From btiwari at ceh.ac.uk Thu Nov 17 10:11:57 2005 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Thu, 17 Nov 2005 15:11:57 +0000 Subject: [Bio-Linux] new packages on Bio-Linux - taverna, estscan and prot4est Message-ID: Hello, This is an email to alert you to new Bio-Linux packages available: 1) Taverna Taverna is a graphical interface allowing you to harness the many bioinformatics functions being offered as web services to create customised pipelines to accomplish tasks from the simple to the complex. Example workflows come with the program to help you get a feel for what is possible. The first time a user runs taverna on Bio-Linux, they are offered the opportunity to copy the examples that come with taverna into their home directory. These example workflow files are saved to a folder called tavernaExamples. Some of the examples are rather complex, but some simpler ones which are easier to understand are provided such as: FetchPDBFlatFile.xml (within the libraries subfolder) blast-compare-retry.xml (under the WBSWorkflows subfolder) or perhaps the best one to start out with: FetchDailyDilbertComic.xml (within the tavernaExamples folder itself) Once installed, taverna can be started by typing "taverna" on the command line, or by choosing the taverna option in the graphical bioinformatics menu. 2) estscan ESTScan is a commane line program that can detect coding regions in DNA seqeunces, even if they are of low quality. It will also try to detect and correct sequence errors that lead to frameshifts. ESTScan uses a Markov model to represent the bias in hexanucleotide use found in coding regions relative to non-coding regions. After installation, ESTScan can be started on Bio-Linux by typing "estscan" on the command line. 3) prot4est This program takes expressed sequence tags and translates them into putative peptide sequences. It makes use of the ESTScan program and can optionally use the decode program also if that is available on the machine. Please note that the User Guide provided with this package is currently out of date. We will add the new version when it becomes available. The important change relevant to Bio-Linux users is that you do not need to do any additional configuration or installation after installing the bio-linux-prot4est package unless you wish to make use of decoder, which is a licensed piece of software. As with all new packages added to the Bio-Linux package listing, these packages will not get installed on your machine automatically. One way to install them is through the synaptic interface. Information on how to do that can be found through the following link: http://envgen.nox.ac.uk/envgen/software/archives/000503.html#Synaptic cheers Bela ************************* Dr. Bela Tiwari Lead Bioinformatician NERC Environmental Bioinformatics Centre CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 ************************* This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any views or opinions expressed are those of the author and do not represent the views of NERC unless otherwise explicitly stated. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and your reply cannot be guaranteed. From ajt at rri.sari.ac.uk Thu Nov 17 17:26:09 2005 From: ajt at rri.sari.ac.uk (Tony Travis) Date: Thu, 17 Nov 2005 22:26:09 +0000 Subject: [Bio-Linux] new packages on Bio-Linux - taverna, estscan and prot4est In-Reply-To: References: Message-ID: <437D0381.5010404@rri.sari.ac.uk> Bela Tiwari wrote: > Hello, > > This is an email to alert you to new Bio-Linux packages available: > > > 1) Taverna > > Taverna is a graphical interface allowing you to harness the many > bioinformatics functions being offered as web services to create > customised pipelines to accomplish tasks from the simple to the > complex. Example workflows come with the program to help you get a > feel for what is possible. The first time a user runs taverna on > Bio-Linux, they are offered the opportunity to copy the examples that > come with taverna into their home directory. These example workflow > files are saved to a folder called tavernaExamples. Some of the > examples are rather complex, but some simpler ones which are easier > to understand are provided such as: Hello, Bela. Good stuff! I noticed Taverna appear in your public deb repository :-) I've installed it from the *.deb repository on wildcat.rri.sari.ac.uk under Debian 'stable' (i.e not under Bio-Linux) but it crashed and burned: can't find the plugins folder. Anyone else had this problem? I've installed the Sun 1.5.0_03 JRE under Debian using java-package, and Jemboss works fine. Best wishes, Tony. -- Dr. A.J.Travis, | mailto:ajt at rri.sari.ac.uk Rowett Research Institute, | http://www.rri.sari.ac.uk/~ajt Greenburn Road, Bucksburn, | phone:+44 (0)1224 712751 Aberdeen AB21 9SB, Scotland, UK. | fax:+44 (0)1224 716687 From keith.jolley at medawar.ox.ac.uk Thu Nov 17 12:23:43 2005 From: keith.jolley at medawar.ox.ac.uk (Keith Jolley) Date: Thu, 17 Nov 2005 17:23:43 -0000 Subject: [Bio-Linux] Firewall rules for browsing virtual host on localhost Message-ID: <20051117172347.19A1CE0003C1@astro.systems.pipex.net> I've run into a problem with the firewall as configured on Bio-Linux. I have a number of web sites hosted on a Bio-Linux server - these are set up as named virtual hosts. What I can't do with the firewall running is to browse these web sites from the Bio-Linux machine itself, although they are visible from other machines. This normally isn't a problem but I would like to use htdig as a search engine on one of these sites, but this needs to be able to browse the local machine. Does anybody know what I need to do with narc.conf or narc-custom.conf in order to enable local browsing of virtual hosts? Thanks Keith From btiwari at ceh.ac.uk Fri Nov 18 11:45:53 2005 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Fri, 18 Nov 2005 16:45:53 +0000 Subject: [Bio-Linux] taverna on Bio-Linux Message-ID: Hello Tony, I've posted this response to the taverna-users mailing list also in case anyone has any comments about the issue you saw. >I've installed it from the *.deb repository on wildcat.rri.sari.ac.uk >under Debian 'stable' (i.e not under Bio-Linux) but it crashed and >burned: can't find the plugins folder. Anyone else had this problem? The bio-linux-taverna package includes a runme_biolinux.sh file which is what is being called when you run taverna after installing the package. That file is very similar to the standard runme.sh file that comes with taverna - it was just hacked a bit (by me...so you know who to blame) to make Taverna run sensibly on a multi-user system like Bio-Linux. Another person here, Chimdi Ekeke, tried to run Taverna (installed from the Bio-Linux package) on a non-Bio-Linux version of Debian (stable) and saw the same issue as you. He then tried running it using the standard runme.sh script (from an appropriate location) and this caused the same problems, which suggests this might be a problem with Taverna 1.3 on standard Debian Sarge installations. If you alter the java command at the very end of the runme_biolinux.sh to rearrange the order of the -D flags such that it looks like: -Dtaverna.home=$TAVERNA_HOME -ea org.embl.ebi.escience.scuflui.workbench.Workbench taverna will work, but according to Chimdi, it then takes on a similar appearance to Taverna version 1.2 rather than what is it, version 1.3. cheers Bela ************************* Dr. Bela Tiwari Lead Bioinformatician NERC Environmental Bioinformatics Centre CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 ************************* This e-mail and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. Any views or opinions expressed are those of the author and do not represent the views of NERC unless otherwise explicitly stated. The information contained in this e-mail may be subject to public disclosure under the Freedom of Information Act 2000. Unless the information is legally exempt from disclosure, the confidentiality of this e-mail and your reply cannot be guaranteed. From keith.jolley at medawar.ox.ac.uk Sat Nov 19 07:06:39 2005 From: keith.jolley at medawar.ox.ac.uk (Keith Jolley) Date: Sat, 19 Nov 2005 12:06:39 -0000 Subject: [Bio-Linux] Firewall rules for browsing virtual host on localhost In-Reply-To: <20051117172347.19A1CE0003C1@astro.systems.pipex.net> Message-ID: <20051119120642.D252CE000266@astro.systems.pipex.net> In case anybody else finds this useful, the solution was to set: LOOPBACK_MODE="loose" In /etc/narc.conf It was originally set to 'normal' which only allows 127.0.0.1 addressed packets through on lo. Keith > -----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 Keith Jolley > Sent: 17 November 2005 17:24 > To: bio-linux at ivsun01.nerc-oxford.ac.uk > Subject: [Bio-Linux] Firewall rules for browsing virtual host on localhost > > I've run into a problem with the firewall as configured on Bio-Linux. I > have a number of web sites hosted on a Bio-Linux server - these are set up > as named virtual hosts. What I can't do with the firewall running is to > browse these web sites from the Bio-Linux machine itself, although they > are > visible from other machines. This normally isn't a problem but I would > like > to use htdig as a search engine on one of these sites, but this needs to > be > able to browse the local machine. > > Does anybody know what I need to do with narc.conf or narc-custom.conf in > order to enable local browsing of virtual hosts? > > Thanks > Keith > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at bioinf.ceh.ac.uk > http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux From bioinformatics.lists at gmail.com Fri Nov 25 05:25:11 2005 From: bioinformatics.lists at gmail.com (Dan Swan) Date: Fri, 25 Nov 2005 10:25:11 +0000 Subject: [Bio-Linux] Bio-Linux EMBOSS and proxies Message-ID: Hi All, just a quick note to say that whilst we were setting up for an MRes practical we ran into an issue with EMBOSS. Not sure if this has been covered before/elsewhere Seqret was returning errors of 'no route to host' when attempting to fetch EMBL records. We eventually traced this to being a proxy issue, seqret doesn't understand $http_proxy. If other institutions access the web via a proxy there are two workarounds: 1) Type this at the command line, or add it into your login scripts: export EMBOSS_PROXY=yourcache.ac.uk:portnum (where yourcache.ac.uk is your proxy host and portnum is your proxy port (eg 8080)) 2) In /usr/local/bioinf/EMBOSS/EMBOSS/emboss/emboss.default add a line such as: SET EMBOSS_PROXY yourcache.ac.uk:portnum it is important *not* to include a leading "http://" to the proxy address. Hope this is useful to someone else. Dan Swan -- Senior Research Associate, Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Framlington Place, University of Newcastle upon Tyne, Newcastle, NE2 4HH Tel: +44 (0)191 222 7253 (Leech offices: Rooms M.2046/M.2046A) Tel: +44 (0)191 246 4833 (Devonshire offices: Rooms G.25/G.26) Website: http://bioinf.ncl.ac.uk/support/ From tmo at ebi.ac.uk Fri Nov 25 09:05:05 2005 From: tmo at ebi.ac.uk (Tom Oinn) Date: Fri, 25 Nov 2005 14:05:05 +0000 Subject: [Bio-Linux] Re: [Taverna-users] taverna on Bio-Linux In-Reply-To: References: Message-ID: <43871A11.9050304@ebi.ac.uk> Bela Tiwari wrote: > Hello Tony, > > I've posted this response to the taverna-users mailing list also in > case anyone has any comments about the issue you saw. > >> I've installed it from the *.deb repository on >> wildcat.rri.sari.ac.uk under Debian 'stable' (i.e not under >> Bio-Linux) but it crashed and burned: can't find the plugins >> folder. Anyone else had this problem? That's nothing to worry about - Taverna 1.3 has a partially working alternate classloader, what you're seeing is the debug output. The 'can't find the plugins folder' message is present on all platforms, it shouldn't have any impact on functionality of the code though. > The bio-linux-taverna package includes a runme_biolinux.sh file which > is what is being called when you run taverna after installing the > package. That file is very similar to the standard runme.sh file that > comes with taverna - it was just hacked a bit (by me...so you know > who to blame) to make Taverna run sensibly on a multi-user system > like Bio-Linux. > > Another person here, Chimdi Ekeke, tried to run Taverna (installed > from the Bio-Linux package) on a non-Bio-Linux version of Debian > (stable) and saw the same issue as you. He then tried running it > using the standard runme.sh script (from an appropriate location) and > this caused the same problems, which suggests this might be a problem > with Taverna 1.3 on standard Debian Sarge installations. > > If you alter the java command at the very end of the > runme_biolinux.sh to rearrange the order of the -D flags such that it > looks like: > > -Dtaverna.home=$TAVERNA_HOME -ea > org.embl.ebi.escience.scuflui.workbench.Workbench > > taverna will work, but according to Chimdi, it then takes on a > similar appearance to Taverna version 1.2 rather than what is it, > version 1.3. That would be rather strange, the only way the code could be picking up 1.2 behaviours would be to have the 1.2 code present somewhere - they just don't exist in 1.3. You might get a different look and feel if you're running different versions of Java but that's the only thing I could think of that would account for it. You might have to be more specific on 'takes on a similar...' etc though, it's rather hard to tell what the problem is. On Java 5 and linux you need to remove the -Dtaverna.scrolldesktop (or similar) from the command line, this disables a feature that has issues with some look and feel classes on JDK5. Tom From mith at ceh.ac.uk Fri Nov 25 12:35:50 2005 From: mith at ceh.ac.uk (Milo Thurston) Date: Fri, 25 Nov 2005 17:35:50 +0000 Subject: [Bio-Linux] Dust Message-ID: <43874B76.8020905@ceh.ac.uk> Has anyone got "dust" running on bio-linux? If so, please would you let me know where you found it? Thanks, Milo Thurston. -- Dr. Milo Thurston, CEH Oxford, Mansfield Road, Oxford, OX1 3SR. 'phone 01865 281975, fax 01865 281696. http://www.genomics.ceh.ac.uk/lab/ From tbooth at ceh.ac.uk Mon Nov 28 05:08:19 2005 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 28 Nov 2005 10:08:19 +0000 Subject: [Bio-Linux] Fast remote desktop for Bio-Linux using FreeNX Message-ID: <1133172500.14790.11.camel@ivpcp044.nox.ac.uk> Hi All, Nic here suggested trying FreeNX for remote connections into Bio-Linux machines. The system promises a full-speed remote desktop even over a home broadband connection, has clients for Windows, Mac and Linux and is available at no cost. I tried it myself this weekend and was very impressed. If you are running remote applications on a Bio-Linux machine and finding them slow, then FreeNX may be the answer. It also allows you to run a remote session on a Windows machine without installing software like Exceed. I have put instructions on how to set it up on our website: http://envgen.nox.ac.uk/envgen/software/archives/000506.html#freenx The homepage for the FreeNX project is: http://freenx.berlios.de/ NX was developed by NoMachine: http://nomachine.com Please let me know if you do try NX and find it useful. Thanks, TIM -- Tim Booth NEBC at CEH Oxford From keith.jolley at medawar.ox.ac.uk Mon Nov 28 05:31:05 2005 From: keith.jolley at medawar.ox.ac.uk (Keith Jolley) Date: Mon, 28 Nov 2005 10:31:05 -0000 Subject: [Bio-Linux] Fast remote desktop for Bio-Linux using FreeNX In-Reply-To: <1133172500.14790.11.camel@ivpcp044.nox.ac.uk> Message-ID: <001301c5f406$d69e8020$4c4901a3@artemis> This is great - I've just tried it and it seems to be what I've been looking for. I'm running a course in Cambridge in January but we will be doing some analysis on a Bio-Linux machine based in Oxford. Last time, I used a VNC session tunnelled via SSH using a simplied desktop (IceWM) - this worked ok, but it entailed manually setting up port forwarding on each client - this is so much easier and faster. Thanks for the pointer. Keith > -----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 Tim Booth > Sent: 28 November 2005 10:08 > To: Bio-Linux mailing list > Subject: [Bio-Linux] Fast remote desktop for Bio-Linux using FreeNX > > Hi All, > > Nic here suggested trying FreeNX for remote connections into Bio-Linux > machines. The system promises a full-speed remote desktop even over a > home broadband connection, has clients for Windows, Mac and > Linux and is > available at no cost. I tried it myself this weekend and was very > impressed. If you are running remote applications on a Bio-Linux > machine and finding them slow, then FreeNX may be the answer. It also > allows you to run a remote session on a Windows machine without > installing software like Exceed. I have put instructions on > how to set > it up on our website: > > http://envgen.nox.ac.uk/envgen/software/archives/000506.html#freenx > > The homepage for the FreeNX project is: > > http://freenx.berlios.de/ > > NX was developed by NoMachine: > > http://nomachine.com > > Please let me know if you do try NX and find it useful. > > Thanks, > > TIM > > -- > Tim Booth > NEBC at CEH Oxford > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at bioinf.ceh.ac.uk > http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux > From ajt at rri.sari.ac.uk Mon Nov 28 06:04:05 2005 From: ajt at rri.sari.ac.uk (Tony Travis) Date: Mon, 28 Nov 2005 11:04:05 +0000 Subject: [Bio-Linux] Fast remote desktop for Bio-Linux using FreeNX In-Reply-To: <1133172500.14790.11.camel@ivpcp044.nox.ac.uk> References: <1133172500.14790.11.camel@ivpcp044.nox.ac.uk> Message-ID: <438AE425.8000407@rri.sari.ac.uk> Tim Booth wrote: > Hi All, > > Nic here suggested trying FreeNX for remote connections into > Bio-Linux machines. The system promises a full-speed remote desktop > even over a home broadband connection, has clients for Windows, Mac > and Linux and is available at no cost. I tried it myself this > weekend and was very impressed. If you are running remote > applications on a Bio-Linux machine and finding them slow, then > FreeNX may be the answer. It also allows you to run a remote session > on a Windows machine without installing software like Exceed. I have > put instructions on how to set it up on our website: Hello, Tim. I've set up Bio-Linux under Debian Sarge with XDMCP and VNC: You can get a Bio-Linux desktop using either the Microsoft Windows VNC viewer, or in a web browser window using the Java VNC viewer applet. Performance is excellent on 2Mb broadband - I'm using a web browser at the moment to run GAP4. I'm using 'TightVNC': http://www.tightvnc.com/ Instructions about setting up VNC under XDMCP are attached. You need to tunnel port 5901 (VNC) through port 22 (SSH) to use VNC through a firewall, and you also need to tunnel port 80 (HTTP) through 22 (SSH) if you want to use the Java applet in a web browser through a firewall. BTW these 'complications' are necessary to ensure security for external use, but are not needed within a firewall. Best wishes, Tony. -- Dr. A.J.Travis, | mailto:ajt at rri.sari.ac.uk Rowett Research Institute, | http://www.rri.sari.ac.uk/~ajt Greenburn Road, Bucksburn, | phone:+44 (0)1224 712751 Aberdeen AB21 9SB, Scotland, UK. | fax:+44 (0)1224 716687 -------------- next part -------------- A non-text attachment was scrubbed... Name: VNCTricks.pdf Type: application/pdf Size: 321503 bytes Desc: not available URL: From a.shirras at lancaster.ac.uk Mon Nov 28 07:28:01 2005 From: a.shirras at lancaster.ac.uk (Shirras, Alan) Date: Mon, 28 Nov 2005 12:28:01 -0000 Subject: [Bio-Linux] Fast remote desktop for Bio-Linux using FreeNX Message-ID: Is it possible to install the server software if you don't have root access? Alan -----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 Tim Booth Sent: 28 November 2005 10:08 To: Bio-Linux mailing list Subject: [Bio-Linux] Fast remote desktop for Bio-Linux using FreeNX Hi All, Nic here suggested trying FreeNX for remote connections into Bio-Linux machines. The system promises a full-speed remote desktop even over a home broadband connection, has clients for Windows, Mac and Linux and is available at no cost. I tried it myself this weekend and was very impressed. If you are running remote applications on a Bio-Linux machine and finding them slow, then FreeNX may be the answer. It also allows you to run a remote session on a Windows machine without installing software like Exceed. I have put instructions on how to set it up on our website: http://envgen.nox.ac.uk/envgen/software/archives/000506.html#freenx The homepage for the FreeNX project is: http://freenx.berlios.de/ NX was developed by NoMachine: http://nomachine.com Please let me know if you do try NX and find it useful. Thanks, TIM -- Tim Booth NEBC at CEH Oxford _______________________________________________ Bio-Linux mailing list Bio-Linux at bioinf.ceh.ac.uk http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux From tbooth at ceh.ac.uk Mon Nov 28 07:42:54 2005 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 28 Nov 2005 12:42:54 +0000 Subject: [Bio-Linux] Fast remote desktop for Bio-Linux using FreeNX In-Reply-To: References: Message-ID: <1133181774.14790.28.camel@ivpcp044.nox.ac.uk> Hi Alan, Unfortunately not. The MX server requires changes to system files and the creation of the 'mx' user account, so you need to get the permission of the system administrator - which on a standard Bio-Linux setup is whoever holds the manager password. As a reminder, to get a root shell open a regular terminal as manager and do: 'sudo bash' (and give the manager password) or open a terminal as any user and do: 'su -' (and give the root password) TIM On Mon, 2005-11-28 at 12:28 +0000, Shirras, Alan wrote: > Is it possible to install the server software if you don't have root access? > > Alan >