overall feel of the=20 system compared to the current Bio-Linux =09 Overall level of user (and administrator)-friendliness =09 Release schedule, automatic updating systems, versions of base system=20 components =09 Licensing issues for redistribution =09 Documentation availability =09 =09 In addition, we will take into account the mechanism by which the OS can=20 be distributed as distribution via hard media rather than the current=20 situation, using SystemImager software, would free a significant amount=20 of time for EGTDC staff providing user support, and allow distribution=20 of the Bio-Linux system to a wider audience with no significant support=20 cost to the EGTDC. Associated with the distribution system, some OS=20 versions provide an easy mechanism to produce "Live CD's" which would=20 allow Bio-Linux to be demonstrated easily, for example at conferences,=20 thus raising its profile. A live CD version would also enable people to=20 run a cut down version of Bio-Linux on machines without dedicating the=20 machine to a Linux installation. =09 Our testing is made up of several stages: =09 from all the Linux distributions, choose those to be tested =09 from those chosen, make choices for further testing based on obvious=20 issues such as hardware incompatibility =09 test a number of distributions further and choose two that will be=20 tested by a larger group =09 on the basis of all the above, decide on the OS on which to base the=20 future development =09 =09 Distributions chosen for testing =09 There are many Linux distributions available. On the basis of our=20 requirements, some distributions were immediately excluded from=20 consideration: =09 Gentoo was considered to be inappropriate for the remit of Bio-Linux as=20 the installation process allows such fine grained control an install can=20 take upwards of a day and you must be extremely competent with Linux=20 already. =09 Debian was excluded on the basis that its install was too complex for=20 people not familiar with Linux. =09 Slackware was excluded as it lacks an integral modern system of package=20 management (deb or rpm). =09 Mandrake was excluded from initial consideration as it was close to=20 receivership last year and there were worries about its long term future. =09 The distributions reviewed include: =09 Knoppix (a Live-CD distribution of Debian) Fedora SuSE DNALinux (a Slackware based Live-CD with some bioinformatics=20 applications bundled) BioBrew Morphix (a "modular" Knoppix derivative ) Mandrake MandrakeMove BioKnoppix =09 Results of testing =09 2 distributions failed to boot on our test hardware due to the inability=20 to deal with 2 CPU machines and were immediately excluded from further=20 consideration: =09 DNALinux Morphix =09 These bugs were reported to the development teams responsible. =09 1 distribution was excluded on the basis that the Live-CD format had no=20 option to install to disk: =09 MandrakeMove. =09 The remaining distributions were tested further: =09 Knoppix Fedora SuSE BioBrew BioKnoppix =09 A brief overview of these distributions is given here, followed by the=20 testing results: =09 Knoppix =09 Knoppix is probably the oldest and best known Live-CD distribution and=20 has a long history of customisation for various purposes (see "Related=20 Projects" at http://www.knopper.net/knoppix-links/index-en.html).=20 Knoppix is of interest as it could be not only used as a Bio-Linux demo=20 system at conferences, but could also be used in a teaching environment=20 and most importantly of all can be installed onto the hard disk of a=20 machine to give a Debian install without the pain of a traditional=20 Debian install. It has excellent hardware detection routines. =09 Fedora =09 The Fedora Project is a Red-Hat-sponsored and community-supported open=20 source project. It is also a proving ground for new technology that may=20 eventually make its way into Red Hat products. It is not a supported=20 product of Red Hat, Inc. Fedora Core 1 is effectively Red Hat 10.=20 Fedora is of interest to us as this will most resemble the system=20 Bio-Linux 3.0 and earlier are based upon. The configuration tools are=20 largely unchanged from Red Hat 9.0. Whilst we can not make a Live-CD=20 for Fedora we would be able to create a distribution based on it. =09 SuSE =09 SuSE is a German, but internationalised, distribution very much in Red=20 Hat's image. They have a heavy focus on enterprise solutions like Red=20 Hat and have recently been acquired by Novell as a platform for the next=20 generation or Novell products. SuSE has a highly integrated=20 configuration GUI, much more advanced than Red Hat's. =09 BioBrew =09 BioBrew is a cluster focused Linux distribution which comes with some=20 bioinformatics software preinstalled. For the most part, the programs=20 included form a subset of those available on Bio-Linux. BioBrew is=20 based on NCAPI/Rocks Linux, a derivative of Red Hat Advanced Server.=20 Bio-Brew has the look and feel of a default Red Hat 7.3 install. =09 Bio-Knoppix =09 A derivative of Knoppix (see above). It includes some bioinformatics=20 tools and is in early beta development (version 0.2 currently, version=20 0.3 was recalled due to mastering problems); essentially it is Knoppix=20 with a new splashscreen and KDE menus for some bioinformatics software=20 (not all of which work). If Bio-Linux 4.0 was to be derived from Knoppix we would be using a clean Knoppix base rather than a derived=20 system such as Bio-Knoppix. =09 Summary of some positive and negative aspects of the different distributions =09 Knoppix =09 Positive: =09 1)Once installed it never has to be upgraded with CD's 2)Exceedingly stable code base 3)Very long release cycle 4)Can be used to make a Live-CD 5)Strong remastering community 6)Can be made to track stable releases, or testing releases when appropriate 7)Installs a perfectly configured Debian system to disk. 8)Excellent hardware detection and configuration =09 Negative: =09 1)Not as advanced GUI for systems administration 2)Debian package management system - will be unfamiliar to RPM users =09 Fedora =09 Positive: =09 1)It's the closest distribution to Bio-Linux 2)Has reasonably advanced GUI configurations 3)Have most in house administration experience on the related RedHat=20 platform 4)Will be familiar to the Environmental Genomics user community 5)Exceedingly easy to install=20 =09 Negative: =09 1)Very new project, despite established base 2)Focus on cutting edge -i.e. FC2 is 2.6 Kernel, 2.6 Gnome and we do not=20 know how this will impact the software included on Bio-Linux 3)Rapid release schedule: 2-3 releases a year to keep up with and remaster 4)Releases not always out on date initially scheduled 5)Cannot be made into a Live CD =09 SuSE =09 Positive: =09 1)Exceedingly easy to install 2)Centralised administration through yast2 3)RPM based, therefore familiar to awardees 4)Likely to be guaranteed to work with Novell products in the future. =09 Negative: =09 1)Licensing terms for redistribution are unclear 2)There are no SuSE-derived releases on the market hence: 3)There are no instructions for remastering SuSE 4)Cannot be made into a Live-CD 5)There is the possibility of it "pulling a Red Hat" and focusing on=20 Enterprise exclusively 6)Will be remastering at least once a year (SuSE are slowing release=20 dates for stability) =09 =09 =09 BioBrew =09 Positive: =09 1)Based on Red Hat and so would be familiar to Bio-Linux users and=20 administrators 2)Large installed base=20 3)Ready to cluster 4)Already has some bioinformatics applications installed =09 Negative: =09 1)Cannot be made into a Live-CD 2)Based on outdated version of RHAS 3)Text mode install=20 4)Not at all focused on desktop usage =09 Bio-Knoppix =09 =09 This distribution has the same base list of positive and negative=20 attributes as Knoppix, but also includes: =09 Positive: =09 1)Has some bioinformatics software preinstalled 2)Some EMBOSS customisation has been done 3)Menu customisations have been already implemented for bioinformatics=20 software =09 Negative: =09 1)Current version is at 0.2 and is clearly labeled beta 2)Not all menus work 3)All added software, bioinformatics and non-bioinformatics, has been=20 installed into /usr/local 4)Even if we used it as a base, we'd end up ripping out everything=20 they've done and remastering it. =09 Linux distributions chosen for further testing =09 On the basis of the above results, two distributions were chosen at the=20 Bio-Linux Development strategy meeting on February 13, 2004 for further=20 testing as potential base systems for Bio-Linux: =09 Fedora Core 1 Knoppix =09 Testing strategy: =09 Two machines will be set up, one for each of the above distributions.=20 Over the next two weeks, EGTDC staff will dedicate time to work on both=20 systems. A final decision for the distribution to be used for further=20 Bio-Linux development will be made on February 27, 2004 on the basis of=20 this testing. =09 For those wishing to read up on what is happening in the Linux world=20 there is an excellent article here on the relative market share of the=20 top Linux variants: =09 http://www.internetnews.com/ent-news/article.php/3313211 --=20 Dr Dan Swan - Bio-Linux Developer | RHCE EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR Tel: 01865 281 658 Fax: 018665 281 696 http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk =09 =09 -- __--__-- =09 _______________________________________________ Bio-Linux mailing list Bio-Linux at bioinf.ceh.ac.uk http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux =09 =09 End of Bio-Linux Digest _____ =20 Do you Yahoo!? Yahoo! Mail SpamGuard 1> - Read only the mail you want. ------_=_NextPart_001_01C3F6E4.17A29E89 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable charset=3Dus-ascii"> /* Font Definitions */ @font-face {font-family:Tahoma; panose-1:2 11 6 4 3 5 4 4 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0cm; margin-bottom:.0001pt; font-size:12.0pt; font-family:"Times New Roman";} a:link, span.MsoHyperlink {color:blue; text-decoration:underline;} a:visited, span.MsoHyperlinkFollowed {color:blue; text-decoration:underline;} p {margin-right:0cm; margin-left:0cm; font-size:12.0pt; font-family:"Times New Roman";} p.Heading, li.Heading, div.Heading {margin:0cm; margin-bottom:.0001pt; text-align:center; font-size:14.0pt; font-family:"Times New Roman"; text-decoration:underline;} span.EmailStyle19 {font-family:Arial; color:navy;} @page Section1 {size:595.3pt 841.9pt; margin:72.0pt 90.0pt 72.0pt 90.0pt;} div.Section1 {page:Section1;} --> style=3D'font-size: 10.0pt;font-family:Arial;color:navy'>It seems that you are asking for a = lot of something that is being given away for free. Remember that EGTDC = have to install, test and support every package that they include in BioLinux and that = takes resources. Would your organization contribute the necessary = resources for EGTDC to be able to include and support all the packages you request = (and any interaction between them)? From a support point of view it is much = simpler to include a core set of applications that cover most of the tasks = people using a BioLinux box are likely to use, and then allow them to install and = support their own specific packages on top of that. There is nothing to = stop you installing your own extra applications on top of the BioLinux 3 = distribution. style=3D'font-size: 10.0pt;font-family:Arial;color:navy'> style=3D'font-size: 10.0pt;font-family:Arial;color:navy'>Rob Anderson style=3D'font-size: 10.0pt;font-family:Arial;color:navy'>Computing Support = Officer style=3D'font-size: 10.0pt;font-family:Arial;color:navy'>Centre for Population = Biology style=3D'font-size: 10.0pt;font-family:Arial;color:navy'>Imperialsize=3D2 color=3Dnavy face=3DArial>style=3D'font-size:10.0pt;font-family:Arial; color:navy'> face=3DArial> = style=3D'font-size:10.0pt;font-family:Arial;color:navy'>Collegeont> face=3DTahoma>lang=3DEN-US style=3D'font-size:10.0pt;font-family:Tahoma'>-----Original Message----- From: = bio-linux-admin at ivsun01.nerc-oxford.ac.uk [mailto:bio-linux-admin at ivsun01.nerc-oxford.ac.uk] style=3D'font-weight: bold'>On Behalf Of M.S YATNATTI Sent: size=3D2 face=3DTahoma>style=3D'font-size:10.0pt;font-family:Tahoma'>19 February 2004lang=3DEN-US style=3D'font-size:10.0pt;font-family:Tahoma'> size=3D2 face=3DTahoma>style=3D'font-size:10.0pt;font-family:Tahoma'>11:54size=3D2 face=3DTahoma>style=3D'font-size:10.0pt;font-family:Tahoma'> To: bio-linux at ivsun01.nerc-oxford.ac.uk Subject: [Bio-Linux] Re: = === message truncated === --------------------------------- Do you Yahoo!? Yahoo! Mail SpamGuard - Read only the mail you want. -------------- next part -------------- An HTML attachment was scrubbed... URL: From M.Ostrowski at warwick.ac.uk Fri Feb 27 13:01:18 2004 From: M.Ostrowski at warwick.ac.uk (Martin Ostrowski) Date: Fri, 27 Feb 2004 18:01:18 +0000 Subject: [Bio-Linux] ARB, broken link to pt_servers in Biolinux 3.0 Message-ID: For those of you that use pt servers with arb the link to the pt servers in /usr/software/arb/arb/lib/pts does not work we fixed the problem by deleting the old one in /usr/software/arb/arb/lib/pts and creating a new link to /home/db/arb_pt_server/lib/pts. We also had to replace the /usr/software/arb/arb/lib arb_tcp.dat with our old version in but it might be possible to create a link to this as well. regards, Martin Dept. Biological Sciences University of Warwick Gibbet Hill Rd Coventry CV4 7AL UK M.Ostrowski at warwick.ac.uk