From gmachnik at sum.edu.pl Wed Apr 1 07:53:33 2009 From: gmachnik at sum.edu.pl (Grzegorz Machnik) Date: Wed, 1 Apr 2009 13:53:33 +0200 Subject: [EMBOSS] Command line on www-interface Message-ID: Hello everybody, If I utilize any of www- based EMBOSS interface, may I use any of the command line qualifiers, i.e. -sreverse2 ? It will be useful for me. Till now I use it succesfuly in UNIX- based software. There is no such options to chose it, even in "advanced options" section. Any advices? Thanks Grzegorz From gbottu at vub.ac.be Wed Apr 1 11:24:12 2009 From: gbottu at vub.ac.be (Guy Bottu) Date: Wed, 01 Apr 2009 17:24:12 +0200 Subject: [EMBOSS] Command line on www-interface In-Reply-To: References: Message-ID: <49D3871C.6030308@vub.ac.be> Grzegorz Machnik wrote: > If I utilize any of www- based EMBOSS interface, may I use any of the command line qualifiers, i.e. -sreverse2 ? It will be useful for me. Till now I use it succesfuly in UNIX- based software. > There is no such options to chose it, even in "advanced options" section. Dear Grzegorz, You present here a good question. GUI's for EMBOSS usually have a script that converts ACD to HTML, XML or whatever language is used to describe the program pages. The "Associated" parameters however do not show up in the ACD files and need some ad hoc programmed module in the ACD parser. The GUI's much differ in what they offer. I think Jemboss is quite complete, at least for sequences. And wEMBOSS at least does support -sbegin1 -send1 -sreverse1 -sbegin2 -send2 -sreverse2. Regards, Guy Bottu, Belgian EMBnet Node and wEMBOSS development team From eric.userlist at gmail.com Mon Apr 6 20:17:35 2009 From: eric.userlist at gmail.com (Eric Userlist) Date: Mon, 6 Apr 2009 17:17:35 -0700 Subject: [EMBOSS] Jemboss installation error Message-ID: Hi I have installed emboss in an intel redhat machine (Linux 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:54:53 EST 2006 i686 i686 i386 GNU/Linux) and tested several commands that seem to work. However I get the following errors after "successful" installing jemboss: Exception in thread "main" java.lang.NoClassDefFoundError: org.emboss.jemboss.Jemboss at gnu.gcj.runtime.FirstThread.run() (/usr/lib/libgcj.so.5.0.0) at _Jv_ThreadRun(java.lang.Thread) (/usr/lib/libgcj.so.5.0.0) at _Jv_RunMain(java.lang.Class, byte const, int, byte const, boolean) (/usr/lib/libgcj.so.5.0.0) I tried to search the emboss website and related discussions in the internet. Some people seem to run into similar problems but no solutions were offered. I hope to get some help here. Thank you very much! Eric From tjc at sanger.ac.uk Tue Apr 7 03:32:35 2009 From: tjc at sanger.ac.uk (Tim Carver) Date: Tue, 07 Apr 2009 08:32:35 +0100 Subject: [EMBOSS] Jemboss installation error In-Reply-To: Message-ID: Hi Eric This looks to me as if it is trying to run with Gnu Java. You probably need to set your PATH to point at Sun Java and also make sure it was compiled with that. Regards Tim On 4/7/09 1:17 AM, "Eric Userlist" wrote: > Hi > I have installed emboss in an intel redhat machine (Linux 2.6.9-34.ELsmp #1 > SMP Fri Feb 24 16:54:53 EST 2006 i686 i686 i386 GNU/Linux) and tested > several commands that seem to work. However I get the following errors after > "successful" installing jemboss: > > Exception in thread "main" java.lang.NoClassDefFoundError: > org.emboss.jemboss.Jemboss > at gnu.gcj.runtime.FirstThread.run() (/usr/lib/libgcj.so.5.0.0) > at _Jv_ThreadRun(java.lang.Thread) (/usr/lib/libgcj.so.5.0.0) > at _Jv_RunMain(java.lang.Class, byte const, int, byte const, boolean) > (/usr/lib/libgcj.so.5.0.0) > > I tried to search the emboss website and related discussions in the > internet. Some people seem to run into similar problems but no solutions > were offered. I hope to get some help here. Thank you very much! > > Eric > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From uludag at ebi.ac.uk Tue Apr 7 04:19:59 2009 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Tue, 07 Apr 2009 09:19:59 +0100 Subject: [EMBOSS] Jemboss installation error In-Reply-To: References: Message-ID: <1239092399.12380.32.camel@emboss2.ebi.ac.uk> Hi Eric, > I get the following errors after > "successful" installing jemboss: > > Exception in thread "main" java.lang.NoClassDefFoundError: > org.emboss.jemboss.Jemboss > at gnu.gcj.runtime.FirstThread.run() (/usr/lib/libgcj.so.5.0.0) > at _Jv_ThreadRun(java.lang.Thread) (/usr/lib/libgcj.so.5.0.0) > at _Jv_RunMain(java.lang.Class, byte const, int, byte const, boolean) > (/usr/lib/libgcj.so.5.0.0) I guess you followed the install procedure described on the following page. I ask this because in my initial attempts i thought jemboss would automatically come out of the box when i install emboss. http://emboss.sourceforge.net/Jemboss/install/standalone.html The second thing to check would be whether you change your current working directory to your ${JEMBOSS_INSTALL_DIR}/share/EMBOSS/jemboss directory before running the runJemboss.sh script. If you find it inconvenient to change directory each time before running the script you can set the JEMBOSS_HOME variable at the top of the script to the above directory. Regards, Mahmut From d.leader at bio.gla.ac.uk Tue Apr 7 11:39:06 2009 From: d.leader at bio.gla.ac.uk (David Leader) Date: Tue, 7 Apr 2009 16:39:06 +0100 Subject: [EMBOSS] Png problem on Mac OS 10.5 Message-ID: <57FCCCBF-8737-4B32-91F5-3D21B7B5AB6A@bio.gla.ac.uk> Turns out that the problem was nothing to do with the version of Mac OS 10 or the type of processor. It was the location of the png libraries when using MacPorts. MacPorts puts everything in a sandpit - /opt/local - so as to shield installs from updates to the operating system. In this case it's irrelevant and a nuisance. Pity, as MacPorts is a very convenient and effective way of getting the libraries for gd (unless you are in a University with web cacheing when it's a teeny bit more complex.) Thanks to David Bauer for suggesting the library location as the problem, and that I should run configure with a library location qualifier, in my case: configure --with-pngdriver=/opt/local Works now. David ___________________________________________________ Dr. David P. Leader, Faculty of Biomedical & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK Phone: +44 (0)141 330 5905 http://doolittle.ibls.gla.ac.uk/leader http://motif.gla.ac.uk/ The University of Glasgow, charity number SC004401 ___________________________________________________ From eric.userlist at gmail.com Tue Apr 7 12:30:19 2009 From: eric.userlist at gmail.com (Eric Userlist) Date: Tue, 7 Apr 2009 09:30:19 -0700 Subject: [EMBOSS] Jemboss installation error In-Reply-To: References: Message-ID: Hi Tim Thanks for your email. I am not a big java guru. Can you point to me how to get a compatible sun java with emboss 6.0.1? Eric On Tue, Apr 7, 2009 at 12:32 AM, Tim Carver wrote: > Hi Eric > > This looks to me as if it is trying to run with Gnu Java. You probably need > to set your PATH to point at Sun Java and also make sure it was compiled > with that. > > Regards > Tim > > > On 4/7/09 1:17 AM, "Eric Userlist" wrote: > > > Hi > > I have installed emboss in an intel redhat machine (Linux 2.6.9-34.ELsmp > #1 > > SMP Fri Feb 24 16:54:53 EST 2006 i686 i686 i386 GNU/Linux) and tested > > several commands that seem to work. However I get the following errors > after > > "successful" installing jemboss: > > > > Exception in thread "main" java.lang.NoClassDefFoundError: > > org.emboss.jemboss.Jemboss > > at gnu.gcj.runtime.FirstThread.run() (/usr/lib/libgcj.so.5.0.0) > > at _Jv_ThreadRun(java.lang.Thread) (/usr/lib/libgcj.so.5.0.0) > > at _Jv_RunMain(java.lang.Class, byte const, int, byte const, boolean) > > (/usr/lib/libgcj.so.5.0.0) > > > > I tried to search the emboss website and related discussions in the > > internet. Some people seem to run into similar problems but no solutions > > were offered. I hope to get some help here. Thank you very much! > > > > Eric > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/emboss > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. > From eric.userlist at gmail.com Tue Apr 7 12:31:54 2009 From: eric.userlist at gmail.com (Eric Userlist) Date: Tue, 7 Apr 2009 09:31:54 -0700 Subject: [EMBOSS] Jemboss installation error In-Reply-To: <1239092399.12380.32.camel@emboss2.ebi.ac.uk> References: <1239092399.12380.32.camel@emboss2.ebi.ac.uk> Message-ID: Thanks Mahmut. I also think that jemboss should be automatically compiled with emboss. Maybe someone can provide a more updated installation procedure. Thanks all. Eric On Tue, Apr 7, 2009 at 1:19 AM, Mahmut Uludag wrote: > Hi Eric, > > > I get the following errors after > > "successful" installing jemboss: > > > > Exception in thread "main" java.lang.NoClassDefFoundError: > > org.emboss.jemboss.Jemboss > > at gnu.gcj.runtime.FirstThread.run() (/usr/lib/libgcj.so.5.0.0) > > at _Jv_ThreadRun(java.lang.Thread) (/usr/lib/libgcj.so.5.0.0) > > at _Jv_RunMain(java.lang.Class, byte const, int, byte const, boolean) > > (/usr/lib/libgcj.so.5.0.0) > > I guess you followed the install procedure described on the following > page. I ask this because in my initial attempts i thought jemboss would > automatically come out of the box when i install emboss. > > http://emboss.sourceforge.net/Jemboss/install/standalone.html > > The second thing to check would be whether you change your current > working directory to your ${JEMBOSS_INSTALL_DIR}/share/EMBOSS/jemboss > directory before running the runJemboss.sh script. If you find it > inconvenient to change directory each time before running the script you > can set the JEMBOSS_HOME variable at the top of the script to the above > directory. > > Regards, > Mahmut > > > From joscott at healthlib.usf.edu Tue Apr 14 14:11:21 2009 From: joscott at healthlib.usf.edu (John Scott) Date: Tue, 14 Apr 2009 14:11:21 -0400 Subject: [EMBOSS] New to EMBOSS Message-ID: <1239732681.4160.7.camel@localhost> Planning on deploying emboss, but can't seem to find how much disk space usage I should plan for. Can someone let me know what I can expect to see on a system with about a hundred users? Thanks. John From gbottu at vub.ac.be Wed Apr 15 03:52:14 2009 From: gbottu at vub.ac.be (Guy Bottu) Date: Wed, 15 Apr 2009 09:52:14 +0200 Subject: [EMBOSS] New to EMBOSS In-Reply-To: <1239732681.4160.7.camel@localhost> References: <1239732681.4160.7.camel@localhost> Message-ID: <49E5922E.9060803@vub.ac.be> John Scott wrote: > Planning on deploying emboss, but can't seem to find how much disk space > usage I should plan for. Can someone let me know what I can expect to > see on a system with about a hundred users? Thanks. Dear John, That is a difficult question. On our computer EMBOSS itself (without the sequence databases but with the motif databases) takes 250 Mbyte. The space your users need depends much on whether they are just grandmotherwise analyzing some sequences of their interest or whether they are in complete genome high throughput analysis. On our computer there is for the moment 49 Gbyte used (about 250 users, but not all are very active). Regards, Guy Bottu, Belgian EMBnet Node From moldoverb at gmail.com Wed Apr 15 07:35:19 2009 From: moldoverb at gmail.com (Brian Moldover) Date: Wed, 15 Apr 2009 07:35:19 -0400 Subject: [EMBOSS] New to EMBOSS In-Reply-To: <49E5922E.9060803@vub.ac.be> References: <1239732681.4160.7.camel@localhost> <49E5922E.9060803@vub.ac.be> Message-ID: <000901c9bdbe$42074b60$c615e220$@com> My basic installation which includes Emboss (and Embassy), and the Blocks, Prints, Prosite, Blimps, and test databases, but no sequence databases, takes 1.23 gb. EMBL is something like 700+ Gb uncompressed. I just installed a 4tb NAS to try and manage the sequence databases. -----Original Message----- From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Guy Bottu Sent: Wednesday, April 15, 2009 3:52 AM To: John Scott Cc: emboss at lists.open-bio.org Subject: Re: [EMBOSS] New to EMBOSS John Scott wrote: > Planning on deploying emboss, but can't seem to find how much disk space > usage I should plan for. Can someone let me know what I can expect to > see on a system with about a hundred users? Thanks. Dear John, That is a difficult question. On our computer EMBOSS itself (without the sequence databases but with the motif databases) takes 250 Mbyte. The space your users need depends much on whether they are just grandmotherwise analyzing some sequences of their interest or whether they are in complete genome high throughput analysis. On our computer there is for the moment 49 Gbyte used (about 250 users, but not all are very active). Regards, Guy Bottu, Belgian EMBnet Node _______________________________________________ EMBOSS mailing list EMBOSS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss No virus found in this incoming message. Checked by AVG - www.avg.com Version: 8.0.238 / Virus Database: 270.11.57/2059 - Release Date: 04/14/09 14:52:00 From koenvanderdrift at gmail.com Wed Apr 15 08:00:47 2009 From: koenvanderdrift at gmail.com (Koen van der Drift) Date: Wed, 15 Apr 2009 08:00:47 -0400 Subject: [EMBOSS] Png problem on Mac OS 10.5 Message-ID: <5cba6b9f0904150500t2f599e4cyf39fe3500cc0b92e@mail.gmail.com> > > Turns out that the problem was nothing to do with the version of Mac > OS 10 or the type of processor. It was the location of the png > libraries when using MacPorts. MacPorts puts everything in a sandpit > - /opt/local - so as to shield installs from updates to the operating > system. In this case it's irrelevant and a nuisance. Pity, as > MacPorts is a very convenient and effective way of getting the > libraries for gd (unless you are in a University with web cacheing > when it's a teeny bit more complex.) Why not install emboss with macports as well, in that case all necessary libraries can be found in the same place (/opt/local) and you don't have to worry about it. This is the way fink works, and I'm sure Macports is not different from that. - Koen. From lueck at ipk-gatersleben.de Fri Apr 17 04:27:30 2009 From: lueck at ipk-gatersleben.de (=?iso-8859-1?Q?Stefanie_L=FCck?=) Date: Fri, 17 Apr 2009 10:27:30 +0200 Subject: [EMBOSS] EmbossWin eprimer3 compilation Message-ID: <002e01c9bf36$596c0380$1022a8c0@ipkgatersleben.de> Hello! I'm using eprimer3 from the EmbossWin package. Now I want to compile my program (written in Python, compiled with py2exe) to make a windows installer. Unfortunatly eprimer3 has a problem after installation of my program. It's gives an error message that emboss.ini was not found and no primers are designed. If EmbossWin is installed then my program works but this is a circumstantially solution since I need only eprimer3 and the user has to install it additionally. Does someone has an idea how I can solve this problem? Thanks in adavance! Stefanie From uludag at ebi.ac.uk Fri Apr 17 06:23:14 2009 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Fri, 17 Apr 2009 11:23:14 +0100 Subject: [EMBOSS] EmbossWin eprimer3 compilation In-Reply-To: <002e01c9bf36$596c0380$1022a8c0@ipkgatersleben.de> References: <002e01c9bf36$596c0380$1022a8c0@ipkgatersleben.de> Message-ID: <1239963794.20536.47.camel@emboss2.ebi.ac.uk> Hi Stefanie, > I'm using eprimer3 from the EmbossWin package. Now I want to compile > my program (written in Python, compiled with py2exe) to make a windows > installer. Unfortunatly eprimer3 has a problem after installation of > my program. It's gives an error message that emboss.ini was not found > and no primers are designed. If EmbossWin is installed then my program > works but this is a circumstantially solution since I need only > eprimer3 and the user has to install it additionally. As far as I understand you want to include only eprimer3 and files essential for running eprimer3. Your installer might be missing some of the steps EmbossWin installer normally does. http://www.interactive-biosoftware.com/embosswin/install.html Do you know there is a new Windows port of EMBOSS since summer 2006? http://emboss.open-bio.org/pipermail/emboss/2007-July/003051.html You may consider using mEMBOSS as it is compatible with most recent versions of EMBOSS and you can get better support. Regards, Mahmut From lueck at ipk-gatersleben.de Fri Apr 17 06:59:01 2009 From: lueck at ipk-gatersleben.de (=?iso-8859-1?Q?Stefanie_L=FCck?=) Date: Fri, 17 Apr 2009 12:59:01 +0200 Subject: [EMBOSS] EmbossWin eprimer3 compilation References: <002e01c9bf36$596c0380$1022a8c0@ipkgatersleben.de> <1239963794.20536.47.camel@emboss2.ebi.ac.uk> Message-ID: <005101c9bf4b$83dd7170$1022a8c0@ipkgatersleben.de> Hi! > > Do you know there is a new Windows port of EMBOSS since summer 2006? > No, I'll try this! Thanks, Stefanie From jeedward at yahoo.com Sat Apr 18 12:57:10 2009 From: jeedward at yahoo.com (John Edward) Date: Sat, 18 Apr 2009 09:57:10 -0700 (PDT) Subject: [EMBOSS] Extended draft paper submission: BCBGC-09 call for papers Message-ID: <505864.94161.qm@web45916.mail.sp1.yahoo.com> Extended draft paper submission: BCBGC-09 call for papers ? This Extended Call for Papers is for those who didn't get a chance to submit the papers for the earlier call for papers. The papers received and accepted in response to this extended call for papers will be included in the final version of the respective conference proceedings. These proceedings will be either ready by the time of the conference (i.e., they will be available during the conference) or soon after the conference (before the end of August 2009), based how fast the proceedings can be prepared. Note: If you have already submitted a paper (whether accepted or rejected or currently under review) for MULTICONF-09, please DO NOT submit that paper again to this extended call for papers. IMPORTANT DATES: Draft paper submission date: May 11, 2009 Acceptance/rejection decision: May 21, 2009 Camera ready paper and copyright and pre-registration due: May 28, 2009 Conference dates: July 13-16, 2009 ? ? The 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) will be held during July 13-16 2009 in Orlando, FL, USA. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include: ????????? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) ????????? International Conference on Automation, Robotics and Control Systems (ARCS-09) ????????? International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) ????????? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) ????????? International Conference on Information Security and Privacy (ISP-09) ????????? International Conference on Recent Advances in Information Technology and Applications (RAITA-09) ????????? International Conference on Software Engineering Theory and Practice (SETP-09) ????????? International Conference on Theory and Applications of Computational Science (TACS-09) ????????? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) ? The website http://www.PromoteResearch.org contains more details. ? Sincerely John Edward Publicity committee From arum at ufl.edu Fri Apr 24 11:49:35 2009 From: arum at ufl.edu (Mccaffery,Michael W) Date: Fri, 24 Apr 2009 11:49:35 -0400 Subject: [EMBOSS] mEMBOSS help Message-ID: I am trying to re-run mEMBOSS on a WinXP SP3 machine. The software worked for a several months - then quit running. Clicking on the "Launch JEMBOSS" icon produces an brief hourglass then nothing. No error messages, just nothing. I have reinstalled JAVA (ver 6 update 13) and resinstalled mEMBOSS (6.0.1 and 6.0.1.3 setup files) to no avail. Any help would be greatly appreciated. Mike McCaffery mwm at ifas.ufl.edu From ajb at ebi.ac.uk Fri Apr 24 15:52:18 2009 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Fri, 24 Apr 2009 20:52:18 +0100 (BST) Subject: [EMBOSS] mEMBOSS help In-Reply-To: References: Message-ID: <33941.86.26.12.63.1240602738.squirrel@webmail.ebi.ac.uk> Hello Mike, Try uninstalling/reinstalling using the following procedure. a) You should use the add/remove programs method, not manual deletion of the mEMBOSS folder. If you didn't use add/remove programs then reinstall mEMBOSS and then remove it immediately using add/remove programs b) Now you can manually delete any remaining mEMBOSS folders that are left. c) Search your computer for any files called 'jemboss.properties' and delete any that are found. d) Check that the following 4 Environment Variables have been removed from the 'System Variables' section of: My Computer->Properties->Advanced->Environment Variables namely: EMBOSS_ACDROOT, EMBOSS_DATA, EMBOSS_ROOT & PLPLOT_LIB if they appear then delete them. While you are looking in that section of the environment variables check that the 'Path' entry looks OK, is not empty, and doesn't refer to any old/corrupt installations. Edit if necessary. e) It should now be OK to reinstall mEMBOSS. As the installation states, it is essential that you choose an installation destination having the property that there are no space characters between the drive letter and that folder nor within the folder name itself. If it still doesn't work then check that the 4 environment variables above have been created and point at/within your installation folder and that the 'Path' variable has an entry for your installation folder too. HTH Alan > I am trying to re-run mEMBOSS on a WinXP SP3 machine. > > The software worked for a several months - then quit running. > Clicking on the "Launch JEMBOSS" icon produces an brief hourglass then > nothing. No error messages, just nothing. > > I have reinstalled JAVA (ver 6 update 13) and resinstalled mEMBOSS (6.0.1 > and 6.0.1.3 setup files) to no avail. > > > Any help would be greatly appreciated. > > Mike McCaffery > mwm at ifas.ufl.edu > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From uludag at ebi.ac.uk Fri Apr 24 19:02:54 2009 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Sat, 25 Apr 2009 00:02:54 +0100 (BST) Subject: [EMBOSS] mEMBOSS help In-Reply-To: References: Message-ID: <43788.86.173.4.141.1240614174.squirrel@webmail.ebi.ac.uk> > Clicking on the "Launch JEMBOSS" icon produces an brief hourglass then > nothing. No error messages, just nothing. Starting Jemboss from Windows "Command Prompt" manually may allow to see errors that are printed on the console. 1-) Open a new Windows Command Prompt Start -> All Programs-> Accessories -> Command Prompt 2-) Change your directory to the 'jemboss\jar' folder under your mEMBOSS folder. For example since my mEMBOSS was installed in my D drive I had to run following 2 commands > d: > cd D:\mEMBOSS\jemboss\jar 3-) Start Jemboss manually (you may need to enter full path of java) > java -jar Jemboss-MS.jar local Regards, Mahmut From achille.zappa at istge.it Thu Apr 30 03:20:31 2009 From: achille.zappa at istge.it (Achille Zappa) Date: Thu, 30 Apr 2009 09:20:31 +0200 (CEST) Subject: [EMBOSS] Applications limits Message-ID: <1165.10.2.0.90.1241076031.squirrel@webmail.istge.it> Hi All ! I'm new in the mailing list and I want to say hello to everyones I want to use some EMBOSS apps as services in a Taverna workflow, but they failed in some cases, I suppose when I use "too many" sequences or alignments as inputs!! Could you tell me if there are some specific limits and what they are?! Especially about "emma", "fproml" and "fneighbor" services ! thanks best regards Achille Aiutaci TU ad aiutare TANTI: Il tuo 5 per MILLE a sostegno della nostra RICERCA. Come fare: Nella prossima dichiarazione dei redditi metti la firma nell'apposito riquadro del 5 per mille, scrivendo anche il codice fiscale dell'Istituto Nazionale per la Ricerca sul Cancro di Genova : c.f. 80 100 850 108 Istituto Nazionale per la Ricerca sul Cancro L.go R. Benzi, 10 -16132 Genova http://www.istge.it From jison at ebi.ac.uk Thu Apr 30 06:08:41 2009 From: jison at ebi.ac.uk (Jon Ison) Date: Thu, 30 Apr 2009 11:08:41 +0100 (BST) Subject: [EMBOSS] Applications limits In-Reply-To: <1165.10.2.0.90.1241076031.squirrel@webmail.istge.it> References: <1165.10.2.0.90.1241076031.squirrel@webmail.istge.it> Message-ID: <37393.84.92.187.247.1241086121.squirrel@webmail.ebi.ac.uk> Hi Achille As a rule, the native EMBOSS applications have no arbitrary limits so you should be able to process as many sequences as your hardware / software setup allows. The applications you mention however use ports of third-party code. These too should have had any arbitrary limits removed but I'm not 100% on that. You might check there are no limits on memory usage in your system, use "unlimit" or some such on Unix. Cheers Jon > Hi All ! > I'm new in the mailing list and I want to say hello to everyones > I want to use some EMBOSS apps as services in a Taverna workflow, but > they failed in some cases, I suppose when I use "too many" sequences or > alignments as inputs!! Could you tell me if there are some specific limits > and what they are?! Especially about "emma", "fproml" and "fneighbor" > services ! > thanks > best regards > Achille > > > > Aiutaci TU ad aiutare TANTI: Il tuo 5 per MILLE a sostegno della nostra RICERCA. > Come fare: > Nella prossima dichiarazione dei redditi metti la firma > nell'apposito riquadro del 5 per mille, > scrivendo anche il codice fiscale dell'Istituto Nazionale per la Ricerca sul Cancro di Genova : > c.f. 80 100 850 108 > Istituto Nazionale per la Ricerca sul Cancro > L.go R. Benzi, 10 -16132 Genova > http://www.istge.it > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From gmachnik at sum.edu.pl Wed Apr 1 11:53:33 2009 From: gmachnik at sum.edu.pl (Grzegorz Machnik) Date: Wed, 1 Apr 2009 13:53:33 +0200 Subject: [EMBOSS] Command line on www-interface Message-ID: Hello everybody, If I utilize any of www- based EMBOSS interface, may I use any of the command line qualifiers, i.e. -sreverse2 ? It will be useful for me. Till now I use it succesfuly in UNIX- based software. There is no such options to chose it, even in "advanced options" section. Any advices? Thanks Grzegorz From gbottu at vub.ac.be Wed Apr 1 15:24:12 2009 From: gbottu at vub.ac.be (Guy Bottu) Date: Wed, 01 Apr 2009 17:24:12 +0200 Subject: [EMBOSS] Command line on www-interface In-Reply-To: References: Message-ID: <49D3871C.6030308@vub.ac.be> Grzegorz Machnik wrote: > If I utilize any of www- based EMBOSS interface, may I use any of the command line qualifiers, i.e. -sreverse2 ? It will be useful for me. Till now I use it succesfuly in UNIX- based software. > There is no such options to chose it, even in "advanced options" section. Dear Grzegorz, You present here a good question. GUI's for EMBOSS usually have a script that converts ACD to HTML, XML or whatever language is used to describe the program pages. The "Associated" parameters however do not show up in the ACD files and need some ad hoc programmed module in the ACD parser. The GUI's much differ in what they offer. I think Jemboss is quite complete, at least for sequences. And wEMBOSS at least does support -sbegin1 -send1 -sreverse1 -sbegin2 -send2 -sreverse2. Regards, Guy Bottu, Belgian EMBnet Node and wEMBOSS development team From eric.userlist at gmail.com Tue Apr 7 00:17:35 2009 From: eric.userlist at gmail.com (Eric Userlist) Date: Mon, 6 Apr 2009 17:17:35 -0700 Subject: [EMBOSS] Jemboss installation error Message-ID: Hi I have installed emboss in an intel redhat machine (Linux 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:54:53 EST 2006 i686 i686 i386 GNU/Linux) and tested several commands that seem to work. However I get the following errors after "successful" installing jemboss: Exception in thread "main" java.lang.NoClassDefFoundError: org.emboss.jemboss.Jemboss at gnu.gcj.runtime.FirstThread.run() (/usr/lib/libgcj.so.5.0.0) at _Jv_ThreadRun(java.lang.Thread) (/usr/lib/libgcj.so.5.0.0) at _Jv_RunMain(java.lang.Class, byte const, int, byte const, boolean) (/usr/lib/libgcj.so.5.0.0) I tried to search the emboss website and related discussions in the internet. Some people seem to run into similar problems but no solutions were offered. I hope to get some help here. Thank you very much! Eric From tjc at sanger.ac.uk Tue Apr 7 07:32:35 2009 From: tjc at sanger.ac.uk (Tim Carver) Date: Tue, 07 Apr 2009 08:32:35 +0100 Subject: [EMBOSS] Jemboss installation error In-Reply-To: Message-ID: Hi Eric This looks to me as if it is trying to run with Gnu Java. You probably need to set your PATH to point at Sun Java and also make sure it was compiled with that. Regards Tim On 4/7/09 1:17 AM, "Eric Userlist" wrote: > Hi > I have installed emboss in an intel redhat machine (Linux 2.6.9-34.ELsmp #1 > SMP Fri Feb 24 16:54:53 EST 2006 i686 i686 i386 GNU/Linux) and tested > several commands that seem to work. However I get the following errors after > "successful" installing jemboss: > > Exception in thread "main" java.lang.NoClassDefFoundError: > org.emboss.jemboss.Jemboss > at gnu.gcj.runtime.FirstThread.run() (/usr/lib/libgcj.so.5.0.0) > at _Jv_ThreadRun(java.lang.Thread) (/usr/lib/libgcj.so.5.0.0) > at _Jv_RunMain(java.lang.Class, byte const, int, byte const, boolean) > (/usr/lib/libgcj.so.5.0.0) > > I tried to search the emboss website and related discussions in the > internet. Some people seem to run into similar problems but no solutions > were offered. I hope to get some help here. Thank you very much! > > Eric > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From uludag at ebi.ac.uk Tue Apr 7 08:19:59 2009 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Tue, 07 Apr 2009 09:19:59 +0100 Subject: [EMBOSS] Jemboss installation error In-Reply-To: References: Message-ID: <1239092399.12380.32.camel@emboss2.ebi.ac.uk> Hi Eric, > I get the following errors after > "successful" installing jemboss: > > Exception in thread "main" java.lang.NoClassDefFoundError: > org.emboss.jemboss.Jemboss > at gnu.gcj.runtime.FirstThread.run() (/usr/lib/libgcj.so.5.0.0) > at _Jv_ThreadRun(java.lang.Thread) (/usr/lib/libgcj.so.5.0.0) > at _Jv_RunMain(java.lang.Class, byte const, int, byte const, boolean) > (/usr/lib/libgcj.so.5.0.0) I guess you followed the install procedure described on the following page. I ask this because in my initial attempts i thought jemboss would automatically come out of the box when i install emboss. http://emboss.sourceforge.net/Jemboss/install/standalone.html The second thing to check would be whether you change your current working directory to your ${JEMBOSS_INSTALL_DIR}/share/EMBOSS/jemboss directory before running the runJemboss.sh script. If you find it inconvenient to change directory each time before running the script you can set the JEMBOSS_HOME variable at the top of the script to the above directory. Regards, Mahmut From d.leader at bio.gla.ac.uk Tue Apr 7 15:39:06 2009 From: d.leader at bio.gla.ac.uk (David Leader) Date: Tue, 7 Apr 2009 16:39:06 +0100 Subject: [EMBOSS] Png problem on Mac OS 10.5 Message-ID: <57FCCCBF-8737-4B32-91F5-3D21B7B5AB6A@bio.gla.ac.uk> Turns out that the problem was nothing to do with the version of Mac OS 10 or the type of processor. It was the location of the png libraries when using MacPorts. MacPorts puts everything in a sandpit - /opt/local - so as to shield installs from updates to the operating system. In this case it's irrelevant and a nuisance. Pity, as MacPorts is a very convenient and effective way of getting the libraries for gd (unless you are in a University with web cacheing when it's a teeny bit more complex.) Thanks to David Bauer for suggesting the library location as the problem, and that I should run configure with a library location qualifier, in my case: configure --with-pngdriver=/opt/local Works now. David ___________________________________________________ Dr. David P. Leader, Faculty of Biomedical & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK Phone: +44 (0)141 330 5905 http://doolittle.ibls.gla.ac.uk/leader http://motif.gla.ac.uk/ The University of Glasgow, charity number SC004401 ___________________________________________________ From eric.userlist at gmail.com Tue Apr 7 16:30:19 2009 From: eric.userlist at gmail.com (Eric Userlist) Date: Tue, 7 Apr 2009 09:30:19 -0700 Subject: [EMBOSS] Jemboss installation error In-Reply-To: References: Message-ID: Hi Tim Thanks for your email. I am not a big java guru. Can you point to me how to get a compatible sun java with emboss 6.0.1? Eric On Tue, Apr 7, 2009 at 12:32 AM, Tim Carver wrote: > Hi Eric > > This looks to me as if it is trying to run with Gnu Java. You probably need > to set your PATH to point at Sun Java and also make sure it was compiled > with that. > > Regards > Tim > > > On 4/7/09 1:17 AM, "Eric Userlist" wrote: > > > Hi > > I have installed emboss in an intel redhat machine (Linux 2.6.9-34.ELsmp > #1 > > SMP Fri Feb 24 16:54:53 EST 2006 i686 i686 i386 GNU/Linux) and tested > > several commands that seem to work. However I get the following errors > after > > "successful" installing jemboss: > > > > Exception in thread "main" java.lang.NoClassDefFoundError: > > org.emboss.jemboss.Jemboss > > at gnu.gcj.runtime.FirstThread.run() (/usr/lib/libgcj.so.5.0.0) > > at _Jv_ThreadRun(java.lang.Thread) (/usr/lib/libgcj.so.5.0.0) > > at _Jv_RunMain(java.lang.Class, byte const, int, byte const, boolean) > > (/usr/lib/libgcj.so.5.0.0) > > > > I tried to search the emboss website and related discussions in the > > internet. Some people seem to run into similar problems but no solutions > > were offered. I hope to get some help here. Thank you very much! > > > > Eric > > _______________________________________________ > > EMBOSS mailing list > > EMBOSS at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/emboss > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. > From eric.userlist at gmail.com Tue Apr 7 16:31:54 2009 From: eric.userlist at gmail.com (Eric Userlist) Date: Tue, 7 Apr 2009 09:31:54 -0700 Subject: [EMBOSS] Jemboss installation error In-Reply-To: <1239092399.12380.32.camel@emboss2.ebi.ac.uk> References: <1239092399.12380.32.camel@emboss2.ebi.ac.uk> Message-ID: Thanks Mahmut. I also think that jemboss should be automatically compiled with emboss. Maybe someone can provide a more updated installation procedure. Thanks all. Eric On Tue, Apr 7, 2009 at 1:19 AM, Mahmut Uludag wrote: > Hi Eric, > > > I get the following errors after > > "successful" installing jemboss: > > > > Exception in thread "main" java.lang.NoClassDefFoundError: > > org.emboss.jemboss.Jemboss > > at gnu.gcj.runtime.FirstThread.run() (/usr/lib/libgcj.so.5.0.0) > > at _Jv_ThreadRun(java.lang.Thread) (/usr/lib/libgcj.so.5.0.0) > > at _Jv_RunMain(java.lang.Class, byte const, int, byte const, boolean) > > (/usr/lib/libgcj.so.5.0.0) > > I guess you followed the install procedure described on the following > page. I ask this because in my initial attempts i thought jemboss would > automatically come out of the box when i install emboss. > > http://emboss.sourceforge.net/Jemboss/install/standalone.html > > The second thing to check would be whether you change your current > working directory to your ${JEMBOSS_INSTALL_DIR}/share/EMBOSS/jemboss > directory before running the runJemboss.sh script. If you find it > inconvenient to change directory each time before running the script you > can set the JEMBOSS_HOME variable at the top of the script to the above > directory. > > Regards, > Mahmut > > > From joscott at healthlib.usf.edu Tue Apr 14 18:11:21 2009 From: joscott at healthlib.usf.edu (John Scott) Date: Tue, 14 Apr 2009 14:11:21 -0400 Subject: [EMBOSS] New to EMBOSS Message-ID: <1239732681.4160.7.camel@localhost> Planning on deploying emboss, but can't seem to find how much disk space usage I should plan for. Can someone let me know what I can expect to see on a system with about a hundred users? Thanks. John From gbottu at vub.ac.be Wed Apr 15 07:52:14 2009 From: gbottu at vub.ac.be (Guy Bottu) Date: Wed, 15 Apr 2009 09:52:14 +0200 Subject: [EMBOSS] New to EMBOSS In-Reply-To: <1239732681.4160.7.camel@localhost> References: <1239732681.4160.7.camel@localhost> Message-ID: <49E5922E.9060803@vub.ac.be> John Scott wrote: > Planning on deploying emboss, but can't seem to find how much disk space > usage I should plan for. Can someone let me know what I can expect to > see on a system with about a hundred users? Thanks. Dear John, That is a difficult question. On our computer EMBOSS itself (without the sequence databases but with the motif databases) takes 250 Mbyte. The space your users need depends much on whether they are just grandmotherwise analyzing some sequences of their interest or whether they are in complete genome high throughput analysis. On our computer there is for the moment 49 Gbyte used (about 250 users, but not all are very active). Regards, Guy Bottu, Belgian EMBnet Node From moldoverb at gmail.com Wed Apr 15 11:35:19 2009 From: moldoverb at gmail.com (Brian Moldover) Date: Wed, 15 Apr 2009 07:35:19 -0400 Subject: [EMBOSS] New to EMBOSS In-Reply-To: <49E5922E.9060803@vub.ac.be> References: <1239732681.4160.7.camel@localhost> <49E5922E.9060803@vub.ac.be> Message-ID: <000901c9bdbe$42074b60$c615e220$@com> My basic installation which includes Emboss (and Embassy), and the Blocks, Prints, Prosite, Blimps, and test databases, but no sequence databases, takes 1.23 gb. EMBL is something like 700+ Gb uncompressed. I just installed a 4tb NAS to try and manage the sequence databases. -----Original Message----- From: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] On Behalf Of Guy Bottu Sent: Wednesday, April 15, 2009 3:52 AM To: John Scott Cc: emboss at lists.open-bio.org Subject: Re: [EMBOSS] New to EMBOSS John Scott wrote: > Planning on deploying emboss, but can't seem to find how much disk space > usage I should plan for. Can someone let me know what I can expect to > see on a system with about a hundred users? Thanks. Dear John, That is a difficult question. On our computer EMBOSS itself (without the sequence databases but with the motif databases) takes 250 Mbyte. The space your users need depends much on whether they are just grandmotherwise analyzing some sequences of their interest or whether they are in complete genome high throughput analysis. On our computer there is for the moment 49 Gbyte used (about 250 users, but not all are very active). Regards, Guy Bottu, Belgian EMBnet Node _______________________________________________ EMBOSS mailing list EMBOSS at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss No virus found in this incoming message. Checked by AVG - www.avg.com Version: 8.0.238 / Virus Database: 270.11.57/2059 - Release Date: 04/14/09 14:52:00 From koenvanderdrift at gmail.com Wed Apr 15 12:00:47 2009 From: koenvanderdrift at gmail.com (Koen van der Drift) Date: Wed, 15 Apr 2009 08:00:47 -0400 Subject: [EMBOSS] Png problem on Mac OS 10.5 Message-ID: <5cba6b9f0904150500t2f599e4cyf39fe3500cc0b92e@mail.gmail.com> > > Turns out that the problem was nothing to do with the version of Mac > OS 10 or the type of processor. It was the location of the png > libraries when using MacPorts. MacPorts puts everything in a sandpit > - /opt/local - so as to shield installs from updates to the operating > system. In this case it's irrelevant and a nuisance. Pity, as > MacPorts is a very convenient and effective way of getting the > libraries for gd (unless you are in a University with web cacheing > when it's a teeny bit more complex.) Why not install emboss with macports as well, in that case all necessary libraries can be found in the same place (/opt/local) and you don't have to worry about it. This is the way fink works, and I'm sure Macports is not different from that. - Koen. From lueck at ipk-gatersleben.de Fri Apr 17 08:27:30 2009 From: lueck at ipk-gatersleben.de (=?iso-8859-1?Q?Stefanie_L=FCck?=) Date: Fri, 17 Apr 2009 10:27:30 +0200 Subject: [EMBOSS] EmbossWin eprimer3 compilation Message-ID: <002e01c9bf36$596c0380$1022a8c0@ipkgatersleben.de> Hello! I'm using eprimer3 from the EmbossWin package. Now I want to compile my program (written in Python, compiled with py2exe) to make a windows installer. Unfortunatly eprimer3 has a problem after installation of my program. It's gives an error message that emboss.ini was not found and no primers are designed. If EmbossWin is installed then my program works but this is a circumstantially solution since I need only eprimer3 and the user has to install it additionally. Does someone has an idea how I can solve this problem? Thanks in adavance! Stefanie From uludag at ebi.ac.uk Fri Apr 17 10:23:14 2009 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Fri, 17 Apr 2009 11:23:14 +0100 Subject: [EMBOSS] EmbossWin eprimer3 compilation In-Reply-To: <002e01c9bf36$596c0380$1022a8c0@ipkgatersleben.de> References: <002e01c9bf36$596c0380$1022a8c0@ipkgatersleben.de> Message-ID: <1239963794.20536.47.camel@emboss2.ebi.ac.uk> Hi Stefanie, > I'm using eprimer3 from the EmbossWin package. Now I want to compile > my program (written in Python, compiled with py2exe) to make a windows > installer. Unfortunatly eprimer3 has a problem after installation of > my program. It's gives an error message that emboss.ini was not found > and no primers are designed. If EmbossWin is installed then my program > works but this is a circumstantially solution since I need only > eprimer3 and the user has to install it additionally. As far as I understand you want to include only eprimer3 and files essential for running eprimer3. Your installer might be missing some of the steps EmbossWin installer normally does. http://www.interactive-biosoftware.com/embosswin/install.html Do you know there is a new Windows port of EMBOSS since summer 2006? http://emboss.open-bio.org/pipermail/emboss/2007-July/003051.html You may consider using mEMBOSS as it is compatible with most recent versions of EMBOSS and you can get better support. Regards, Mahmut From lueck at ipk-gatersleben.de Fri Apr 17 10:59:01 2009 From: lueck at ipk-gatersleben.de (=?iso-8859-1?Q?Stefanie_L=FCck?=) Date: Fri, 17 Apr 2009 12:59:01 +0200 Subject: [EMBOSS] EmbossWin eprimer3 compilation References: <002e01c9bf36$596c0380$1022a8c0@ipkgatersleben.de> <1239963794.20536.47.camel@emboss2.ebi.ac.uk> Message-ID: <005101c9bf4b$83dd7170$1022a8c0@ipkgatersleben.de> Hi! > > Do you know there is a new Windows port of EMBOSS since summer 2006? > No, I'll try this! Thanks, Stefanie From jeedward at yahoo.com Sat Apr 18 16:57:10 2009 From: jeedward at yahoo.com (John Edward) Date: Sat, 18 Apr 2009 09:57:10 -0700 (PDT) Subject: [EMBOSS] Extended draft paper submission: BCBGC-09 call for papers Message-ID: <505864.94161.qm@web45916.mail.sp1.yahoo.com> Extended draft paper submission: BCBGC-09 call for papers ? This Extended Call for Papers is for those who didn't get a chance to submit the papers for the earlier call for papers. The papers received and accepted in response to this extended call for papers will be included in the final version of the respective conference proceedings. These proceedings will be either ready by the time of the conference (i.e., they will be available during the conference) or soon after the conference (before the end of August 2009), based how fast the proceedings can be prepared. Note: If you have already submitted a paper (whether accepted or rejected or currently under review) for MULTICONF-09, please DO NOT submit that paper again to this extended call for papers. IMPORTANT DATES: Draft paper submission date: May 11, 2009 Acceptance/rejection decision: May 21, 2009 Camera ready paper and copyright and pre-registration due: May 28, 2009 Conference dates: July 13-16, 2009 ? ? The 2009 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09) (website: http://www.PromoteResearch.org ) will be held during July 13-16 2009 in Orlando, FL, USA. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include: ????????? International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) ????????? International Conference on Automation, Robotics and Control Systems (ARCS-09) ????????? International Conference on Enterprise Information Systems and Web Technologies (EISWT-09) ????????? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) ????????? International Conference on Information Security and Privacy (ISP-09) ????????? International Conference on Recent Advances in Information Technology and Applications (RAITA-09) ????????? International Conference on Software Engineering Theory and Practice (SETP-09) ????????? International Conference on Theory and Applications of Computational Science (TACS-09) ????????? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09) ? The website http://www.PromoteResearch.org contains more details. ? Sincerely John Edward Publicity committee From arum at ufl.edu Fri Apr 24 15:49:35 2009 From: arum at ufl.edu (Mccaffery,Michael W) Date: Fri, 24 Apr 2009 11:49:35 -0400 Subject: [EMBOSS] mEMBOSS help Message-ID: I am trying to re-run mEMBOSS on a WinXP SP3 machine. The software worked for a several months - then quit running. Clicking on the "Launch JEMBOSS" icon produces an brief hourglass then nothing. No error messages, just nothing. I have reinstalled JAVA (ver 6 update 13) and resinstalled mEMBOSS (6.0.1 and 6.0.1.3 setup files) to no avail. Any help would be greatly appreciated. Mike McCaffery mwm at ifas.ufl.edu From ajb at ebi.ac.uk Fri Apr 24 19:52:18 2009 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Fri, 24 Apr 2009 20:52:18 +0100 (BST) Subject: [EMBOSS] mEMBOSS help In-Reply-To: References: Message-ID: <33941.86.26.12.63.1240602738.squirrel@webmail.ebi.ac.uk> Hello Mike, Try uninstalling/reinstalling using the following procedure. a) You should use the add/remove programs method, not manual deletion of the mEMBOSS folder. If you didn't use add/remove programs then reinstall mEMBOSS and then remove it immediately using add/remove programs b) Now you can manually delete any remaining mEMBOSS folders that are left. c) Search your computer for any files called 'jemboss.properties' and delete any that are found. d) Check that the following 4 Environment Variables have been removed from the 'System Variables' section of: My Computer->Properties->Advanced->Environment Variables namely: EMBOSS_ACDROOT, EMBOSS_DATA, EMBOSS_ROOT & PLPLOT_LIB if they appear then delete them. While you are looking in that section of the environment variables check that the 'Path' entry looks OK, is not empty, and doesn't refer to any old/corrupt installations. Edit if necessary. e) It should now be OK to reinstall mEMBOSS. As the installation states, it is essential that you choose an installation destination having the property that there are no space characters between the drive letter and that folder nor within the folder name itself. If it still doesn't work then check that the 4 environment variables above have been created and point at/within your installation folder and that the 'Path' variable has an entry for your installation folder too. HTH Alan > I am trying to re-run mEMBOSS on a WinXP SP3 machine. > > The software worked for a several months - then quit running. > Clicking on the "Launch JEMBOSS" icon produces an brief hourglass then > nothing. No error messages, just nothing. > > I have reinstalled JAVA (ver 6 update 13) and resinstalled mEMBOSS (6.0.1 > and 6.0.1.3 setup files) to no avail. > > > Any help would be greatly appreciated. > > Mike McCaffery > mwm at ifas.ufl.edu > > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From uludag at ebi.ac.uk Fri Apr 24 23:02:54 2009 From: uludag at ebi.ac.uk (uludag at ebi.ac.uk) Date: Sat, 25 Apr 2009 00:02:54 +0100 (BST) Subject: [EMBOSS] mEMBOSS help In-Reply-To: References: Message-ID: <43788.86.173.4.141.1240614174.squirrel@webmail.ebi.ac.uk> > Clicking on the "Launch JEMBOSS" icon produces an brief hourglass then > nothing. No error messages, just nothing. Starting Jemboss from Windows "Command Prompt" manually may allow to see errors that are printed on the console. 1-) Open a new Windows Command Prompt Start -> All Programs-> Accessories -> Command Prompt 2-) Change your directory to the 'jemboss\jar' folder under your mEMBOSS folder. For example since my mEMBOSS was installed in my D drive I had to run following 2 commands > d: > cd D:\mEMBOSS\jemboss\jar 3-) Start Jemboss manually (you may need to enter full path of java) > java -jar Jemboss-MS.jar local Regards, Mahmut From achille.zappa at istge.it Thu Apr 30 07:20:31 2009 From: achille.zappa at istge.it (Achille Zappa) Date: Thu, 30 Apr 2009 09:20:31 +0200 (CEST) Subject: [EMBOSS] Applications limits Message-ID: <1165.10.2.0.90.1241076031.squirrel@webmail.istge.it> Hi All ! I'm new in the mailing list and I want to say hello to everyones I want to use some EMBOSS apps as services in a Taverna workflow, but they failed in some cases, I suppose when I use "too many" sequences or alignments as inputs!! Could you tell me if there are some specific limits and what they are?! Especially about "emma", "fproml" and "fneighbor" services ! thanks best regards Achille Aiutaci TU ad aiutare TANTI: Il tuo 5 per MILLE a sostegno della nostra RICERCA. Come fare: Nella prossima dichiarazione dei redditi metti la firma nell'apposito riquadro del 5 per mille, scrivendo anche il codice fiscale dell'Istituto Nazionale per la Ricerca sul Cancro di Genova : c.f. 80 100 850 108 Istituto Nazionale per la Ricerca sul Cancro L.go R. Benzi, 10 -16132 Genova http://www.istge.it From jison at ebi.ac.uk Thu Apr 30 10:08:41 2009 From: jison at ebi.ac.uk (Jon Ison) Date: Thu, 30 Apr 2009 11:08:41 +0100 (BST) Subject: [EMBOSS] Applications limits In-Reply-To: <1165.10.2.0.90.1241076031.squirrel@webmail.istge.it> References: <1165.10.2.0.90.1241076031.squirrel@webmail.istge.it> Message-ID: <37393.84.92.187.247.1241086121.squirrel@webmail.ebi.ac.uk> Hi Achille As a rule, the native EMBOSS applications have no arbitrary limits so you should be able to process as many sequences as your hardware / software setup allows. The applications you mention however use ports of third-party code. These too should have had any arbitrary limits removed but I'm not 100% on that. You might check there are no limits on memory usage in your system, use "unlimit" or some such on Unix. Cheers Jon > Hi All ! > I'm new in the mailing list and I want to say hello to everyones > I want to use some EMBOSS apps as services in a Taverna workflow, but > they failed in some cases, I suppose when I use "too many" sequences or > alignments as inputs!! Could you tell me if there are some specific limits > and what they are?! Especially about "emma", "fproml" and "fneighbor" > services ! > thanks > best regards > Achille > > > > Aiutaci TU ad aiutare TANTI: Il tuo 5 per MILLE a sostegno della nostra RICERCA. > Come fare: > Nella prossima dichiarazione dei redditi metti la firma > nell'apposito riquadro del 5 per mille, > scrivendo anche il codice fiscale dell'Istituto Nazionale per la Ricerca sul Cancro di Genova : > c.f. 80 100 850 108 > Istituto Nazionale per la Ricerca sul Cancro > L.go R. Benzi, 10 -16132 Genova > http://www.istge.it > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss >