From quintric at sb-roscoff.fr Mon May 3 07:56:05 2004 From: quintric at sb-roscoff.fr (Laure Quintric) Date: Mon, 03 May 2004 13:56:05 +0200 Subject: [EMBOSS] little question about EMBOSS win Message-ID: <40963355.6020509@sb-roscoff.fr> Hi ! I'd like to know when EMBOSSWIN was created and if it's still under construction or not? Thanks ! Laure. ----- Laure Quintric mail : quintric at sb-roscoff.fr From postmaster at 2020.net Tue May 4 09:20:29 2004 From: postmaster at 2020.net (System Administrator) Date: Tue, 4 May 2004 09:20:29 -0400 Subject: [EMBOSS] Undeliverable:{Spam?} Message-ID: <63ECD1C77009D646B4CA1309051A5E7397297A@srv-mail1.ho.wan.2020.net> Your message To: Marketing Subject: {Spam?} Sent: Sun, 6 Mar 1994 04:26:41 -0400 did not reach the following recipient(s): Marketing on Sun, 6 Mar 1994 08:26:41 -0400 User Marketing (Marketing at mks-laval) not listed in public Name & Address Book -------------- next part -------------- An embedded message was scrubbed... From: "emboss at embnet.org@SMTP at Exchange" Subject: {Spam?} Date: Sun, 6 Mar 1994 04:26:41 -0400 Size: 1345 Url: http://lists.open-bio.org/pipermail/emboss/attachments/20040504/cefa00ae/attachment.mht From ablavier at wanadoo.fr Tue May 4 15:45:08 2004 From: ablavier at wanadoo.fr (=?ISO-8859-1?Q?Andr=E9_Blavier?=) Date: Tue, 04 May 2004 21:45:08 +0200 Subject: [EMBOSS] little question about EMBOSS win In-Reply-To: <40963355.6020509@sb-roscoff.fr> References: <40963355.6020509@sb-roscoff.fr> Message-ID: <4097F2C4.6030908@wanadoo.fr> The first version of EMBOSSWIN was released in May 2003. The latest version was released in October 2003; it's a port of EMBOSS version 2.7.1 (see http://perso.wanadoo.fr/ablavier/embosswin/embosswin.html). Indeed, EMBOSSWIN is still under construction, and will probably always be. I didn't receive a lot of feedback about this Windows port, so it is only maintained on demand. -- Andr? Blavier Laure Quintric wrote: > Hi ! > I'd like to know when EMBOSSWIN was created and if it's still under > construction or not? > Thanks ! > > Laure. > > ----- > Laure Quintric > mail : quintric at sb-roscoff.fr > From postmaster at ebi.ac.uk Tue May 4 23:23:48 2004 From: postmaster at ebi.ac.uk (MailScanner) Date: Wed, 5 May 2004 04:23:48 +0100 (BST) Subject: [EMBOSS] Warning: E-mail containing attachment(s) blocked Message-ID: <200405050323.i453NmR06223@maui.ebi.ac.uk> Our MailScanner has blocked a message that you sent:- To: dali-help at ebi.ac.uk Subject: Mail Delivery (failure dali-help at ebi.ac.uk) Date: Wed May 5 04:23:48 2004 This is because it contains one or more attachments that we do not allow. Please rename any attachments to be in the form: filename.clean and resend the message (don't forget to tell the recipient the attachment type). If you have not actually sent this email it is possible that it has been forged (so that it appeared to be from you). MailScanner Report: Windows Screensavers are often used to hide viruses (message.scr) -- MailScanner Email Virus Scanner www.mailscanner.info From sghk100 at sghms.ac.uk Wed May 5 05:48:22 2004 From: sghk100 at sghms.ac.uk (David Winterbourne) Date: Wed, 05 May 2004 10:48:22 +0100 Subject: [EMBOSS] little question about EMBOSS win References: <40963355.6020509@sb-roscoff.fr> <4097F2C4.6030908@wanadoo.fr> Message-ID: <4098B866.98376B30@sghms.ac.uk> I only recently downloaded EMBOSSWIN and was very pleased with the result (thanks, Andr?). It was easy to instal and I have not seen any problems with the applications that I have tried. However, I would prefer not to work in a DOS window most of the time and it would be nice to run the programs from Staden's Spin, which I had installed on my Windows XP machine before installing EMBOSSWIN. The Windows version of Spin shows all the Emboss programs greyed out - is it possible to direct Spin to the EMBOSSWIN folder, what file would need to be modified to do that? Surprisingly, although Spin has not identified the EMBOSSWIN applications, it has picked up the settings I made in emboss.ini to get data from EBI and Entrez. -- David Winterbourne Andr? Blavier wrote: > The first version of EMBOSSWIN was released in May 2003. > The latest version was released in October 2003; it's a port of EMBOSS > version 2.7.1 (see > http://perso.wanadoo.fr/ablavier/embosswin/embosswin.html). > Indeed, EMBOSSWIN is still under construction, and will probably always > be. I didn't receive a lot of feedback about this Windows port, so it is > only maintained on demand. > > -- Andr? Blavier > > Laure Quintric wrote: > > Hi ! > > I'd like to know when EMBOSSWIN was created and if it's still under > > construction or not? > > Thanks ! > > > > Laure. > > > > ----- > > Laure Quintric > > mail : quintric at sb-roscoff.fr > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From alex.li at pioneer.com Wed May 5 15:38:45 2004 From: alex.li at pioneer.com (Li, Alex) Date: Wed, 5 May 2004 14:38:45 -0500 Subject: [EMBOSS] ENBOSS: compilation failed Message-ID: Dear ENBOSS expert: I downloaded the latest ENBOSS package. "./configuration --prefix=/mypath" went fine, but when I tried to compile it I got the following errors: gdpng.c:24:16: gd.h: No such file or directory gdpng.c:51: parse error before "im_out" gdpng.c:51: warning: data definition has no type or storage class gdpng.c: In function `fill_polygon': gdpng.c:233: `gdPoint' undeclared (first use in this function) gdpng.c:233: (Each undeclared identifier is reported only once gdpng.c:233: for each function it appears in.) gdpng.c:233: `points' undeclared (first use in this function) make[2]: *** [gdpng.lo] Error 1 make[2]: Leaving directory `/home/f198883/test/EMBOSS-2.8.0/plplot' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/f198883/test/EMBOSS-2.8.0/plplot' make: *** [all-recursive] Error 1 I noticed that there was an error when I was untar-ing the tarball: tar: directory checksum error Is it possible that some directories and files are not tar-ed properly? Thanks for any help in advance! Alex Li Bioinformatics Dept. Pioneer Hi-Bred - A DuPont Company alex.li at pioneer.com 515-334-4736 This communication is for use by the intended recipient and contains information that may be privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html From humberto at hpcf.upr.edu Thu May 6 15:30:27 2004 From: humberto at hpcf.upr.edu (humberto at hpcf.upr.edu) Date: Thu, 06 May 2004 15:30:27 -0400 Subject: [EMBOSS] Standalone Jemboss: where does output go? Message-ID: <200405061930.i46JURkE011146@daleth.hpcf.upr.edu> I'm one of the co-developers of bioknoppix. We've set up a standalone Jemboss on the CD, and one of our users sent us a note that Jemboss ran and didn't produce output. The Jemboss makefile contains the follwing fragment: echo "(cd $(prefix)/share/$(PACKAGE)/jemboss; java org/emboss/jemboss/Jemboss &)" >> $(bindir)/runJemboss.csh; but mere mortals don't have write access to $(prefix)/share/$(PACKAGE)/jemboss (actually, on our CD, neither does ROOT). Removing the cd command allows text output to work. Graphical programs just dump a bunch of png files into the current directory. Is this expected behavior or did we break something? -- Humberto Ortiz Zuazaga Programmer-Archaeologist High Performance Computing facility University of Puerto Rico http://www.hpcf.upr.edu/~humberto/ -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 241 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20040506/013f2358/attachment.bin From e-offers at freelotto.com Sat May 8 23:53:44 2004 From: e-offers at freelotto.com (e-offers at freelotto.com) Date: Sat, 08 May 2004 23:53:44 -0400 Subject: [EMBOSS] Auto-reply In-Reply-To: Message-ID: Dear FreeLotto Player, Thank you for your message to Customer Service at FreeLotto. If you are having a problem with our service we appreciate that you are taking the time to tell us. If you like our games, please tell your friends and we appreciate hearing your nice comments! To best serve you and provide a quick answer to your question, please click on the following icons at the top of our FreeLotto website. Most questions our players ask are answered there. HelpDesk F.A.S.T - for Monthly Subscription Service Rules How it Works PLEASE DO NOT RESPOND TO THIS MESSAGE. SEE BELOW. When you send a message to us, please indicate your topic in the Subject line: For Example: "Click2Win Tournaments" Directions to our most Frequently Asked Questions: How to Play: There are six different games played in sequence which each user can play once each day. See http://www.freelotto.com/faq/Faq.asp#1 http://www.freelotto.com/Rules.asp How many user ids can I use to play FreeLotto each day? Each person Can play each set of games 1 time each day. http://www.freelotto.com/faq/Faq.asp#2 http://www.freelotto.com/Rules.asp FreeLotto is available worldwide - with a few exceptions. http://www.freelotto.com/faq/Faq.asp#3 http://www.freelotto.com/Rules.asp Not receiving confirmations. http://www.freelotto.com/faq/Faq.asp#7 Not receiving Results. http://www.freelotto.com/faq/Faq.asp#8 Unsubscribe from FreeLotto e-mails: http://www.freelotto.com/faq/Faq.asp#9 F.A.S.T. Subscription account - Edit or deactivate http://www.freelotto.com/faq/Faq.asp#4 http://www.freelotto.com/LottoPicker/subscribe_faq.asp Change mailing address or e-mail address. http://www.freelotto.com/faq/Faq.asp#10 Forgot Password. http://www.freelotto.com/faq/Faq.asp#11 See previous results. http://www.freelotto.com/faq/Faq.asp#14 How to receive FREELOTTO prizes. http://www.freelotto.com/faq/Faq.asp#6 If your question is not answered, please write to us by clicking on the link below. Please make sure that your topic is in the subject line. http://www.freelotto.com/Contact.asp?type=questions Thank you for your patience and support. Customer Service If you are a Postmaster or Webmaster, please send your request to the email address listed above. If you are requesting action regarding a specific user, please be sure to include the user's email address and/or user id so we can best serve you and quickly respond to your request. From Sean.Maceachern at dpi.vic.gov.au Mon May 10 00:36:39 2004 From: Sean.Maceachern at dpi.vic.gov.au (Sean.Maceachern at dpi.vic.gov.au) Date: Mon, 10 May 2004 14:36:39 +1000 Subject: [EMBOSS] coderet problems Message-ID: Hi, I'm having problems with coderet. I have put in 27 956 entries from a genbank flat file and I am only getting 27 711 sequences returned. I have tried all of the -verbose options etc but I can not get information on which of the 200 sequences failed. Does anyone know what the problem might be or how I might be able to get this information? Any help would be appreciated. Cheers, Sean MacEachern From d.m.a.martin at dundee.ac.uk Tue May 11 07:22:13 2004 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Tue, 11 May 2004 12:22:13 +0100 Subject: [EMBOSS] Installing the Jemboss server Message-ID: Has anyone actually managed to do this outside HGMP (oops, RFCGR)? I have been battling with the install script for a few days with varying degrees of success. First issue: It doesn't take into account the additional arguements given for an EMBOSS install (eg. --bindir= --libdir=) which then break it later. This is easily fixed with a manual edit. Second issue: It has problems finding various files. Excerpts from the install included below with comments -- java.io.FileNotFoundException: /site/share/EMBOSS/jemboss/resources/wossname.jar (No such file or directory) at java.io.FileOutputStream.open(Native Method) at java.io.FileOutputStream.(FileOutputStream.java:102) at java.io.FileOutputStream.(FileOutputStream.java:62) at sun.tools.jar.Main.run(Main.java:134) at sun.tools.jar.Main.main(Main.java:904) java.io.FileNotFoundException: /site/share/EMBOSS/jemboss/resources/resources.ja r (No such file or directory) at java.io.FileOutputStream.open(Native Method) at java.io.FileOutputStream.(FileOutputStream.java:102) at java.io.FileOutputStream.(FileOutputStream.java:62) at sun.tools.jar.Main.run(Main.java:134) at sun.tools.jar.Main.main(Main.java:904) -- I had removed /site/share/EMBOSS/jemboss before running the script. /site/share/EMBOSS/jemboss/resources/ points to the axis web application directory under tomcat. (axis/WEB-INF/classes/resources) -- error: cannot read: /site/share/EMBOSS/jemboss/org/emboss/jemboss/server/Jemboss AuthServer.java 1 error error: cannot read: /site/share/EMBOSS/jemboss/org/emboss/jemboss/server/Jemboss FileAuthServer.java 1 error -- the relevant files have for some reason been installed under /site/share/EMBOSS/jemboss/org/org/emboss/jemboss/server by the install script. and it goes on with many more file not found errors. If these are ignored then further problems arise later. ..d -- David Martin PhD Post-Genomics and Molecular Interactions Centre University of Dundee ICQ: 337640638 From tjc at sanger.ac.uk Tue May 11 08:43:36 2004 From: tjc at sanger.ac.uk (Timothy Carver) Date: Tue, 11 May 2004 13:43:36 +0100 (BST) Subject: [EMBOSS] Installing the Jemboss server (fwd) Message-ID: Hi David On Tue, 11 May 2004, David Martin wrote: > Has anyone actually managed to do this outside HGMP (oops, RFCGR)? Errr yes. Many sites have installed this and most people are successful using the script. It has been tested on all EMBOSS supported platforms.... Linux, MacOSX, SunOS, AIX.... > First issue: It doesn't take into account the additional arguements given > for an EMBOSS install (eg. --bindir= --libdir=) which then break it later. > This is easily fixed with a manual edit. Why do you need to use those? This possibly cannot be described as a standard install then. You don't say what you edit so I cannot comment other than that the script does certainly allow you to add lines to the configure. > Second issue: It has problems finding various files. Excerpts from the > install included below with comments > -- > java.io.FileNotFoundException: > /site/share/EMBOSS/jemboss/resources/wossname.jar > (No such file or directory) > at java.io.FileOutputStream.open(Native Method) > at java.io.FileOutputStream.(FileOutputStream.java:102) > at java.io.FileOutputStream.(FileOutputStream.java:62) > at sun.tools.jar.Main.run(Main.java:134) > at sun.tools.jar.Main.main(Main.java:904) > java.io.FileNotFoundException: > /site/share/EMBOSS/jemboss/resources/resources.ja > r (No such file or directory) > at java.io.FileOutputStream.open(Native Method) > at java.io.FileOutputStream.(FileOutputStream.java:102) > at java.io.FileOutputStream.(FileOutputStream.java:62) > at sun.tools.jar.Main.run(Main.java:134) > at sun.tools.jar.Main.main(Main.java:904) > -- > I had removed /site/share/EMBOSS/jemboss before running the script. > /site/share/EMBOSS/jemboss/resources/ points to the axis web application > directory under tomcat. (axis/WEB-INF/classes/resources) > -- > error: cannot read: > /site/share/EMBOSS/jemboss/org/emboss/jemboss/server/Jemboss > AuthServer.java > 1 error > error: cannot read: > /site/share/EMBOSS/jemboss/org/emboss/jemboss/server/Jemboss > FileAuthServer.java > 1 error > -- > the relevant files have for some reason been installed under > /site/share/EMBOSS/jemboss/org/org/emboss/jemboss/server > by the install script. > > and it goes on with many more file not found errors. If these are ignored > then further problems arise later. No point ignoring errors like that and hoping it will work. Again from what you provide I can only guess at what the problem may be. Do you delete tomcat, axis and EMBOSS (download & installation) before doing a fresh install? Anyway it would be better to start with a standard working installation and then hack it about from there if you really have to. Tim From MAILER-DAEMON at mailfilter1.voicenet.com Sat May 15 05:10:49 2004 From: MAILER-DAEMON at mailfilter1.voicenet.com (MAILER-DAEMON at mailfilter1.voicenet.com) Date: 15 May 2004 09:10:49 -0000 Subject: [EMBOSS] failure notice Message-ID: <20040515091050.635347D2AB@mercury.hgmp.mrc.ac.uk> Hi. This is the qmail-send program at mailfilter1.voicenet.com. I'm afraid I wasn't able to deliver your message to the following addresses. This is a permanent error; I've given up. Sorry it didn't work out. : Sorry, no mailbox here by that name. (#5.1.1) --- Below this line is a copy of the message. Return-Path: Received: (qmail 16906 invoked from network); 15 May 2004 09:10:40 -0000 Received: from 62-128-170-156.iwayafrica.com (HELO voicenet.com) (62.128.170.156) by mailfilter1.voicenet.com with SMTP; 15 May 2004 09:10:40 -0000 X-Matched: 62-128-170-156.iwayafrica.com [62.128.170.156] From: emboss at embnet.org To: gatgul at voicenet.com Subject: Re: Re: Message Date: Sat, 15 May 2004 19:10:13 +0300 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0001_00006497.000017C0" X-Priority: 3 X-MSMail-Priority: Normal This is a multi-part message in MIME format. ------=_NextPart_000_0001_00006497.000017C0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit Please have a look at the attached file. ------=_NextPart_000_0001_00006497.000017C0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit IMPORTANT NOTICE: A Virus has been found and removed from this email. Anti-virus software has detected that this email message was infected with the "W32/Netsky.D-mm" virus. To protect our network and help prevent your computer from receiving this virus, the following file or attachment has been removed: "message_details.pif". If you know the sender and believe that the inclusion of the virus was inadvertent on their part, it is your option to contact them and have the email resent ONLY after they have scanned it first for viruses. Thank you, Voicenet Support support at voicenet.com ------=_NextPart_000_0001_00006497.000017C0-- From m.tagaya at nippon-shinyaku.co.jp Sun May 16 21:00:44 2004 From: m.tagaya at nippon-shinyaku.co.jp (Mitsuhiro Tagaya) Date: Mon, 17 May 2004 10:00:44 +0900 Subject: [EMBOSS] mailing list for Japanese Users Message-ID: <20040517094352.3131.M.TAGAYA@nippon-shinyaku.co.jp> Hi, We JAMBO (Japan EMBOSS Users Group) made a mailing list for Japanese EMBOSS Users. The URL of JAMBO is: http://jambo.sourceforge.jp/ and the mailing list is: http://lists.sourceforge.jp/mailman/listinfo/jambo-users ---- Tagaya Mitsuhiro m.tagaya at nippon-shinyaku.co.jp Jambo! Habari yako? http://jambo.sourceforge.jp/ From pmr at ebi.ac.uk Mon May 17 05:58:33 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 17 May 2004 10:58:33 +0100 Subject: [EMBOSS] mailing list for Japanese Users In-Reply-To: <20040517094352.3131.M.TAGAYA@nippon-shinyaku.co.jp> References: <20040517094352.3131.M.TAGAYA@nippon-shinyaku.co.jp> Message-ID: <40A88CC9.9040003@ebi.ac.uk> Mitsuhiro Tagaya wrote: > Hi, We JAMBO (Japan EMBOSS Users Group) made a mailing list > for Japanese EMBOSS Users. Welcome to our Japanese friends. We can try to read the list using a translation service, but it would be helpful if someone could act as moderator and pass on questions to emboss-bug. I see one question about fasta sequence IDs from FANTOM. We can try to fix that by extending the sequence ID rules if someone can send us an example sequence file. regards, Peter Rice From mad at biol.unlp.edu.ar Mon May 17 11:17:09 2004 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Mon, 17 May 2004 12:17:09 -0300 Subject: [EMBOSS] wEMBOSS-1.1 release Message-ID: <40A8D775.3000800@biol.unlp.edu.ar> Version 1.1 of wEMBOSS is out. You can download it here http://bigben.vub.ac.be:6080/wEMBOSS/Folder.2003-09-11.4050/Folder.2003-09-11.4318C/wEMBOSS-1.1.tar.gz Some of the new features are: 1) results sort by date or alphabetically 2) rename projects 3) move projects The wEMBOSS Portal is at http://www.ar.embnet.org/wEMBOSS Regards, the wEMBOSS team -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From Marc.Logghe at devgen.com Tue May 18 03:00:23 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Tue, 18 May 2004 09:00:23 +0200 Subject: [EMBOSS] rformat option epestfind missing Message-ID: Hi, Just wanted to mention that the rformat option is 'missing' for epestfind. Al least I expected to have it there; I mean I have the impression as soon as an EMBOSS application returns 'regions' you may obtain them as features via the rformat opton. No ? Cheers, Marc From pmr at ebi.ac.uk Tue May 18 04:29:13 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 18 May 2004 09:29:13 +0100 Subject: [EMBOSS] rformat option epestfind missing In-Reply-To: References: Message-ID: <40A9C959.5060806@ebi.ac.uk> Marc Logghe wrote: > Just wanted to mention that the rformat option is 'missing' for epestfind. Al least I expected to have it there; I mean I have the impression as soon as an EMBOSS application returns 'regions' you may obtain them as features via the rformat opton. No ? rformat is available for any application that has a "report" output. You are right - the "outfile" in epestfind should be a report. The problem is that the original program had its own output format - but all we need to do is add a new rformat as the default. Then you would be able to use -rformat to get a feature file. I will take a look. regards, Peter Rice From henrikki.almusa at helsinki.fi Tue May 18 04:43:19 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Tue, 18 May 2004 11:43:19 +0300 Subject: [EMBOSS] rformat option epestfind missing In-Reply-To: <40A9C959.5060806@ebi.ac.uk> References: <40A9C959.5060806@ebi.ac.uk> Message-ID: <200405181143.19985.henrikki.almusa@helsinki.fi> On Tuesday 18 May 2004 11:29, Peter Rice wrote: > Marc Logghe wrote: > > Just wanted to mention that the rformat option is 'missing' for > > epestfind. Al least I expected to have it there; I mean I have the > > impression as soon as an EMBOSS application returns 'regions' you may > > obtain them as features via the rformat opton. No ? > > rformat is available for any application that has a "report" output. > > You are right - the "outfile" in epestfind should be a report. > > The problem is that the original program had its own output format - but > all we need to do is add a new rformat as the default. Then you would be > able to use -rformat to get a feature file. > > I will take a look. I sent a patch to change the epestfind (and newcpgreport) output into report format into emboss-submit few weeks ago. Did they get through (meaning the notice on emboss webpages about MRC) ? I can resend them to you if that will help. Regards, -- Henrikki Almusa From d.gatherer at vir.gla.ac.uk Tue May 18 05:17:55 2004 From: d.gatherer at vir.gla.ac.uk (Derek Gatherer) Date: Tue, 18 May 2004 10:17:55 +0100 Subject: [EMBOSS] EMBOSS mailing list archive final resting place In-Reply-To: <200405181143.19985.henrikki.almusa@helsinki.fi> References: <40A9C959.5060806@ebi.ac.uk> <40A9C959.5060806@ebi.ac.uk> Message-ID: <5.2.1.1.1.20040518095759.0352a400@udcf.gla.ac.uk> When RFCGR finally sadly closes next year, will there still be this mailing list? and will the archives of the list be preserved in the new sourceforge site? I think that the list archives are an invaluable resource for problem solving, and in fact I often consult them to remind myself of the answers to questions I previously asked. Even if there's no active list, it would be good to keep the archive for reference. cheers Derek _________________________ Derek Gatherer Ph.D. Cert.Ed. Computer Officer Institute of Virology Church St. Glasgow G11 5JR Phone: +44 141 330 6268 Fax: +44 141 337 2236 Email: d.gatherer at vir.gla.ac.uk Website: http://www.vir.gla.ac.uk From ableasby at hgmp.mrc.ac.uk Tue May 18 05:22:45 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Tue, 18 May 2004 10:22:45 +0100 (BST) Subject: [EMBOSS] EMBOSS mailing list archive final resting place Message-ID: <200405180922.i4I9Mjfv013631@bromine.hgmp.mrc.ac.uk> The intention is to move the lists plus archives to another site. It may turn out to be a mixture of sourceforge and EBI. We'll let people know as soon as we do. Alan From pmr at ebi.ac.uk Tue May 18 05:24:53 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 18 May 2004 10:24:53 +0100 Subject: [EMBOSS] EMBOSS mailing list archive final resting place In-Reply-To: <5.2.1.1.1.20040518095759.0352a400@udcf.gla.ac.uk> References: <40A9C959.5060806@ebi.ac.uk> <40A9C959.5060806@ebi.ac.uk> <5.2.1.1.1.20040518095759.0352a400@udcf.gla.ac.uk> Message-ID: <40A9D665.30006@ebi.ac.uk> Derek Gatherer wrote: > When RFCGR finally sadly closes next year, will there still be this > mailing list? and will the archives of the list be preserved in the new > sourceforge site? I think that the list archives are an invaluable > resource for problem solving, and in fact I often consult them to remind > myself of the answers to questions I previously asked. Even if there's > no active list, it would be good to keep the archive for reference. Yes, the list will continue and will be active (assuming of course everyone keeps posting to it :-). One reason for using the embnet.org address was to keep the list going if EMBOSS moved (as it did, from Sanger to HGMP/RFCGR in July 2000). Sourceforge does provide an alternative for mailing lists - and we do use it already for tracking bug and feature requests. The list archives will be preserved and maintained - after all, we use them too! regards, Peter Rice From Marc.Logghe at devgen.com Tue May 18 05:40:02 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Tue, 18 May 2004 11:40:02 +0200 Subject: [EMBOSS] rformat option epestfind missing Message-ID: > > The problem is that the original program had its own output > format - but > > all we need to do is add a new rformat as the default. Then > you would be > > able to use -rformat to get a feature file. > > > > I will take a look. > > I sent a patch to change the epestfind (and newcpgreport) > output into report > format into emboss-submit few weeks ago. Did they get through > (meaning the > notice on emboss webpages about MRC) ? I can resend them to > you if that will > help. How should I proceed ? Watch out for a cvs commit and rebuild the individual application ? Thanks all ! Cheers, Marc From Joerg.Schaber at uv.es Tue May 18 07:49:55 2004 From: Joerg.Schaber at uv.es (Joerg Schaber) Date: Tue, 18 May 2004 13:49:55 +0200 Subject: [EMBOSS] dbiflat problem Message-ID: <40A9F863.7080505@uv.es> Hi, I am indexing a genbank database on Linux RH7.3 with EMBOSS 2.8.0 and running dbiflat -idformat gb -directory "." -filename "*.gbk" -dbname "ncbibac" -release "1.3" -date "18/05/04" -fields acnum,des,taxon I keep geeting the following mistake: EMBOSS An error in embdbi.c at line 693: Cannot open ncbibac.idsrt for reading Any idea what's the problem here? Thanks, joerg From Imogene at fiestabrava.com Tue May 18 12:03:48 2004 From: Imogene at fiestabrava.com (Eugenio Watts) Date: Tue, 18 May 2004 19:03:48 +0300 (CST) Subject: [EMBOSS] Softwares CDS all software under 15$ and 99$! slut Message-ID: <14050440263761.BI41njWXkua74@workbench6.danny89cocolee.net> >Life begins at forty Sensation!! We opened a NEW site with unbeatable prices and products. 1500 WORLD BEST software with 90% discount - that is a really BEST offer just imagine, you can buy ALL software that you ever need and pay price of just one of it! Office 2003 for 50$ - nice deal right ? ;) retail price is 700$ - great savings, huh? Please spend few moments of yours precious time to check our offer - it is more than worth it! http://constantine.reachsoftware.com/?driveway >Absence makes the heart go wander. >The squeaky wheel gets the grease. >Every dog has his day >Lean liberty is better than fat slavery >A place for everything and everything in its place. >Yesterday is ashes; tomorrow wood Only today does the fire burn brightly >There is a time and a place for everything >March winds and April showers bring forth May flowers >A fair exchange is no robbery. >Shame face ah feel like cent ice. >And say, How have I hated instruction, and my heart despised reproof. >Promises are like babies Easy to make, hard to deliver >Don't cross your bridges before you come to them. >Tis better to get things for free, than to work up a sweat >There is no such thing as a free lunch >It is in vain to cast your net where there is no fish >Everything must have a beginning >Rain, Rain, go away, come back another day >Artificial intelligence is no match for natural stupidity From deejoe at iastate.edu Tue May 18 13:04:23 2004 From: deejoe at iastate.edu (D. Joe Anderson) Date: Tue, 18 May 2004 12:04:23 -0500 Subject: [EMBOSS] dbiflat problem In-Reply-To: <40A9F863.7080505@uv.es> References: <40A9F863.7080505@uv.es> Message-ID: <20040518170423.GA15431@iastate.edu> On Tue, May 18, 2004 at 01:49:55PM +0200, Joerg Schaber wrote: > EMBOSS An error in embdbi.c at line 693: > Cannot open ncbibac.idsrt for reading Sorry if this seems too obvious, but can you find the file ncbibac.idsrt, and if so, what are it's permissions and ownership? --Joe From VZWUBanks at fwfaq.com Wed May 19 00:18:59 2004 From: VZWUBanks at fwfaq.com (Barbara Forbes) Date: Wed, 19 May 2004 07:18:59 +0300 Subject: [EMBOSS] Name brand software at generic prices. mint Message-ID: An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20040519/6a49a10e/attachment.html From luisa.pugliese at safan-bioinformatics.it Wed May 19 08:59:49 2004 From: luisa.pugliese at safan-bioinformatics.it (luisa pugliese) Date: Wed, 19 May 2004 14:59:49 +0200 Subject: [EMBOSS] emboss on amd64 Message-ID: <00ba01c43da1$2affe960$f3ee669e@chagall> Hi all, I would like to run EMBOSS on an AMD64 processor with mandrake 9.2 for amd64. I downloaded the rpm distributions for EMBOSS2.8 and libEMBOSS2.8 and I installed them. However when I try to run the emboss programs (I tryed water and needle) I get a segmentation fault. I saw that in your tutorial there is something about 64-bit machines configuration, but the details are present only for Irix. I wonder if you could be so kind to help me in finding what could be the problem.a I also downloaded the tar file from the emboss web site, I compiled it and I get the same error. I wonder if anybody knows and is so kind to let me know what should I do in order to get EMBOSS running on the AMD64. Best regards Luisa ============================= Luisa Pugliese, Ph.D. luisa.pugliese at safan-bioinformatics.it S.A.F.AN. BIOINFORMATICS Corso Tazzoli 215/13 -10137 Torino - ITALY tel +39 011 3026230 cell. +39 333 6130644 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20040519/2c126c30/attachment.html From postmaster at navair.navy.mil Wed May 19 09:04:51 2004 From: postmaster at navair.navy.mil (System Administrator) Date: Wed, 19 May 2004 09:04:51 -0400 Subject: [EMBOSS] Undeliverable: Re: Re: Document Message-ID: <14A4447570FE374E8906CA5AA6261AB7028BF7B7@neim05.navair.navy.mil> Your message To: corpusgd at navair.navy.mil Subject: Re: Re: Document Sent: Wed, 19 May 2004 09:07:46 -0400 did not reach the following recipient(s): CORPUSGD at NAVAIR.NAVY.MIL on Wed, 19 May 2004 09:04:49 -0400 The recipient name is not recognized The MTS-ID of the original message is: c=us;a= ;p=organization;l=NEIM050405191304LD3ACB8Q MSEXCH:IMS:ORGANIZATION:NAVAIREAST:NEIM05 0 (000C05A6) Unknown Recipient -------------- next part -------------- An embedded message was scrubbed... From: emboss at embnet.org Subject: Re: Re: Document Date: Wed, 19 May 2004 09:07:46 -0400 Size: 763 Url: http://lists.open-bio.org/pipermail/emboss/attachments/20040519/f10a1fc6/attachment.mht From ableasby at hgmp.mrc.ac.uk Wed May 19 09:08:31 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Wed, 19 May 2004 14:08:31 +0100 (BST) Subject: [EMBOSS] emboss on amd64 Message-ID: <200405191308.i4JD8Vpq029072@bromine.hgmp.mrc.ac.uk> Dear Luisa, This is becoming a more common query so I'll post the answer to the list. Before compiling EMBOSS 2.8.0 you need to get the following files: ftp://ftp.rfcgr.mrc.ac.uk/pub/EMBOSS/patchfiles/ajfmt.c ftp://ftp.rfcgr.mrc.ac.uk/pub/EMBOSS/patchfiles/ajfmt.h and use them to replace the files in the ajax directory. Hopefully your compiler will predefine __amd64__ but, if not, setenv CFLAGS "__amd64__" before configuring EMBOSS. These modifications have already been added to the CVS version. HTH Alan Bleasby RFCGR From ableasby at hgmp.mrc.ac.uk Wed May 19 09:17:06 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Wed, 19 May 2004 14:17:06 +0100 (BST) Subject: [EMBOSS] emboss on amd64 Message-ID: <200405191317.i4JDH67f029679@bromine.hgmp.mrc.ac.uk> Correction: That should, of course, be: setenv CFLAGS "-D__amd64__" or the sh equivalent. AJB From gombar at email.unc.edu Wed May 19 10:23:08 2004 From: gombar at email.unc.edu (gombar at email.unc.edu) Date: Wed, 19 May 2004 10:23:08 -0400 Subject: [EMBOSS] Eprimer3 Issue Message-ID: <1084976588.40ab6dccd9764@webmail0.isis.unc.edu> Hello, My name is Saurabh Gombar and I work in the Biology department at UNC Chapel Hill. I had a question regarding your Eprimer3 application. In your Eprimer3 information page it says "eprimer3 takes as input a Sequence Quality list for use." However, looking through the rest of the documentation I could not find how specify the Quality List to Eprimer3 as well as minimum quality values to consider. Thanks, Saurabh Gombar From gwilliam at hgmp.mrc.ac.uk Wed May 19 10:28:08 2004 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Wed, 19 May 2004 15:28:08 +0100 Subject: [EMBOSS] Eprimer3 Issue References: <1084976588.40ab6dccd9764@webmail0.isis.unc.edu> Message-ID: <40AB6EF8.E5B87477@hgmp.mrc.ac.uk> Saurabh, You are correct. The eprimer3 program doesn't read in a Sequence Quality list. I will change the documentation. Gary gombar at email.unc.edu wrote: > > Hello, > My name is Saurabh Gombar and I work in the Biology department at > UNC Chapel Hill. I had a question regarding your Eprimer3 application. > In your Eprimer3 information page it says "eprimer3 takes as input > a Sequence Quality list for use." However, looking through the rest > of the documentation I could not find how specify the Quality List to > Eprimer3 as well as minimum quality values to consider. > Thanks, > Saurabh Gombar -- Gary Williams MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494522 Fax: +44 1223 494512 E-mail: gwilliam at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk From alex.li at pioneer.com Thu May 20 14:23:08 2004 From: alex.li at pioneer.com (Li, Alex) Date: Thu, 20 May 2004 13:23:08 -0500 Subject: [EMBOSS] more info about Codon Usage Table (.cut) files? Message-ID: Hello, there, Some filenames of .cut files under .../EMBOSS/data/CODONS are intuitive (eg: Echicken.cut for chickens), but most are not. I assume filenames imply species names. Where can I get the info that maps between filenames and more DETAILED species info? Thanks in advance. Alex Li Bioinformatics Dept. Pioneer Hi-Bred. Voice: 515-334-4736 Fax: 515-334-6634 This communication is for use by the intended recipient and contains information that may be privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html From postmaster at ebi.ac.uk Fri May 21 03:51:20 2004 From: postmaster at ebi.ac.uk (MailScanner) Date: Fri, 21 May 2004 08:51:20 +0100 (BST) Subject: [EMBOSS] Warning: E-mail containing attachment(s) blocked Message-ID: <200405210751.i4L7pKU29148@maui.ebi.ac.uk> Our MailScanner has blocked a message that you sent:- To: datalib at ebi.ac.uk Subject: Mail Delivery (failure datalib at ebi.ac.uk) Date: Fri May 21 08:51:20 2004 This is because it contains one or more attachments that we do not allow. Please rename any attachments to be in the form: filename.clean and resend the message (don't forget to tell the recipient the attachment type). If you have not actually sent this email it is possible that it has been forged (so that it appeared to be from you). MailScanner Report: Windows Screensavers are often used to hide viruses (message.scr) -- MailScanner Email Virus Scanner www.mailscanner.info From henrikki.almusa at helsinki.fi Fri May 21 05:59:11 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Fri, 21 May 2004 12:59:11 +0300 Subject: [EMBOSS] PLPLOT_LIB enviromental variable Message-ID: <200405211259.11917.henrikki.almusa@helsinki.fi> Hello, To get emboss programs with graphics to work PLPLOT_LIB enviromental variable needs to be set, even if graph is set null or none. I tried to set this in emboss.properties, but it didn't work with "set PLPLOT_LIB /emboss/path/EMBOSS/share". Is is possible to make it so that it can be set from properties file asl well? Thanks, -- Henrikki Almusa From team at domeus.it Fri May 21 07:12:10 2004 From: team at domeus.it (Team domeus) Date: Fri, 21 May 2004 13:12:10 +0200 (CEST) Subject: [EMBOSS] RICHIESTA DI CONFERMA: Per cortesia conferma l'iscrizione al gruppo MailingList Aperta tutti scrivono a tutti Message-ID: <24858905.1085137930121.ecMessenger@domeus.it> Ciao grazie per esserti iscritto al gruppo MailingList Aperta tutti scrivono a tutti (cryomail at domeus.it). Se intendi davvero iscriverti, rispondi a quest'eMail utilizzando la funzione "Reply"/"Rispondi" o, in alternativa, cliccando su questo link: http://www.domeus.it/public/subscribe.jsp?tsp=1085137930111&gid=292685&uid=28311913&sig=EPOEOLBMEALHCHID&action=subscribeToSingleGroup Se non sei interessato ad unirti al gruppo, ignora semplicemente quest'eMail e non ne riceverai altre da parte nostra. Se il tuo indirizzo eMail ? stato aggiunto a questa lista senza il tuo consenso e non desideri ricevere eMail da Domeus, inoltra questo messaggio a: set_account_inactive at domeus.it. Ci? non ti permetter? di utilizzare il tuo indirizzo eMail tramite il sistema Domeus. DEVI RISPONDERE A QUESTO MESSAGGIO PER UNIRTI DEFINITIVAMENTE A QUESTO GRUPPO! Se intendi utilizzare in modo completo tutti i servizi, entra semplicemente in http://www.domeus.it utilizzando i seguenti dati d'accesso: username: emboss at embnet.org password: wabakil4 A presto, Il team di domeus.it -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20040521/c1d0185f/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 2422 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20040521/c1d0185f/attachment.gif -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 1458 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20040521/c1d0185f/attachment-0001.gif From team at domeus.it Fri May 21 08:47:08 2004 From: team at domeus.it (Team domeus) Date: Fri, 21 May 2004 14:47:08 +0200 (CEST) Subject: [EMBOSS] Benvenuto nel gruppo MailingList Aperta tutti scrivono a tutti Message-ID: <7862244.1085143628314.ecMessenger@domeus.it> Ciao emboss at embnet.org, sei stato aggiunto al gruppo MailingList Aperta tutti scrivono a tutti (cryomail at domeus.it). Il proprietario del gruppo ti invia il seguente messaggio di benvenuto: ---------------------------- ---------------------------- Se non desideri ricevere email da questo gruppo invia un eMail a cryomail-unsubscribe at domeus.it. Per cancellarti direttamenet tramite web, utilizza il seguente link: http://www.domeus.it/public/unsubscribe.jsp?tsp=1085143628294&gid=292685&uid=28311913&sig=GGOMLIIEIDECEPKO In ogni modo sarai cancellato dalla lista di distribuzione. Per qualsiasi domanda o problema puoi contattare il moderatore di questo gruppo scrivendo a cryomail-moderators at domeus.it. A presto, Il team di domeus.it -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20040521/73631f25/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... 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Da questo momento in poi non riceverai ulteriori messaggi dal gruppo. grazie per essere stato con noi.... lo sapevi che sul sito del cryogenteam trovi anche... ______________________________________________________ abbiamo lottato e vinto per la vita di safiya , ora stiamo lottando per per la vita di amina .. unisciti a noi, un form anonimo ti aspetta !! http://www.cryogenteam.com/safiya.htm calendario ribelle soft e hot del 2002 le ragazze del cryogenteam.com http://www.cryogenteam.com/calendario.htm sexy chat immagini in diretta chat sexy sexy videochat chat in html video chat videoconferenza video conferenza http://www.cryogenteam.com/chat.html - games & jokes - giochi e scherzi programmi gioco scherzi divertenti http://www.cryogenteam.com/game.htm loghi e suonerie per cellulari nokia ericsson motorola sagem siemens philips panasonic siemens creati il tuo logo personalizzato !! http://www.cryogenteam.com/loghisuonerie.htm software e utility programmi completi guide in italiano recensioni - manuali - software - guide - informazioni - consigli - programmi - giochi - satellite http://www.cryogenteam.com/software.htm free webcam - webcam in diretta dal web gratuite o gratis ragazze asiatiche in diretta regazze orientali in diretta cam http://www.cryogenteam.com/webcam.htm foto soft e hot - foto annunci - singoli coppie gay trans escort - totalmente amatoriali reali e gratuiti http://www.cryogenteam.com/animeribelli/ _________________________________________ _________________________________________ _________________________________________ _________________________________________ _________________________________________ A presto, Il team di domeus.it -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20040521/afdadc72/attachment.html -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 2422 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20040521/afdadc72/attachment.gif -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/gif Size: 1458 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20040521/afdadc72/attachment-0001.gif From tnetkxflase at jomani.com.br Sun May 23 16:17:05 2004 From: tnetkxflase at jomani.com.br (Rubens F. Galutti) Date: Sun, 23 May 2004 17:17:05 -0300 Subject: [EMBOSS] Rendimento com Internet Message-ID: <20040523201700.56D257D1BC@mercury.hgmp.mrc.ac.uk> Procuramos Pessoas, Profissionais e Empres?rios, para Trabalho e Parceria de Neg?cios, com uso da Internet e de outras ferramentas. Pode ser feito em tempo parcial ou integral e com Altos Ganhos. Visite: http://www.hipernegocio.net Rubens F. Galutti WTRCorp - D?vidas pelo email wtrcorp at ibest.com.br Para ser removido de futuros correios, por favor, envie email para ngtcad at ibest.com.br, com o assunto REMOVER. Obrigado. From d.m.a.martin at dundee.ac.uk Mon May 24 11:46:33 2004 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Mon, 24 May 2004 16:46:33 +0100 Subject: [EMBOSS] 'Resources' in the emboss.default file Message-ID: I was browsing the ajnam.c code and noticed that there is what looks like a 'resource' type that can be defined in emboss.default. (causes namParseType to be set to TYPE_RESOURCE) What does this resource beast look like as I cannot find any documentation for it? My initial guess is that it looks like a database definition. Or am I barking up the wrong tree? -- David Martin PhD Post-Genomics and Molecular Interactions Centre University of Dundee ICQ: 337640638 From pmr at ebi.ac.uk Tue May 25 01:57:34 2004 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Tue, 25 May 2004 06:57:34 +0100 (BST) Subject: [EMBOSS] 'Resources' in the emboss.default file In-Reply-To: References: Message-ID: <1110.217.134.89.40.1085464654.squirrel@webmail.ebi.ac.uk> David, > I was browsing the ajnam.c code and noticed that there is what looks like > a > 'resource' type that can be defined in emboss.default. (causes > namParseType > to be set to TYPE_RESOURCE) What does this resource beast look like as I > cannot find any documentation for it? > > My initial guess is that it looks like a database definition. Pretty close! It looks like a database definition, but is intended to define "non-database resources". So far it has not been used, but I do have a blast wrapper submitted that will need this mechanism to define available blast databases, and have considered using it for other resources such as codon usage and genetic codes to make ACD files rather simpler. The definitions could be dynamic (seacrhing for files of a certain type and returning a list of files) or static (simply defining the list of allowed values). This reminds me I need to put some examples in before 3.0.0 :-) Any other suggestions welcome. regards, Peter Rice From asonyadi at cp.co.id Wed May 26 07:01:57 2004 From: asonyadi at cp.co.id (Sony) Date: Wed, 26 May 2004 07:01:57 -0400 Subject: [EMBOSS] Can not install emboss on mandrake 9.2 Message-ID: Dear friends I try to install emboss 2.8.0 on my mandrake 9.2, I have already done ./configure prefix=/usr/local/emboss/, make, make install, but after I modify bashrc with the following suggested code " PLPLOT_LIB=/site/prog/emboss/lib PATH=/site/prog/emboss/bin:\$PATH export PLPLOT_LIB PATH" then the command line can not recognized common command such as ls, cp, etc except cd. When I try to log out, I can not back to my x windows because mandrake system reject my username and password (before changing the bashrc the username and password are working properly). Does anyone know how to solve the problem? Do I have to change my distribution, once I have ever installed it in redhat 9, and it work properly without experiencing this case Thank you very much for help Sony Adi S From deejoe at iastate.edu Wed May 26 12:36:01 2004 From: deejoe at iastate.edu (D. Joe Anderson) Date: Wed, 26 May 2004 11:36:01 -0500 Subject: [EMBOSS] Can not install emboss on mandrake 9.2 In-Reply-To: References: Message-ID: <20040526163601.GK14459@iastate.edu> On Wed, May 26, 2004 at 07:01:57AM -0400, Sony wrote: > Dear friends > > I try to install emboss 2.8.0 on my mandrake 9.2, I have already done > ./configure prefix=/usr/local/emboss/, make, make install, but after I > modify bashrc with the following suggested code " > PLPLOT_LIB=/site/prog/emboss/lib PATH=/site/prog/emboss/bin:\$PATH export > PLPLOT_LIB PATH" then the command line can not recognized common command > such as ls, cp, etc except cd. Just for clarity, let's unwrap those commands onto one line per command: PLPLOT_LIB=/site/prog/emboss/lib PATH=/site/prog/emboss/bin:\$PATH export PLPLOT_LIB PATH Leave out the \ Instead of adding something to your PATH, you are obliterating your PATH and replacing it with directories that lack useful and necessary programs. With the \, the $ is escaped and not recognized as a special character. This keeps the $PATH variable from being interpreted and its value included. You want to include PATH's former value, as it tells the system where to find ls, cp, etc. It finds cd just fine because that is a command built-in to the bash shell. Also, you should not have to set the prefix, if ./configure's defaults are set right, it should put things in /usr/local. At that point, what you want to add to PATH is not /site/proc/emboss/bin but rather /usr/local/bin. You can set the PATH variable from the shell prompt. Doing so is a good way to test a PATH setting before committing it to a configuration file like bashrc For instance, if you manage to again get a shell prompt, issuing this command may restore your path to a useable state: export PATH=/bin:/sbin:/usr/bin:/usr/sbin you can then try issuing export PATH=/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/emboss/bin to see if you can execute any of the programs installed by your earlier invocation of "make install" > When I try to log out, I can not back to my > x windows because mandrake system reject my username and password (before > changing the bashrc the username and password are working properly). Which bashrc file did you modify? You are better off to modify the bashrc file in the home directory of a non-root account. For instance, if you have a regular user account called "sony" then this would be /home/sony/.bashrc or ~sony/.bashrc for short. Or, if you are logged-in as "sony" then this would be ~/.bashrc Once this file is modified to work properly, and if you need to make this change effective systemwide (for instance, if other people are to use this machine and you want them to be able to use the copy of emboss you have installed), then it might be appropriate to edit the system-wide copies in /etc Also, what account's do and don't work for you? If you have a regular user account that isn't working, you should be able to log in as the root user and make any changes. If what you have done have made it impossible for you to log in as root, then more drastic measures may be necessary. > Does anyone know how to solve the problem? You could try logging-in through a virtual terminal, instead of via X Windows. Hit Ctl-Alt-F1 to switch to a virtual terminal. Log in to the console window there and make any repairs necessary. When done, log out and switch back to X with Alt-F7. You could try booting into single-user mode, and to reverse your changes using that. You might try to boot the system with the Mandrake installation CD in rescue mode, and try to find the bashrc file you changed, and to change it back. It's been a while since I used Mandrake so I can't offer more detailed instructions. You might also try to choose GNOME or some other window manager from the X Windows login screen, instead of KDE. It might be that, with screwed-up dotfiles, KDE cannot find certain subdirectories in your home directory that it needs, and so login fails. > Do I have to change my > distribution, once I have ever installed it in redhat 9, and it work > properly without experiencing this case My guess is the success with redhat 9 was due more to happenstance than to any advantage emboss has on that distribution. So, I don't see that changing back to Redhat 9 would help per se. It might be that GNOME is more forgiving of dotfile configuration mishaps and that it therefore lets you log in via X Windows. You may find it easiest to re-install Mandrake (or any other distribution) but a change in distribution won't solve the basic difficulty, which seems to be an unfamiliarity with the basic system administration. You may be best to seek out local help with Linux basics. Linux.org shows 7 user groups in Indonesia: http://www.linux.org/groups/indonesia.html among which, this one ranks high in google: http://www.linux.or.id/ They may be better positioned to help you with answers and advice troubleshooting general problems like these with running X Windows, GNU software, and Linux. Regards, --Joe From tchiang at bioinfo.sickkids.on.ca Wed May 26 16:20:08 2004 From: tchiang at bioinfo.sickkids.on.ca (Ted Chiang) Date: Wed, 26 May 2004 16:20:08 -0400 (EDT) Subject: [EMBOSS] getorf question.. Message-ID: Hi, I'm using getorf as follows: $ getorf sequence.fasta -find 1 -noreverse -minsize 100 Among the results one of the ORFs I get is: MMSNSSSEIDVQEPNIVSDASCNTEEQLKTVDDVLIHCQVIYDALQNLDKKIDVIRRKVS KIQRFHARSLWTNHKRYGYKKHSYRLVKKLKLQKMKKNEVYETFSYPESYSPTLPVSRRE NNSPSNLPRPSFCMEEYQRAELEEDPILSRTPSPVHPSDFSEHNCQPYYASDGATYGSSS GLCLGNPRADSIHNTYSTDHASAAPPSVTRSPVENDGYIEEGSITKHPSTWSVEAVVLFL KQTDPLALCPLVDLFRSHEIDGKALLLLTSDVLLKHLGVKLGTAVKLCYYIDRLKQGKCF EN However, it does not give me a smaller ORF that begins with the marked '^' below: MMSNSSSEIDVQEPNIVSDASCNTEEQLKTVDDVLIHCQVIYDALQNLDKKIDVIRRKVS KIQRFHARSLWTNHKRYGYKKHSYRLVKKLKLQKMKKNEVYETFSYPESYSPTLPVSRRE ^ NNSPSNLPRPSFCMEEYQRAELEEDPILSRTPSPVHPSDFSEHNCQPYYASDGATYGSSS GLCLGNPRADSIHNTYSTDHASAAPPSVTRSPVENDGYIEEGSITKHPSTWSVEAVVLFL KQTDPLALCPLVDLFRSHEIDGKALLLLTSDVLLKHLGVKLGTAVKLCYYIDRLKQGKCF EN Is there a bug or am I missing something? The DNA input sequence is: >sequence.fasta ggtgtcgcgggagctctctgatccactcaggggtcagggcatcactggtctcgcgtgcgc gtgaccaggcccggtttccggtgccaggacctttccgaagcgtcgagtggcctaacggtc acagctgtcgcccatcggagaggcaggactactgcgagcagttttaccgcgacctccgga ggccggcgtgacaggctctgtcactaaaataggagtagaggtttaccactcttaggtgac taagcagtatcacaaataaaccctccagcaagtttaaaaataattaggtccaactcagag gaagtggagtttctcctgttgcacaaaaatgatgtctaacagctccagtgaaatcgatgt gcaggaaccgaatattgtatctgacgcatcctgtaatactgaagagcaactgaagacagt tgatgatgtccttattcattgccaggttatatatgatgctctgcaaaacctggataagaa gattgatgtgattcgtagaaaggtttcaaaaatccaacgtttccatgcgagatccctgtg gacaaatcataagcgatatggatataaaaagcattcttaccggcttgttaaaaagcttaa actccagaaaatgaagaaaaatgaggtttacgagacattctcctaccctgaaagttacag ccccactttaccagtgtcaaggcgtgagaataattccccgagcaaccttccaaggccatc cttttgcatggaagaataccagcgagctgagctggaggaggacccgatcctcagccgcac tccgagtccagtgcatccctcagatttctctgagcataattgtcagccgtattatgcatc tgatggtgcaacgtatggttcttcttcagggctctgccttggcaaccctcgggctgacag catccacaacacttactcaactgaccatgcttctgcagcaccaccttcagttacaaggtc accagttgaaaatgacggttacatagaggaaggaagcatcactaagcacccttcaacctg gtcggtggaagcagtggtcctatttctaaaacaaacagatcctcttgcattatgccctct tgtcgacctcttcagaagccatgaaattgacgggaaggctctgctcctactcacgagtga cgtgttgctgaagcacttgggggtgaagctgggaacggctgtgaagctatgctactacat tgaccgacttaaacaaggaaaatgctttgaaaattgaaaaaatccttgtgcaaatttaga ttgggccaacttctagaggcaccaatgccttcttagtgtggaatcatttttctgcccttt agtcgtttttgttttgtagaaagtatctctcaaaatatattatagctagaattgtagaac tatgttatagtccagtctacttctttaaaaaccatttaaactgctagatagtattagaat agtccaatagaaaattcattctttataggtctttaaaaattacttttattatattgttta caaatatatttcatgcaagaaacagaaaaaaaaaaaaccctttgattctggttcatctcg atacagagaaccaaaacagctaagagaggtattatcagggttgacaactcctatgattga atctatgggaattattcctcagaagagaatttaaaggtgtacccatatatatctctttct ggagtattttatctgtctgatgttgcagtattctacaagtttccagaaagagaatagcca tataaattattttcctttctgctattatttctctatatgttttatttattcagatttaga gtaaaaaataagcatataaacttttattatgtgctcttaacagttttaagataaactata ggatagatagaatggttattttatgcaagaaatattgtaccgcaagggtggtttggatga agtctgactactttttttcaaacaaactattatattaaaactgtcatattttggctaagt ttggacctataactacactttcattgtttgcatctctctatgaagatacgtctgtccaaa cttttaaaaggcataactgtattttatgtgtttattctttatatagatagtattttatat tttattctcacccgaagtattcacacaatctttttaaaaaaaatttgaaatggcattttg tattgccacagaggtaggatgagccatatattagtgaaatgttttattttgtaaaatata aatggattatttgccatcattagtacctctcaacttactttttagaggacaagaaacaat ctgtagattggtttccatacagggaagttctccgtcctatgcaatgtttctaattaattt gcttaattctgagccattaatcctgctacactttgaatgatacattaattcagactaatc tttgggggctttattttgtaagttagaactttcaagggaaacatgttcaacactattatt ttgttataaatttataactttgttattacattgtgtaacaaatataaggtttacgagcta tgagaattggtgctatcaccattagctatttgctgtaatgtcaagaaaatgttcaccaga tgcaagaatgtaccttttctttttagaaagccaaatgtactttagacatgaatgcaacta tttaaagaatagcttcatcaatgttattccttacatgtcataagattcttacttaaactt ggtcttctttcaaattgtttgtatgaagatgctgtacccacttgaacagtcctcaggtgt ttacataaatactatgttttacagttttcatattttaaaatattaataaagttaaatcac aatagttcaaaaaaaaaaaaaaaa -Ted =================================== Ted Chiang, Analyst Centre for Computational Biology Hospital for Sick Children, Toronto t: 416.813.7028 e: tchiang at sickkids.ca =================================== From gbottu at ben.vub.ac.be Thu May 27 03:52:19 2004 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Thu, 27 May 2004 09:52:19 +0200 Subject: [EMBOSS] getorf question.. In-Reply-To: References: Message-ID: <20040527075219.GA22818@bigben.ulb.ac.be> Dear Ted, It is the "logic" of the algorithm. getorf defines an ORF as a region that : - begins with a start codon - ends with a stop codon - has inside no stop codon (but can have start codons) In translation it will give an as long as possible protein. It does not give a set of proteins that overlap at the COOH-end and where the start methionine of one is an internal methionine of another. Guy Bottu, Belgian EMBnet Node From akira.onozuka at shionogi.co.jp Thu May 27 22:15:05 2004 From: akira.onozuka at shionogi.co.jp (Akira Onozuka) Date: Fri, 28 May 2004 11:15:05 +0900 Subject: [EMBOSS] Can't connect internal SRSWWW ver7 Message-ID: Dear EMBOSS users I would like to ask a very primitive question. I installed EMBOSS 2.8 on linux environment and we have SRSWWW internally on other host machine without proxy configuration. Our emboss.default file is vary simple as follows. ############## DB GENBANK [ type: N method: srswww format: genbank url: http://hostname:8080/srs71bin/cgi-bin/wgetz dbalias: GENBANK fields: "sv des org key" comment: "Genbank IDs" ] ############# But, when I typed seqret -sequence DDBJ:AB001611 -outseq AB001611.fasta -osformat fasta machine returns Reads and writes (returns) sequences Error: failed to open filename 'DDBJ' Error: Unable to read sequence 'DDBJ:AB001611' Died: seqret terminated: Bad value for '-sequence' and no prompt I can't specify which process has the issue for connecting with SRS. If we tried to jump to internet SRSWWW , we need proxy with user authentication, so it is difficult to verify with other outer resources in current EMBOSS version. The possibility could be (1)EMBOSS can't recognize SRS7?? (2)Some configuration trouble in emboss.default file and others....... But anyway, I would like to know which process has the issue for retrieving sequence from SRSWWW. How can I see that?? Any suggestions will be highly welcomed. Regards, Akira Onozuka ##################################################### Shionogi & Co., Ltd 12-4, Sagisu 5-chome, Fukushima-ku, Osaka 553-0002, Japan Sr.Research Scientist TEL:+81-6-6455-2015??FAX :+81-6-6455-2066 E-mail akira.onozuka at shionogi.co.jp ##################################################### From David.Bauer at schering.de Fri May 28 03:45:23 2004 From: David.Bauer at schering.de (David.Bauer at schering.de) Date: Fri, 28 May 2004 09:45:23 +0200 Subject: Antwort: [EMBOSS] Can't connect internal SRSWWW ver7 Message-ID: Hello Akira, one answer and one more question (I guess Peter is listening :-) In your emboss.default the database name is GENBANK. (DB GENBANK) So you must use GENBANK:AB001611 to get the sequence. The dbalias specifies the name of the database within SRS. This is used to formulate the wgetz request. If you want to query more than one database you can put the list in this place. In SRS GenBank and RefSeq are separate databases. So I use dbalias: "{genbank%20refseq}" If it still does not work use -debug. Seqret (like all other emboss programs) then writes a file seqret.dbg which contains the complete communication log of seqret with the srs server. Hope this helps, David. And now my question to Peter: I would like to use in fields also the GI number. In ajsrsdb I see queries for sv, org, des etc. But even if I specify this in fields of emboss.default the SRS request is only for ID and ACC. So what to do, if I want to be able to retrieve by SV ? Dear EMBOSS users I would like to ask a very primitive question. I installed EMBOSS 2.8 on linux environment and we have SRSWWW internally on other host machine without proxy configuration. Our emboss.default file is vary simple as follows. ############## DB GENBANK [ type: N method: srswww format: genbank url: http://hostname:8080/srs71bin/cgi-bin/wgetz dbalias: GENBANK fields: "sv des org key" comment: "Genbank IDs" ] ############# But, when I typed seqret -sequence DDBJ:AB001611 -outseq AB001611.fasta -osformat fasta machine returns Reads and writes (returns) sequences Error: failed to open filename 'DDBJ' Error: Unable to read sequence 'DDBJ:AB001611' Died: seqret terminated: Bad value for '-sequence' and no prompt I can't specify which process has the issue for connecting with SRS. If we tried to jump to internet SRSWWW , we need proxy with user authentication, so it is difficult to verify with other outer resources in current EMBOSS version. The possibility could be (1)EMBOSS can't recognize SRS7?? (2)Some configuration trouble in emboss.default file and others....... But anyway, I would like to know which process has the issue for retrieving sequence from SRSWWW. How can I see that?? Any suggestions will be highly welcomed. Regards, Akira Onozuka ##################################################### Shionogi & Co., Ltd 12-4, Sagisu 5-chome, Fukushima-ku, Osaka 553-0002, Japan Sr.Research Scientist TEL:+81-6-6455-2015??FAX :+81-6-6455-2066 E-mail akira.onozuka at shionogi.co.jp ##################################################### From idrummon at receptor.mgh.harvard.edu Fri May 28 15:58:18 2004 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Fri, 28 May 2004 15:58:18 -0400 Subject: [EMBOSS] size limits on extractseq? Message-ID: Is there an upper limit on the file size that extractseq can handle? I run into a problem using extractseq to get segments out of mouse chromosome files. It will only access the first 19.7 MB or so of a 185 MB file. The files are fasta files of the mouse genome build 32 from NCBI. Here is what the problem looks like: (real file sizes are ls'd below) $ extractseq Extract regions from a sequence Input sequence: mm_chr1.fa Regions to extract (eg: 4-57,78-94) [1-19589943]: $ extractseq Extract regions from a sequence Input sequence: mm_chr2.fa Regions to extract (eg: 4-57,78-94) [1-19704910]: $ ls -l total 3782918 -rw-r--r-- 1 nobody nobody 200460727 May 25 23:56 mm_chr1.fa -rw-r--r-- 1 nobody nobody 135604265 May 26 15:16 mm_chr10.fa -rw-r--r-- 1 nobody nobody 123799904 May 26 15:17 mm_chr11.fa -rw-r--r-- 1 nobody nobody 120032577 May 26 15:19 mm_chr12.fa -rw-r--r-- 1 nobody nobody 119608375 May 26 15:20 mm_chr13.fa -rw-r--r-- 1 nobody nobody 185168052 May 26 14:28 mm_chr2.fa -- Iain Drummond, Ph.D. Assistant Professor Department of Medicine, Harvard Medical School and Renal Unit, Massachusetts General Hospital Mailing address: Renal Unit / MGH 149-8000 149 13th St. Charlestown, MA 02129 Tel: 617 726 5647 Fax: 617 726 5669 idrummond at partners.org idrummon at receptor.mgh.harvard.edu Lab Home Page: http://danio.mgh.harvard.edu From w2hgcg at netscape.net Mon May 31 06:49:37 2004 From: w2hgcg at netscape.net (w2hgcg at netscape.net) Date: Mon, 31 May 2004 06:49:37 -0400 Subject: [EMBOSS] ontology for emboss Message-ID: <6AD3D204.3BCDE0D5.000665E2@netscape.net> >From reading the Project meeting file corresponding to the 12th of December I noticed a mention to an ontology for emboss, I would like to know if there is such an ontology, and if so from where can I download it, cheers. __________________________________________________________________ Introducing the New Netscape Internet Service. Only $9.95 a month -- Sign up today at http://isp.netscape.com/register Netscape. Just the Net You Need. New! Netscape Toolbar for Internet Explorer Search from anywhere on the Web and block those annoying pop-ups. Download now at http://channels.netscape.com/ns/search/install.jsp From idrummon at receptor.mgh.harvard.edu Mon May 31 08:18:50 2004 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Mon, 31 May 2004 08:18:50 -0400 Subject: [EMBOSS] SUMMARY: size limits on extractseq? In-Reply-To: <1085978250.40bab68a704f1@webmail.utm.utoronto.ca> Message-ID: This turned out to be operator error. extractseq works fine on large files. The NCBI mouse chromosome files are actually a collection of contigs; extractseq looks only at the first file. Both comments from Clinton and Peter are on the mark; the problem was the sequence file. -- Iain Drummond, Ph.D. Assistant Professor Department of Medicine, Harvard Medical School and Renal Unit, Massachusetts General Hospital Mailing address: Renal Unit / MGH 149-8000 149 13th St. Charlestown, MA 02129 Tel: 617 726 5647 Fax: 617 726 5669 idrummond at partners.org idrummon at receptor.mgh.harvard.edu Lab Home Page: http://danio.mgh.harvard.edu > From: Clinton Fernandes > Reply-To: clintonf at interchange.ubc.ca > Date: Sun, 30 May 2004 21:37:30 -0700 > To: Iain Drummond > Subject: Re: [EMBOSS] size limits on extractseq? > > It may be the source of the file. > > I have experienced difficulty sometimes saving a file in a Windows environment > and working with the file in a Linux environment. While I obviously don't know > the specifics of your environment, this may be something you haven't > considered. > > I never had a problem with extractseq, but what I was experiencing seemed > somewhat similar to your problem. A sequence I downloaded from the internet > had > invisible characters that dos2unix did not remove. This resulted in some very > quirky behaviour in an extraction program that I had coded. I had to copy the > sequence to the clipboard and paste it into a text editor in my Linux machine. > > Again, what I have described may be completely left-field to what you are > experiencing, but it may bear looking into if the situations are similar. > > -- > Clinton Fernandes > Bioinformatician > UBC, Dept. of Microbiology > Wesbrook Bldg, Room 224 > 6174 University Blvd, > Vancouver, BC, Canada > > (604) 827-5160 > e-mail: clintonf at interchange.ubc.ca > > > Quoting Iain Drummond : > >> Is there an upper limit on the file size that extractseq can handle? >> >> I run into a problem using extractseq to get segments out of mouse >> chromosome files. It will only access the first 19.7 MB or so of a 185 MB >> file. The files are fasta files of the mouse genome build 32 from NCBI. Here >> is what the problem looks like: (real file sizes are ls'd below) >> >> $ extractseq >> Extract regions from a sequence >> Input sequence: mm_chr1.fa >> Regions to extract (eg: 4-57,78-94) [1-19589943]: >> >> $ extractseq >> Extract regions from a sequence >> Input sequence: mm_chr2.fa >> Regions to extract (eg: 4-57,78-94) [1-19704910]: >> >> $ ls -l >> total 3782918 >> -rw-r--r-- 1 nobody nobody 200460727 May 25 23:56 mm_chr1.fa >> -rw-r--r-- 1 nobody nobody 135604265 May 26 15:16 mm_chr10.fa >> -rw-r--r-- 1 nobody nobody 123799904 May 26 15:17 mm_chr11.fa >> -rw-r--r-- 1 nobody nobody 120032577 May 26 15:19 mm_chr12.fa >> -rw-r--r-- 1 nobody nobody 119608375 May 26 15:20 mm_chr13.fa >> -rw-r--r-- 1 nobody nobody 185168052 May 26 14:28 mm_chr2.fa >> >> -- >> >> Iain Drummond, Ph.D. >> Assistant Professor >> Department of Medicine, Harvard Medical School and >> Renal Unit, Massachusetts General Hospital >> >> Mailing address: >> Renal Unit / MGH 149-8000 >> 149 13th St. >> Charlestown, MA 02129 >> >> Tel: 617 726 5647 >> Fax: 617 726 5669 >> >> idrummond at partners.org >> idrummon at receptor.mgh.harvard.edu >> >> Lab Home Page: >> http://danio.mgh.harvard.edu >> >> >> > From SUPPORT at INVESTIGATE-BACKGROUND.US Mon May 31 23:54:24 2004 From: SUPPORT at INVESTIGATE-BACKGROUND.US (SUPPORT at INVESTIGATE-BACKGROUND.US) Date: Mon, 31 May 2004 19:54:24 -0800 Subject: [EMBOSS] A user is searching for information re: emboss@embnet.org Message-ID: ****NOT COMMERCIAL EMAIL**** Someone is researching your background at our website. Someone has begun the process of meeting people who know you via our website. This email was sent to you to make you aware of this fact. Our world is one of increasing internationalization, mobility of labor, immigration and upward mobility in the workforce. As a result, towns and neighborhoods where everyone knows each other are increasingly rare. It is increasingly less common for a person to work at the same company for their entire life, or to even live in the same city or town. In life today we are exposed to and meet a greater variety of people, and with the advent of the Internet we can meet people far outside of our geographical area of residence. To learn about the research being done use this link: http://h.womr.biz/sel.php?a=search&b=5&c=emboss%40embnet.org Our website is a valuable background research tool that enables its users to access the information source known as word-of-mouth on an intrnational scale. To add this email address to our Do Not Email List - http://j.womr.us/sel.php?a=donotemail&b=emboss%40embnet.org Once you have searched for connections at our site a few times you will understand that it is something you will want to do regularly. A Connection could be submitted about you or someone interesting to you at anytime. Most users want to learn immediately when interesting connections have been submitted, so we developed Daily Automatic New Connection Searching. A Daily Automatic New Connection Search is like a manual search except that it occurs automatically every day. After the search completes our system sends you an automatic email to confirm that the search has been performed. If any search results are found a link will be included in the email for your convenience. You can change the searches you want our system to perform through our automatic searching page. These searches occur daily and only search through connections that have been submitted since the last utomatic search. Regards, WOM Support Department From quintric at sb-roscoff.fr Mon May 3 11:56:05 2004 From: quintric at sb-roscoff.fr (Laure Quintric) Date: Mon, 03 May 2004 13:56:05 +0200 Subject: [EMBOSS] little question about EMBOSS win Message-ID: <40963355.6020509@sb-roscoff.fr> Hi ! I'd like to know when EMBOSSWIN was created and if it's still under construction or not? Thanks ! Laure. ----- Laure Quintric mail : quintric at sb-roscoff.fr From postmaster at 2020.net Tue May 4 13:20:29 2004 From: postmaster at 2020.net (System Administrator) Date: Tue, 4 May 2004 09:20:29 -0400 Subject: [EMBOSS] Undeliverable:{Spam?} Message-ID: <63ECD1C77009D646B4CA1309051A5E7397297A@srv-mail1.ho.wan.2020.net> Your message To: Marketing Subject: {Spam?} Sent: Sun, 6 Mar 1994 04:26:41 -0400 did not reach the following recipient(s): Marketing on Sun, 6 Mar 1994 08:26:41 -0400 User Marketing (Marketing at mks-laval) not listed in public Name & Address Book -------------- next part -------------- An embedded message was scrubbed... From: "emboss at embnet.org@SMTP at Exchange" Subject: {Spam?} Date: Sun, 6 Mar 1994 04:26:41 -0400 Size: 1345 URL: From ablavier at wanadoo.fr Tue May 4 19:45:08 2004 From: ablavier at wanadoo.fr (=?ISO-8859-1?Q?Andr=E9_Blavier?=) Date: Tue, 04 May 2004 21:45:08 +0200 Subject: [EMBOSS] little question about EMBOSS win In-Reply-To: <40963355.6020509@sb-roscoff.fr> References: <40963355.6020509@sb-roscoff.fr> Message-ID: <4097F2C4.6030908@wanadoo.fr> The first version of EMBOSSWIN was released in May 2003. The latest version was released in October 2003; it's a port of EMBOSS version 2.7.1 (see http://perso.wanadoo.fr/ablavier/embosswin/embosswin.html). Indeed, EMBOSSWIN is still under construction, and will probably always be. I didn't receive a lot of feedback about this Windows port, so it is only maintained on demand. -- Andr? Blavier Laure Quintric wrote: > Hi ! > I'd like to know when EMBOSSWIN was created and if it's still under > construction or not? > Thanks ! > > Laure. > > ----- > Laure Quintric > mail : quintric at sb-roscoff.fr > From postmaster at ebi.ac.uk Wed May 5 03:23:48 2004 From: postmaster at ebi.ac.uk (MailScanner) Date: Wed, 5 May 2004 04:23:48 +0100 (BST) Subject: [EMBOSS] Warning: E-mail containing attachment(s) blocked Message-ID: <200405050323.i453NmR06223@maui.ebi.ac.uk> Our MailScanner has blocked a message that you sent:- To: dali-help at ebi.ac.uk Subject: Mail Delivery (failure dali-help at ebi.ac.uk) Date: Wed May 5 04:23:48 2004 This is because it contains one or more attachments that we do not allow. Please rename any attachments to be in the form: filename.clean and resend the message (don't forget to tell the recipient the attachment type). If you have not actually sent this email it is possible that it has been forged (so that it appeared to be from you). MailScanner Report: Windows Screensavers are often used to hide viruses (message.scr) -- MailScanner Email Virus Scanner www.mailscanner.info From sghk100 at sghms.ac.uk Wed May 5 09:48:22 2004 From: sghk100 at sghms.ac.uk (David Winterbourne) Date: Wed, 05 May 2004 10:48:22 +0100 Subject: [EMBOSS] little question about EMBOSS win References: <40963355.6020509@sb-roscoff.fr> <4097F2C4.6030908@wanadoo.fr> Message-ID: <4098B866.98376B30@sghms.ac.uk> I only recently downloaded EMBOSSWIN and was very pleased with the result (thanks, Andr?). It was easy to instal and I have not seen any problems with the applications that I have tried. However, I would prefer not to work in a DOS window most of the time and it would be nice to run the programs from Staden's Spin, which I had installed on my Windows XP machine before installing EMBOSSWIN. The Windows version of Spin shows all the Emboss programs greyed out - is it possible to direct Spin to the EMBOSSWIN folder, what file would need to be modified to do that? Surprisingly, although Spin has not identified the EMBOSSWIN applications, it has picked up the settings I made in emboss.ini to get data from EBI and Entrez. -- David Winterbourne Andr? Blavier wrote: > The first version of EMBOSSWIN was released in May 2003. > The latest version was released in October 2003; it's a port of EMBOSS > version 2.7.1 (see > http://perso.wanadoo.fr/ablavier/embosswin/embosswin.html). > Indeed, EMBOSSWIN is still under construction, and will probably always > be. I didn't receive a lot of feedback about this Windows port, so it is > only maintained on demand. > > -- Andr? Blavier > > Laure Quintric wrote: > > Hi ! > > I'd like to know when EMBOSSWIN was created and if it's still under > > construction or not? > > Thanks ! > > > > Laure. > > > > ----- > > Laure Quintric > > mail : quintric at sb-roscoff.fr > > -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From alex.li at pioneer.com Wed May 5 19:38:45 2004 From: alex.li at pioneer.com (Li, Alex) Date: Wed, 5 May 2004 14:38:45 -0500 Subject: [EMBOSS] ENBOSS: compilation failed Message-ID: Dear ENBOSS expert: I downloaded the latest ENBOSS package. "./configuration --prefix=/mypath" went fine, but when I tried to compile it I got the following errors: gdpng.c:24:16: gd.h: No such file or directory gdpng.c:51: parse error before "im_out" gdpng.c:51: warning: data definition has no type or storage class gdpng.c: In function `fill_polygon': gdpng.c:233: `gdPoint' undeclared (first use in this function) gdpng.c:233: (Each undeclared identifier is reported only once gdpng.c:233: for each function it appears in.) gdpng.c:233: `points' undeclared (first use in this function) make[2]: *** [gdpng.lo] Error 1 make[2]: Leaving directory `/home/f198883/test/EMBOSS-2.8.0/plplot' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/f198883/test/EMBOSS-2.8.0/plplot' make: *** [all-recursive] Error 1 I noticed that there was an error when I was untar-ing the tarball: tar: directory checksum error Is it possible that some directories and files are not tar-ed properly? Thanks for any help in advance! Alex Li Bioinformatics Dept. Pioneer Hi-Bred - A DuPont Company alex.li at pioneer.com 515-334-4736 This communication is for use by the intended recipient and contains information that may be privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html From humberto at hpcf.upr.edu Thu May 6 19:30:27 2004 From: humberto at hpcf.upr.edu (humberto at hpcf.upr.edu) Date: Thu, 06 May 2004 15:30:27 -0400 Subject: [EMBOSS] Standalone Jemboss: where does output go? Message-ID: <200405061930.i46JURkE011146@daleth.hpcf.upr.edu> I'm one of the co-developers of bioknoppix. We've set up a standalone Jemboss on the CD, and one of our users sent us a note that Jemboss ran and didn't produce output. The Jemboss makefile contains the follwing fragment: echo "(cd $(prefix)/share/$(PACKAGE)/jemboss; java org/emboss/jemboss/Jemboss &)" >> $(bindir)/runJemboss.csh; but mere mortals don't have write access to $(prefix)/share/$(PACKAGE)/jemboss (actually, on our CD, neither does ROOT). Removing the cd command allows text output to work. Graphical programs just dump a bunch of png files into the current directory. Is this expected behavior or did we break something? -- Humberto Ortiz Zuazaga Programmer-Archaeologist High Performance Computing facility University of Puerto Rico http://www.hpcf.upr.edu/~humberto/ -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 241 bytes Desc: not available URL: From e-offers at freelotto.com Sun May 9 03:53:44 2004 From: e-offers at freelotto.com (e-offers at freelotto.com) Date: Sat, 08 May 2004 23:53:44 -0400 Subject: [EMBOSS] Auto-reply In-Reply-To: Message-ID: Dear FreeLotto Player, Thank you for your message to Customer Service at FreeLotto. If you are having a problem with our service we appreciate that you are taking the time to tell us. If you like our games, please tell your friends and we appreciate hearing your nice comments! To best serve you and provide a quick answer to your question, please click on the following icons at the top of our FreeLotto website. Most questions our players ask are answered there. HelpDesk F.A.S.T - for Monthly Subscription Service Rules How it Works PLEASE DO NOT RESPOND TO THIS MESSAGE. SEE BELOW. When you send a message to us, please indicate your topic in the Subject line: For Example: "Click2Win Tournaments" Directions to our most Frequently Asked Questions: How to Play: There are six different games played in sequence which each user can play once each day. See http://www.freelotto.com/faq/Faq.asp#1 http://www.freelotto.com/Rules.asp How many user ids can I use to play FreeLotto each day? Each person Can play each set of games 1 time each day. http://www.freelotto.com/faq/Faq.asp#2 http://www.freelotto.com/Rules.asp FreeLotto is available worldwide - with a few exceptions. http://www.freelotto.com/faq/Faq.asp#3 http://www.freelotto.com/Rules.asp Not receiving confirmations. http://www.freelotto.com/faq/Faq.asp#7 Not receiving Results. http://www.freelotto.com/faq/Faq.asp#8 Unsubscribe from FreeLotto e-mails: http://www.freelotto.com/faq/Faq.asp#9 F.A.S.T. Subscription account - Edit or deactivate http://www.freelotto.com/faq/Faq.asp#4 http://www.freelotto.com/LottoPicker/subscribe_faq.asp Change mailing address or e-mail address. http://www.freelotto.com/faq/Faq.asp#10 Forgot Password. http://www.freelotto.com/faq/Faq.asp#11 See previous results. http://www.freelotto.com/faq/Faq.asp#14 How to receive FREELOTTO prizes. http://www.freelotto.com/faq/Faq.asp#6 If your question is not answered, please write to us by clicking on the link below. Please make sure that your topic is in the subject line. http://www.freelotto.com/Contact.asp?type=questions Thank you for your patience and support. Customer Service If you are a Postmaster or Webmaster, please send your request to the email address listed above. If you are requesting action regarding a specific user, please be sure to include the user's email address and/or user id so we can best serve you and quickly respond to your request. From Sean.Maceachern at dpi.vic.gov.au Mon May 10 04:36:39 2004 From: Sean.Maceachern at dpi.vic.gov.au (Sean.Maceachern at dpi.vic.gov.au) Date: Mon, 10 May 2004 14:36:39 +1000 Subject: [EMBOSS] coderet problems Message-ID: Hi, I'm having problems with coderet. I have put in 27 956 entries from a genbank flat file and I am only getting 27 711 sequences returned. I have tried all of the -verbose options etc but I can not get information on which of the 200 sequences failed. Does anyone know what the problem might be or how I might be able to get this information? Any help would be appreciated. Cheers, Sean MacEachern From d.m.a.martin at dundee.ac.uk Tue May 11 11:22:13 2004 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Tue, 11 May 2004 12:22:13 +0100 Subject: [EMBOSS] Installing the Jemboss server Message-ID: Has anyone actually managed to do this outside HGMP (oops, RFCGR)? I have been battling with the install script for a few days with varying degrees of success. First issue: It doesn't take into account the additional arguements given for an EMBOSS install (eg. --bindir= --libdir=) which then break it later. This is easily fixed with a manual edit. Second issue: It has problems finding various files. Excerpts from the install included below with comments -- java.io.FileNotFoundException: /site/share/EMBOSS/jemboss/resources/wossname.jar (No such file or directory) at java.io.FileOutputStream.open(Native Method) at java.io.FileOutputStream.(FileOutputStream.java:102) at java.io.FileOutputStream.(FileOutputStream.java:62) at sun.tools.jar.Main.run(Main.java:134) at sun.tools.jar.Main.main(Main.java:904) java.io.FileNotFoundException: /site/share/EMBOSS/jemboss/resources/resources.ja r (No such file or directory) at java.io.FileOutputStream.open(Native Method) at java.io.FileOutputStream.(FileOutputStream.java:102) at java.io.FileOutputStream.(FileOutputStream.java:62) at sun.tools.jar.Main.run(Main.java:134) at sun.tools.jar.Main.main(Main.java:904) -- I had removed /site/share/EMBOSS/jemboss before running the script. /site/share/EMBOSS/jemboss/resources/ points to the axis web application directory under tomcat. (axis/WEB-INF/classes/resources) -- error: cannot read: /site/share/EMBOSS/jemboss/org/emboss/jemboss/server/Jemboss AuthServer.java 1 error error: cannot read: /site/share/EMBOSS/jemboss/org/emboss/jemboss/server/Jemboss FileAuthServer.java 1 error -- the relevant files have for some reason been installed under /site/share/EMBOSS/jemboss/org/org/emboss/jemboss/server by the install script. and it goes on with many more file not found errors. If these are ignored then further problems arise later. ..d -- David Martin PhD Post-Genomics and Molecular Interactions Centre University of Dundee ICQ: 337640638 From tjc at sanger.ac.uk Tue May 11 12:43:36 2004 From: tjc at sanger.ac.uk (Timothy Carver) Date: Tue, 11 May 2004 13:43:36 +0100 (BST) Subject: [EMBOSS] Installing the Jemboss server (fwd) Message-ID: Hi David On Tue, 11 May 2004, David Martin wrote: > Has anyone actually managed to do this outside HGMP (oops, RFCGR)? Errr yes. Many sites have installed this and most people are successful using the script. It has been tested on all EMBOSS supported platforms.... Linux, MacOSX, SunOS, AIX.... > First issue: It doesn't take into account the additional arguements given > for an EMBOSS install (eg. --bindir= --libdir=) which then break it later. > This is easily fixed with a manual edit. Why do you need to use those? This possibly cannot be described as a standard install then. You don't say what you edit so I cannot comment other than that the script does certainly allow you to add lines to the configure. > Second issue: It has problems finding various files. Excerpts from the > install included below with comments > -- > java.io.FileNotFoundException: > /site/share/EMBOSS/jemboss/resources/wossname.jar > (No such file or directory) > at java.io.FileOutputStream.open(Native Method) > at java.io.FileOutputStream.(FileOutputStream.java:102) > at java.io.FileOutputStream.(FileOutputStream.java:62) > at sun.tools.jar.Main.run(Main.java:134) > at sun.tools.jar.Main.main(Main.java:904) > java.io.FileNotFoundException: > /site/share/EMBOSS/jemboss/resources/resources.ja > r (No such file or directory) > at java.io.FileOutputStream.open(Native Method) > at java.io.FileOutputStream.(FileOutputStream.java:102) > at java.io.FileOutputStream.(FileOutputStream.java:62) > at sun.tools.jar.Main.run(Main.java:134) > at sun.tools.jar.Main.main(Main.java:904) > -- > I had removed /site/share/EMBOSS/jemboss before running the script. > /site/share/EMBOSS/jemboss/resources/ points to the axis web application > directory under tomcat. (axis/WEB-INF/classes/resources) > -- > error: cannot read: > /site/share/EMBOSS/jemboss/org/emboss/jemboss/server/Jemboss > AuthServer.java > 1 error > error: cannot read: > /site/share/EMBOSS/jemboss/org/emboss/jemboss/server/Jemboss > FileAuthServer.java > 1 error > -- > the relevant files have for some reason been installed under > /site/share/EMBOSS/jemboss/org/org/emboss/jemboss/server > by the install script. > > and it goes on with many more file not found errors. If these are ignored > then further problems arise later. No point ignoring errors like that and hoping it will work. Again from what you provide I can only guess at what the problem may be. Do you delete tomcat, axis and EMBOSS (download & installation) before doing a fresh install? Anyway it would be better to start with a standard working installation and then hack it about from there if you really have to. Tim From MAILER-DAEMON at mailfilter1.voicenet.com Sat May 15 09:10:49 2004 From: MAILER-DAEMON at mailfilter1.voicenet.com (MAILER-DAEMON at mailfilter1.voicenet.com) Date: 15 May 2004 09:10:49 -0000 Subject: [EMBOSS] failure notice Message-ID: <20040515091050.635347D2AB@mercury.hgmp.mrc.ac.uk> Hi. This is the qmail-send program at mailfilter1.voicenet.com. I'm afraid I wasn't able to deliver your message to the following addresses. This is a permanent error; I've given up. Sorry it didn't work out. : Sorry, no mailbox here by that name. (#5.1.1) --- Below this line is a copy of the message. Return-Path: Received: (qmail 16906 invoked from network); 15 May 2004 09:10:40 -0000 Received: from 62-128-170-156.iwayafrica.com (HELO voicenet.com) (62.128.170.156) by mailfilter1.voicenet.com with SMTP; 15 May 2004 09:10:40 -0000 X-Matched: 62-128-170-156.iwayafrica.com [62.128.170.156] From: emboss at embnet.org To: gatgul at voicenet.com Subject: Re: Re: Message Date: Sat, 15 May 2004 19:10:13 +0300 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0001_00006497.000017C0" X-Priority: 3 X-MSMail-Priority: Normal This is a multi-part message in MIME format. ------=_NextPart_000_0001_00006497.000017C0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit Please have a look at the attached file. ------=_NextPart_000_0001_00006497.000017C0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit IMPORTANT NOTICE: A Virus has been found and removed from this email. Anti-virus software has detected that this email message was infected with the "W32/Netsky.D-mm" virus. To protect our network and help prevent your computer from receiving this virus, the following file or attachment has been removed: "message_details.pif". If you know the sender and believe that the inclusion of the virus was inadvertent on their part, it is your option to contact them and have the email resent ONLY after they have scanned it first for viruses. Thank you, Voicenet Support support at voicenet.com ------=_NextPart_000_0001_00006497.000017C0-- From m.tagaya at nippon-shinyaku.co.jp Mon May 17 01:00:44 2004 From: m.tagaya at nippon-shinyaku.co.jp (Mitsuhiro Tagaya) Date: Mon, 17 May 2004 10:00:44 +0900 Subject: [EMBOSS] mailing list for Japanese Users Message-ID: <20040517094352.3131.M.TAGAYA@nippon-shinyaku.co.jp> Hi, We JAMBO (Japan EMBOSS Users Group) made a mailing list for Japanese EMBOSS Users. The URL of JAMBO is: http://jambo.sourceforge.jp/ and the mailing list is: http://lists.sourceforge.jp/mailman/listinfo/jambo-users ---- Tagaya Mitsuhiro m.tagaya at nippon-shinyaku.co.jp Jambo! Habari yako? http://jambo.sourceforge.jp/ From pmr at ebi.ac.uk Mon May 17 09:58:33 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 17 May 2004 10:58:33 +0100 Subject: [EMBOSS] mailing list for Japanese Users In-Reply-To: <20040517094352.3131.M.TAGAYA@nippon-shinyaku.co.jp> References: <20040517094352.3131.M.TAGAYA@nippon-shinyaku.co.jp> Message-ID: <40A88CC9.9040003@ebi.ac.uk> Mitsuhiro Tagaya wrote: > Hi, We JAMBO (Japan EMBOSS Users Group) made a mailing list > for Japanese EMBOSS Users. Welcome to our Japanese friends. We can try to read the list using a translation service, but it would be helpful if someone could act as moderator and pass on questions to emboss-bug. I see one question about fasta sequence IDs from FANTOM. We can try to fix that by extending the sequence ID rules if someone can send us an example sequence file. regards, Peter Rice From mad at biol.unlp.edu.ar Mon May 17 15:17:09 2004 From: mad at biol.unlp.edu.ar (=?ISO-8859-1?Q?Mart=EDn_Sarachu?=) Date: Mon, 17 May 2004 12:17:09 -0300 Subject: [EMBOSS] wEMBOSS-1.1 release Message-ID: <40A8D775.3000800@biol.unlp.edu.ar> Version 1.1 of wEMBOSS is out. You can download it here http://bigben.vub.ac.be:6080/wEMBOSS/Folder.2003-09-11.4050/Folder.2003-09-11.4318C/wEMBOSS-1.1.tar.gz Some of the new features are: 1) results sort by date or alphabetically 2) rename projects 3) move projects The wEMBOSS Portal is at http://www.ar.embnet.org/wEMBOSS Regards, the wEMBOSS team -- Mart?n Sarachu mad at biol.unlp.edu.ar EMBNet Argentina http://www.ar.embnet.org From Marc.Logghe at devgen.com Tue May 18 07:00:23 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Tue, 18 May 2004 09:00:23 +0200 Subject: [EMBOSS] rformat option epestfind missing Message-ID: Hi, Just wanted to mention that the rformat option is 'missing' for epestfind. Al least I expected to have it there; I mean I have the impression as soon as an EMBOSS application returns 'regions' you may obtain them as features via the rformat opton. No ? Cheers, Marc From pmr at ebi.ac.uk Tue May 18 08:29:13 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 18 May 2004 09:29:13 +0100 Subject: [EMBOSS] rformat option epestfind missing In-Reply-To: References: Message-ID: <40A9C959.5060806@ebi.ac.uk> Marc Logghe wrote: > Just wanted to mention that the rformat option is 'missing' for epestfind. Al least I expected to have it there; I mean I have the impression as soon as an EMBOSS application returns 'regions' you may obtain them as features via the rformat opton. No ? rformat is available for any application that has a "report" output. You are right - the "outfile" in epestfind should be a report. The problem is that the original program had its own output format - but all we need to do is add a new rformat as the default. Then you would be able to use -rformat to get a feature file. I will take a look. regards, Peter Rice From henrikki.almusa at helsinki.fi Tue May 18 08:43:19 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Tue, 18 May 2004 11:43:19 +0300 Subject: [EMBOSS] rformat option epestfind missing In-Reply-To: <40A9C959.5060806@ebi.ac.uk> References: <40A9C959.5060806@ebi.ac.uk> Message-ID: <200405181143.19985.henrikki.almusa@helsinki.fi> On Tuesday 18 May 2004 11:29, Peter Rice wrote: > Marc Logghe wrote: > > Just wanted to mention that the rformat option is 'missing' for > > epestfind. Al least I expected to have it there; I mean I have the > > impression as soon as an EMBOSS application returns 'regions' you may > > obtain them as features via the rformat opton. No ? > > rformat is available for any application that has a "report" output. > > You are right - the "outfile" in epestfind should be a report. > > The problem is that the original program had its own output format - but > all we need to do is add a new rformat as the default. Then you would be > able to use -rformat to get a feature file. > > I will take a look. I sent a patch to change the epestfind (and newcpgreport) output into report format into emboss-submit few weeks ago. Did they get through (meaning the notice on emboss webpages about MRC) ? I can resend them to you if that will help. Regards, -- Henrikki Almusa From d.gatherer at vir.gla.ac.uk Tue May 18 09:17:55 2004 From: d.gatherer at vir.gla.ac.uk (Derek Gatherer) Date: Tue, 18 May 2004 10:17:55 +0100 Subject: [EMBOSS] EMBOSS mailing list archive final resting place In-Reply-To: <200405181143.19985.henrikki.almusa@helsinki.fi> References: <40A9C959.5060806@ebi.ac.uk> <40A9C959.5060806@ebi.ac.uk> Message-ID: <5.2.1.1.1.20040518095759.0352a400@udcf.gla.ac.uk> When RFCGR finally sadly closes next year, will there still be this mailing list? and will the archives of the list be preserved in the new sourceforge site? I think that the list archives are an invaluable resource for problem solving, and in fact I often consult them to remind myself of the answers to questions I previously asked. Even if there's no active list, it would be good to keep the archive for reference. cheers Derek _________________________ Derek Gatherer Ph.D. Cert.Ed. Computer Officer Institute of Virology Church St. Glasgow G11 5JR Phone: +44 141 330 6268 Fax: +44 141 337 2236 Email: d.gatherer at vir.gla.ac.uk Website: http://www.vir.gla.ac.uk From ableasby at hgmp.mrc.ac.uk Tue May 18 09:22:45 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Tue, 18 May 2004 10:22:45 +0100 (BST) Subject: [EMBOSS] EMBOSS mailing list archive final resting place Message-ID: <200405180922.i4I9Mjfv013631@bromine.hgmp.mrc.ac.uk> The intention is to move the lists plus archives to another site. It may turn out to be a mixture of sourceforge and EBI. We'll let people know as soon as we do. Alan From pmr at ebi.ac.uk Tue May 18 09:24:53 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 18 May 2004 10:24:53 +0100 Subject: [EMBOSS] EMBOSS mailing list archive final resting place In-Reply-To: <5.2.1.1.1.20040518095759.0352a400@udcf.gla.ac.uk> References: <40A9C959.5060806@ebi.ac.uk> <40A9C959.5060806@ebi.ac.uk> <5.2.1.1.1.20040518095759.0352a400@udcf.gla.ac.uk> Message-ID: <40A9D665.30006@ebi.ac.uk> Derek Gatherer wrote: > When RFCGR finally sadly closes next year, will there still be this > mailing list? and will the archives of the list be preserved in the new > sourceforge site? I think that the list archives are an invaluable > resource for problem solving, and in fact I often consult them to remind > myself of the answers to questions I previously asked. Even if there's > no active list, it would be good to keep the archive for reference. Yes, the list will continue and will be active (assuming of course everyone keeps posting to it :-). One reason for using the embnet.org address was to keep the list going if EMBOSS moved (as it did, from Sanger to HGMP/RFCGR in July 2000). Sourceforge does provide an alternative for mailing lists - and we do use it already for tracking bug and feature requests. The list archives will be preserved and maintained - after all, we use them too! regards, Peter Rice From Marc.Logghe at devgen.com Tue May 18 09:40:02 2004 From: Marc.Logghe at devgen.com (Marc Logghe) Date: Tue, 18 May 2004 11:40:02 +0200 Subject: [EMBOSS] rformat option epestfind missing Message-ID: > > The problem is that the original program had its own output > format - but > > all we need to do is add a new rformat as the default. Then > you would be > > able to use -rformat to get a feature file. > > > > I will take a look. > > I sent a patch to change the epestfind (and newcpgreport) > output into report > format into emboss-submit few weeks ago. Did they get through > (meaning the > notice on emboss webpages about MRC) ? I can resend them to > you if that will > help. How should I proceed ? Watch out for a cvs commit and rebuild the individual application ? Thanks all ! Cheers, Marc From Joerg.Schaber at uv.es Tue May 18 11:49:55 2004 From: Joerg.Schaber at uv.es (Joerg Schaber) Date: Tue, 18 May 2004 13:49:55 +0200 Subject: [EMBOSS] dbiflat problem Message-ID: <40A9F863.7080505@uv.es> Hi, I am indexing a genbank database on Linux RH7.3 with EMBOSS 2.8.0 and running dbiflat -idformat gb -directory "." -filename "*.gbk" -dbname "ncbibac" -release "1.3" -date "18/05/04" -fields acnum,des,taxon I keep geeting the following mistake: EMBOSS An error in embdbi.c at line 693: Cannot open ncbibac.idsrt for reading Any idea what's the problem here? Thanks, joerg From Imogene at fiestabrava.com Tue May 18 16:03:48 2004 From: Imogene at fiestabrava.com (Eugenio Watts) Date: Tue, 18 May 2004 19:03:48 +0300 (CST) Subject: [EMBOSS] Softwares CDS all software under 15$ and 99$! slut Message-ID: <14050440263761.BI41njWXkua74@workbench6.danny89cocolee.net> >Life begins at forty Sensation!! We opened a NEW site with unbeatable prices and products. 1500 WORLD BEST software with 90% discount - that is a really BEST offer just imagine, you can buy ALL software that you ever need and pay price of just one of it! Office 2003 for 50$ - nice deal right ? ;) retail price is 700$ - great savings, huh? Please spend few moments of yours precious time to check our offer - it is more than worth it! http://constantine.reachsoftware.com/?driveway >Absence makes the heart go wander. >The squeaky wheel gets the grease. >Every dog has his day >Lean liberty is better than fat slavery >A place for everything and everything in its place. >Yesterday is ashes; tomorrow wood Only today does the fire burn brightly >There is a time and a place for everything >March winds and April showers bring forth May flowers >A fair exchange is no robbery. >Shame face ah feel like cent ice. >And say, How have I hated instruction, and my heart despised reproof. >Promises are like babies Easy to make, hard to deliver >Don't cross your bridges before you come to them. >Tis better to get things for free, than to work up a sweat >There is no such thing as a free lunch >It is in vain to cast your net where there is no fish >Everything must have a beginning >Rain, Rain, go away, come back another day >Artificial intelligence is no match for natural stupidity From deejoe at iastate.edu Tue May 18 17:04:23 2004 From: deejoe at iastate.edu (D. Joe Anderson) Date: Tue, 18 May 2004 12:04:23 -0500 Subject: [EMBOSS] dbiflat problem In-Reply-To: <40A9F863.7080505@uv.es> References: <40A9F863.7080505@uv.es> Message-ID: <20040518170423.GA15431@iastate.edu> On Tue, May 18, 2004 at 01:49:55PM +0200, Joerg Schaber wrote: > EMBOSS An error in embdbi.c at line 693: > Cannot open ncbibac.idsrt for reading Sorry if this seems too obvious, but can you find the file ncbibac.idsrt, and if so, what are it's permissions and ownership? --Joe From VZWUBanks at fwfaq.com Wed May 19 04:18:59 2004 From: VZWUBanks at fwfaq.com (Barbara Forbes) Date: Wed, 19 May 2004 07:18:59 +0300 Subject: [EMBOSS] Name brand software at generic prices. mint Message-ID: An HTML attachment was scrubbed... URL: From luisa.pugliese at safan-bioinformatics.it Wed May 19 12:59:49 2004 From: luisa.pugliese at safan-bioinformatics.it (luisa pugliese) Date: Wed, 19 May 2004 14:59:49 +0200 Subject: [EMBOSS] emboss on amd64 Message-ID: <00ba01c43da1$2affe960$f3ee669e@chagall> Hi all, I would like to run EMBOSS on an AMD64 processor with mandrake 9.2 for amd64. I downloaded the rpm distributions for EMBOSS2.8 and libEMBOSS2.8 and I installed them. However when I try to run the emboss programs (I tryed water and needle) I get a segmentation fault. I saw that in your tutorial there is something about 64-bit machines configuration, but the details are present only for Irix. I wonder if you could be so kind to help me in finding what could be the problem.a I also downloaded the tar file from the emboss web site, I compiled it and I get the same error. I wonder if anybody knows and is so kind to let me know what should I do in order to get EMBOSS running on the AMD64. Best regards Luisa ============================= Luisa Pugliese, Ph.D. luisa.pugliese at safan-bioinformatics.it S.A.F.AN. BIOINFORMATICS Corso Tazzoli 215/13 -10137 Torino - ITALY tel +39 011 3026230 cell. +39 333 6130644 -------------- next part -------------- An HTML attachment was scrubbed... URL: From postmaster at navair.navy.mil Wed May 19 13:04:51 2004 From: postmaster at navair.navy.mil (System Administrator) Date: Wed, 19 May 2004 09:04:51 -0400 Subject: [EMBOSS] Undeliverable: Re: Re: Document Message-ID: <14A4447570FE374E8906CA5AA6261AB7028BF7B7@neim05.navair.navy.mil> Your message To: corpusgd at navair.navy.mil Subject: Re: Re: Document Sent: Wed, 19 May 2004 09:07:46 -0400 did not reach the following recipient(s): CORPUSGD at NAVAIR.NAVY.MIL on Wed, 19 May 2004 09:04:49 -0400 The recipient name is not recognized The MTS-ID of the original message is: c=us;a= ;p=organization;l=NEIM050405191304LD3ACB8Q MSEXCH:IMS:ORGANIZATION:NAVAIREAST:NEIM05 0 (000C05A6) Unknown Recipient -------------- next part -------------- An embedded message was scrubbed... From: emboss at embnet.org Subject: Re: Re: Document Date: Wed, 19 May 2004 09:07:46 -0400 Size: 763 URL: From ableasby at hgmp.mrc.ac.uk Wed May 19 13:08:31 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Wed, 19 May 2004 14:08:31 +0100 (BST) Subject: [EMBOSS] emboss on amd64 Message-ID: <200405191308.i4JD8Vpq029072@bromine.hgmp.mrc.ac.uk> Dear Luisa, This is becoming a more common query so I'll post the answer to the list. Before compiling EMBOSS 2.8.0 you need to get the following files: ftp://ftp.rfcgr.mrc.ac.uk/pub/EMBOSS/patchfiles/ajfmt.c ftp://ftp.rfcgr.mrc.ac.uk/pub/EMBOSS/patchfiles/ajfmt.h and use them to replace the files in the ajax directory. Hopefully your compiler will predefine __amd64__ but, if not, setenv CFLAGS "__amd64__" before configuring EMBOSS. These modifications have already been added to the CVS version. HTH Alan Bleasby RFCGR From ableasby at hgmp.mrc.ac.uk Wed May 19 13:17:06 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Wed, 19 May 2004 14:17:06 +0100 (BST) Subject: [EMBOSS] emboss on amd64 Message-ID: <200405191317.i4JDH67f029679@bromine.hgmp.mrc.ac.uk> Correction: That should, of course, be: setenv CFLAGS "-D__amd64__" or the sh equivalent. AJB From gombar at email.unc.edu Wed May 19 14:23:08 2004 From: gombar at email.unc.edu (gombar at email.unc.edu) Date: Wed, 19 May 2004 10:23:08 -0400 Subject: [EMBOSS] Eprimer3 Issue Message-ID: <1084976588.40ab6dccd9764@webmail0.isis.unc.edu> Hello, My name is Saurabh Gombar and I work in the Biology department at UNC Chapel Hill. I had a question regarding your Eprimer3 application. In your Eprimer3 information page it says "eprimer3 takes as input a Sequence Quality list for use." However, looking through the rest of the documentation I could not find how specify the Quality List to Eprimer3 as well as minimum quality values to consider. Thanks, Saurabh Gombar From gwilliam at hgmp.mrc.ac.uk Wed May 19 14:28:08 2004 From: gwilliam at hgmp.mrc.ac.uk (Gary Williams, Tel 01223 494522) Date: Wed, 19 May 2004 15:28:08 +0100 Subject: [EMBOSS] Eprimer3 Issue References: <1084976588.40ab6dccd9764@webmail0.isis.unc.edu> Message-ID: <40AB6EF8.E5B87477@hgmp.mrc.ac.uk> Saurabh, You are correct. The eprimer3 program doesn't read in a Sequence Quality list. I will change the documentation. Gary gombar at email.unc.edu wrote: > > Hello, > My name is Saurabh Gombar and I work in the Biology department at > UNC Chapel Hill. I had a question regarding your Eprimer3 application. > In your Eprimer3 information page it says "eprimer3 takes as input > a Sequence Quality list for use." However, looking through the rest > of the documentation I could not find how specify the Quality List to > Eprimer3 as well as minimum quality values to consider. > Thanks, > Saurabh Gombar -- Gary Williams MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494522 Fax: +44 1223 494512 E-mail: gwilliam at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk From alex.li at pioneer.com Thu May 20 18:23:08 2004 From: alex.li at pioneer.com (Li, Alex) Date: Thu, 20 May 2004 13:23:08 -0500 Subject: [EMBOSS] more info about Codon Usage Table (.cut) files? Message-ID: Hello, there, Some filenames of .cut files under .../EMBOSS/data/CODONS are intuitive (eg: Echicken.cut for chickens), but most are not. I assume filenames imply species names. Where can I get the info that maps between filenames and more DETAILED species info? Thanks in advance. Alex Li Bioinformatics Dept. Pioneer Hi-Bred. Voice: 515-334-4736 Fax: 515-334-6634 This communication is for use by the intended recipient and contains information that may be privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html From postmaster at ebi.ac.uk Fri May 21 07:51:20 2004 From: postmaster at ebi.ac.uk (MailScanner) Date: Fri, 21 May 2004 08:51:20 +0100 (BST) Subject: [EMBOSS] Warning: E-mail containing attachment(s) blocked Message-ID: <200405210751.i4L7pKU29148@maui.ebi.ac.uk> Our MailScanner has blocked a message that you sent:- To: datalib at ebi.ac.uk Subject: Mail Delivery (failure datalib at ebi.ac.uk) Date: Fri May 21 08:51:20 2004 This is because it contains one or more attachments that we do not allow. Please rename any attachments to be in the form: filename.clean and resend the message (don't forget to tell the recipient the attachment type). If you have not actually sent this email it is possible that it has been forged (so that it appeared to be from you). MailScanner Report: Windows Screensavers are often used to hide viruses (message.scr) -- MailScanner Email Virus Scanner www.mailscanner.info From henrikki.almusa at helsinki.fi Fri May 21 09:59:11 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Fri, 21 May 2004 12:59:11 +0300 Subject: [EMBOSS] PLPLOT_LIB enviromental variable Message-ID: <200405211259.11917.henrikki.almusa@helsinki.fi> Hello, To get emboss programs with graphics to work PLPLOT_LIB enviromental variable needs to be set, even if graph is set null or none. I tried to set this in emboss.properties, but it didn't work with "set PLPLOT_LIB /emboss/path/EMBOSS/share". Is is possible to make it so that it can be set from properties file asl well? Thanks, -- Henrikki Almusa From team at domeus.it Fri May 21 11:12:10 2004 From: team at domeus.it (Team domeus) Date: Fri, 21 May 2004 13:12:10 +0200 (CEST) Subject: [EMBOSS] RICHIESTA DI CONFERMA: Per cortesia conferma l'iscrizione al gruppo MailingList Aperta tutti scrivono a tutti Message-ID: <24858905.1085137930121.ecMessenger@domeus.it> Ciao grazie per esserti iscritto al gruppo MailingList Aperta tutti scrivono a tutti (cryomail at domeus.it). Se intendi davvero iscriverti, rispondi a quest'eMail utilizzando la funzione "Reply"/"Rispondi" o, in alternativa, cliccando su questo link: http://www.domeus.it/public/subscribe.jsp?tsp=1085137930111&gid=292685&uid=28311913&sig=EPOEOLBMEALHCHID&action=subscribeToSingleGroup Se non sei interessato ad unirti al gruppo, ignora semplicemente quest'eMail e non ne riceverai altre da parte nostra. Se il tuo indirizzo eMail ? stato aggiunto a questa lista senza il tuo consenso e non desideri ricevere eMail da Domeus, inoltra questo messaggio a: set_account_inactive at domeus.it. Ci? non ti permetter? di utilizzare il tuo indirizzo eMail tramite il sistema Domeus. DEVI RISPONDERE A QUESTO MESSAGGIO PER UNIRTI DEFINITIVAMENTE A QUESTO GRUPPO! Se intendi utilizzare in modo completo tutti i servizi, entra semplicemente in http://www.domeus.it utilizzando i seguenti dati d'accesso: username: emboss at embnet.org password: wabakil4 A presto, Il team di domeus.it -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: logo.gif Type: image/gif Size: 2422 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: corner.gif Type: image/gif Size: 1458 bytes Desc: not available URL: From team at domeus.it Fri May 21 12:47:08 2004 From: team at domeus.it (Team domeus) Date: Fri, 21 May 2004 14:47:08 +0200 (CEST) Subject: [EMBOSS] Benvenuto nel gruppo MailingList Aperta tutti scrivono a tutti Message-ID: <7862244.1085143628314.ecMessenger@domeus.it> Ciao emboss at embnet.org, sei stato aggiunto al gruppo MailingList Aperta tutti scrivono a tutti (cryomail at domeus.it). Il proprietario del gruppo ti invia il seguente messaggio di benvenuto: ---------------------------- ---------------------------- Se non desideri ricevere email da questo gruppo invia un eMail a cryomail-unsubscribe at domeus.it. Per cancellarti direttamenet tramite web, utilizza il seguente link: http://www.domeus.it/public/unsubscribe.jsp?tsp=1085143628294&gid=292685&uid=28311913&sig=GGOMLIIEIDECEPKO In ogni modo sarai cancellato dalla lista di distribuzione. Per qualsiasi domanda o problema puoi contattare il moderatore di questo gruppo scrivendo a cryomail-moderators at domeus.it. A presto, Il team di domeus.it -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: logo.gif Type: image/gif Size: 2422 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: corner.gif Type: image/gif Size: 1458 bytes Desc: not available URL: From team at domeus.it Fri May 21 13:28:15 2004 From: team at domeus.it (Team domeus) Date: Fri, 21 May 2004 15:28:15 +0200 (CEST) Subject: [EMBOSS] La tua cancellazione dal gruppo cryomail (Cancellazione MailingList avvenuta) Message-ID: <19242560.1085146095667.ecMessenger@domeus.it> Ciao emboss at embnet.org, la tua cancellazione dal gruppo cryomail at domeus.it ? avvenuta con successo. Da questo momento in poi non riceverai ulteriori messaggi dal gruppo. grazie per essere stato con noi.... lo sapevi che sul sito del cryogenteam trovi anche... ______________________________________________________ abbiamo lottato e vinto per la vita di safiya , ora stiamo lottando per per la vita di amina .. unisciti a noi, un form anonimo ti aspetta !! http://www.cryogenteam.com/safiya.htm calendario ribelle soft e hot del 2002 le ragazze del cryogenteam.com http://www.cryogenteam.com/calendario.htm sexy chat immagini in diretta chat sexy sexy videochat chat in html video chat videoconferenza video conferenza http://www.cryogenteam.com/chat.html - games & jokes - giochi e scherzi programmi gioco scherzi divertenti http://www.cryogenteam.com/game.htm loghi e suonerie per cellulari nokia ericsson motorola sagem siemens philips panasonic siemens creati il tuo logo personalizzato !! http://www.cryogenteam.com/loghisuonerie.htm software e utility programmi completi guide in italiano recensioni - manuali - software - guide - informazioni - consigli - programmi - giochi - satellite http://www.cryogenteam.com/software.htm free webcam - webcam in diretta dal web gratuite o gratis ragazze asiatiche in diretta regazze orientali in diretta cam http://www.cryogenteam.com/webcam.htm foto soft e hot - foto annunci - singoli coppie gay trans escort - totalmente amatoriali reali e gratuiti http://www.cryogenteam.com/animeribelli/ _________________________________________ _________________________________________ _________________________________________ _________________________________________ _________________________________________ A presto, Il team di domeus.it -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: logo.gif Type: image/gif Size: 2422 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: corner.gif Type: image/gif Size: 1458 bytes Desc: not available URL: From tnetkxflase at jomani.com.br Sun May 23 20:17:05 2004 From: tnetkxflase at jomani.com.br (Rubens F. Galutti) Date: Sun, 23 May 2004 17:17:05 -0300 Subject: [EMBOSS] Rendimento com Internet Message-ID: <20040523201700.56D257D1BC@mercury.hgmp.mrc.ac.uk> Procuramos Pessoas, Profissionais e Empres?rios, para Trabalho e Parceria de Neg?cios, com uso da Internet e de outras ferramentas. Pode ser feito em tempo parcial ou integral e com Altos Ganhos. Visite: http://www.hipernegocio.net Rubens F. Galutti WTRCorp - D?vidas pelo email wtrcorp at ibest.com.br Para ser removido de futuros correios, por favor, envie email para ngtcad at ibest.com.br, com o assunto REMOVER. Obrigado. From d.m.a.martin at dundee.ac.uk Mon May 24 15:46:33 2004 From: d.m.a.martin at dundee.ac.uk (David Martin) Date: Mon, 24 May 2004 16:46:33 +0100 Subject: [EMBOSS] 'Resources' in the emboss.default file Message-ID: I was browsing the ajnam.c code and noticed that there is what looks like a 'resource' type that can be defined in emboss.default. (causes namParseType to be set to TYPE_RESOURCE) What does this resource beast look like as I cannot find any documentation for it? My initial guess is that it looks like a database definition. Or am I barking up the wrong tree? -- David Martin PhD Post-Genomics and Molecular Interactions Centre University of Dundee ICQ: 337640638 From pmr at ebi.ac.uk Tue May 25 05:57:34 2004 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Tue, 25 May 2004 06:57:34 +0100 (BST) Subject: [EMBOSS] 'Resources' in the emboss.default file In-Reply-To: References: Message-ID: <1110.217.134.89.40.1085464654.squirrel@webmail.ebi.ac.uk> David, > I was browsing the ajnam.c code and noticed that there is what looks like > a > 'resource' type that can be defined in emboss.default. (causes > namParseType > to be set to TYPE_RESOURCE) What does this resource beast look like as I > cannot find any documentation for it? > > My initial guess is that it looks like a database definition. Pretty close! It looks like a database definition, but is intended to define "non-database resources". So far it has not been used, but I do have a blast wrapper submitted that will need this mechanism to define available blast databases, and have considered using it for other resources such as codon usage and genetic codes to make ACD files rather simpler. The definitions could be dynamic (seacrhing for files of a certain type and returning a list of files) or static (simply defining the list of allowed values). This reminds me I need to put some examples in before 3.0.0 :-) Any other suggestions welcome. regards, Peter Rice From asonyadi at cp.co.id Wed May 26 11:01:57 2004 From: asonyadi at cp.co.id (Sony) Date: Wed, 26 May 2004 07:01:57 -0400 Subject: [EMBOSS] Can not install emboss on mandrake 9.2 Message-ID: Dear friends I try to install emboss 2.8.0 on my mandrake 9.2, I have already done ./configure prefix=/usr/local/emboss/, make, make install, but after I modify bashrc with the following suggested code " PLPLOT_LIB=/site/prog/emboss/lib PATH=/site/prog/emboss/bin:\$PATH export PLPLOT_LIB PATH" then the command line can not recognized common command such as ls, cp, etc except cd. When I try to log out, I can not back to my x windows because mandrake system reject my username and password (before changing the bashrc the username and password are working properly). Does anyone know how to solve the problem? Do I have to change my distribution, once I have ever installed it in redhat 9, and it work properly without experiencing this case Thank you very much for help Sony Adi S From deejoe at iastate.edu Wed May 26 16:36:01 2004 From: deejoe at iastate.edu (D. Joe Anderson) Date: Wed, 26 May 2004 11:36:01 -0500 Subject: [EMBOSS] Can not install emboss on mandrake 9.2 In-Reply-To: References: Message-ID: <20040526163601.GK14459@iastate.edu> On Wed, May 26, 2004 at 07:01:57AM -0400, Sony wrote: > Dear friends > > I try to install emboss 2.8.0 on my mandrake 9.2, I have already done > ./configure prefix=/usr/local/emboss/, make, make install, but after I > modify bashrc with the following suggested code " > PLPLOT_LIB=/site/prog/emboss/lib PATH=/site/prog/emboss/bin:\$PATH export > PLPLOT_LIB PATH" then the command line can not recognized common command > such as ls, cp, etc except cd. Just for clarity, let's unwrap those commands onto one line per command: PLPLOT_LIB=/site/prog/emboss/lib PATH=/site/prog/emboss/bin:\$PATH export PLPLOT_LIB PATH Leave out the \ Instead of adding something to your PATH, you are obliterating your PATH and replacing it with directories that lack useful and necessary programs. With the \, the $ is escaped and not recognized as a special character. This keeps the $PATH variable from being interpreted and its value included. You want to include PATH's former value, as it tells the system where to find ls, cp, etc. It finds cd just fine because that is a command built-in to the bash shell. Also, you should not have to set the prefix, if ./configure's defaults are set right, it should put things in /usr/local. At that point, what you want to add to PATH is not /site/proc/emboss/bin but rather /usr/local/bin. You can set the PATH variable from the shell prompt. Doing so is a good way to test a PATH setting before committing it to a configuration file like bashrc For instance, if you manage to again get a shell prompt, issuing this command may restore your path to a useable state: export PATH=/bin:/sbin:/usr/bin:/usr/sbin you can then try issuing export PATH=/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/emboss/bin to see if you can execute any of the programs installed by your earlier invocation of "make install" > When I try to log out, I can not back to my > x windows because mandrake system reject my username and password (before > changing the bashrc the username and password are working properly). Which bashrc file did you modify? You are better off to modify the bashrc file in the home directory of a non-root account. For instance, if you have a regular user account called "sony" then this would be /home/sony/.bashrc or ~sony/.bashrc for short. Or, if you are logged-in as "sony" then this would be ~/.bashrc Once this file is modified to work properly, and if you need to make this change effective systemwide (for instance, if other people are to use this machine and you want them to be able to use the copy of emboss you have installed), then it might be appropriate to edit the system-wide copies in /etc Also, what account's do and don't work for you? If you have a regular user account that isn't working, you should be able to log in as the root user and make any changes. If what you have done have made it impossible for you to log in as root, then more drastic measures may be necessary. > Does anyone know how to solve the problem? You could try logging-in through a virtual terminal, instead of via X Windows. Hit Ctl-Alt-F1 to switch to a virtual terminal. Log in to the console window there and make any repairs necessary. When done, log out and switch back to X with Alt-F7. You could try booting into single-user mode, and to reverse your changes using that. You might try to boot the system with the Mandrake installation CD in rescue mode, and try to find the bashrc file you changed, and to change it back. It's been a while since I used Mandrake so I can't offer more detailed instructions. You might also try to choose GNOME or some other window manager from the X Windows login screen, instead of KDE. It might be that, with screwed-up dotfiles, KDE cannot find certain subdirectories in your home directory that it needs, and so login fails. > Do I have to change my > distribution, once I have ever installed it in redhat 9, and it work > properly without experiencing this case My guess is the success with redhat 9 was due more to happenstance than to any advantage emboss has on that distribution. So, I don't see that changing back to Redhat 9 would help per se. It might be that GNOME is more forgiving of dotfile configuration mishaps and that it therefore lets you log in via X Windows. You may find it easiest to re-install Mandrake (or any other distribution) but a change in distribution won't solve the basic difficulty, which seems to be an unfamiliarity with the basic system administration. You may be best to seek out local help with Linux basics. Linux.org shows 7 user groups in Indonesia: http://www.linux.org/groups/indonesia.html among which, this one ranks high in google: http://www.linux.or.id/ They may be better positioned to help you with answers and advice troubleshooting general problems like these with running X Windows, GNU software, and Linux. Regards, --Joe From tchiang at bioinfo.sickkids.on.ca Wed May 26 20:20:08 2004 From: tchiang at bioinfo.sickkids.on.ca (Ted Chiang) Date: Wed, 26 May 2004 16:20:08 -0400 (EDT) Subject: [EMBOSS] getorf question.. Message-ID: Hi, I'm using getorf as follows: $ getorf sequence.fasta -find 1 -noreverse -minsize 100 Among the results one of the ORFs I get is: MMSNSSSEIDVQEPNIVSDASCNTEEQLKTVDDVLIHCQVIYDALQNLDKKIDVIRRKVS KIQRFHARSLWTNHKRYGYKKHSYRLVKKLKLQKMKKNEVYETFSYPESYSPTLPVSRRE NNSPSNLPRPSFCMEEYQRAELEEDPILSRTPSPVHPSDFSEHNCQPYYASDGATYGSSS GLCLGNPRADSIHNTYSTDHASAAPPSVTRSPVENDGYIEEGSITKHPSTWSVEAVVLFL KQTDPLALCPLVDLFRSHEIDGKALLLLTSDVLLKHLGVKLGTAVKLCYYIDRLKQGKCF EN However, it does not give me a smaller ORF that begins with the marked '^' below: MMSNSSSEIDVQEPNIVSDASCNTEEQLKTVDDVLIHCQVIYDALQNLDKKIDVIRRKVS KIQRFHARSLWTNHKRYGYKKHSYRLVKKLKLQKMKKNEVYETFSYPESYSPTLPVSRRE ^ NNSPSNLPRPSFCMEEYQRAELEEDPILSRTPSPVHPSDFSEHNCQPYYASDGATYGSSS GLCLGNPRADSIHNTYSTDHASAAPPSVTRSPVENDGYIEEGSITKHPSTWSVEAVVLFL KQTDPLALCPLVDLFRSHEIDGKALLLLTSDVLLKHLGVKLGTAVKLCYYIDRLKQGKCF EN Is there a bug or am I missing something? The DNA input sequence is: >sequence.fasta ggtgtcgcgggagctctctgatccactcaggggtcagggcatcactggtctcgcgtgcgc gtgaccaggcccggtttccggtgccaggacctttccgaagcgtcgagtggcctaacggtc acagctgtcgcccatcggagaggcaggactactgcgagcagttttaccgcgacctccgga ggccggcgtgacaggctctgtcactaaaataggagtagaggtttaccactcttaggtgac taagcagtatcacaaataaaccctccagcaagtttaaaaataattaggtccaactcagag gaagtggagtttctcctgttgcacaaaaatgatgtctaacagctccagtgaaatcgatgt gcaggaaccgaatattgtatctgacgcatcctgtaatactgaagagcaactgaagacagt tgatgatgtccttattcattgccaggttatatatgatgctctgcaaaacctggataagaa gattgatgtgattcgtagaaaggtttcaaaaatccaacgtttccatgcgagatccctgtg gacaaatcataagcgatatggatataaaaagcattcttaccggcttgttaaaaagcttaa actccagaaaatgaagaaaaatgaggtttacgagacattctcctaccctgaaagttacag ccccactttaccagtgtcaaggcgtgagaataattccccgagcaaccttccaaggccatc cttttgcatggaagaataccagcgagctgagctggaggaggacccgatcctcagccgcac tccgagtccagtgcatccctcagatttctctgagcataattgtcagccgtattatgcatc tgatggtgcaacgtatggttcttcttcagggctctgccttggcaaccctcgggctgacag catccacaacacttactcaactgaccatgcttctgcagcaccaccttcagttacaaggtc accagttgaaaatgacggttacatagaggaaggaagcatcactaagcacccttcaacctg gtcggtggaagcagtggtcctatttctaaaacaaacagatcctcttgcattatgccctct tgtcgacctcttcagaagccatgaaattgacgggaaggctctgctcctactcacgagtga cgtgttgctgaagcacttgggggtgaagctgggaacggctgtgaagctatgctactacat tgaccgacttaaacaaggaaaatgctttgaaaattgaaaaaatccttgtgcaaatttaga ttgggccaacttctagaggcaccaatgccttcttagtgtggaatcatttttctgcccttt agtcgtttttgttttgtagaaagtatctctcaaaatatattatagctagaattgtagaac tatgttatagtccagtctacttctttaaaaaccatttaaactgctagatagtattagaat agtccaatagaaaattcattctttataggtctttaaaaattacttttattatattgttta caaatatatttcatgcaagaaacagaaaaaaaaaaaaccctttgattctggttcatctcg atacagagaaccaaaacagctaagagaggtattatcagggttgacaactcctatgattga atctatgggaattattcctcagaagagaatttaaaggtgtacccatatatatctctttct ggagtattttatctgtctgatgttgcagtattctacaagtttccagaaagagaatagcca tataaattattttcctttctgctattatttctctatatgttttatttattcagatttaga gtaaaaaataagcatataaacttttattatgtgctcttaacagttttaagataaactata ggatagatagaatggttattttatgcaagaaatattgtaccgcaagggtggtttggatga agtctgactactttttttcaaacaaactattatattaaaactgtcatattttggctaagt ttggacctataactacactttcattgtttgcatctctctatgaagatacgtctgtccaaa cttttaaaaggcataactgtattttatgtgtttattctttatatagatagtattttatat tttattctcacccgaagtattcacacaatctttttaaaaaaaatttgaaatggcattttg tattgccacagaggtaggatgagccatatattagtgaaatgttttattttgtaaaatata aatggattatttgccatcattagtacctctcaacttactttttagaggacaagaaacaat ctgtagattggtttccatacagggaagttctccgtcctatgcaatgtttctaattaattt gcttaattctgagccattaatcctgctacactttgaatgatacattaattcagactaatc tttgggggctttattttgtaagttagaactttcaagggaaacatgttcaacactattatt ttgttataaatttataactttgttattacattgtgtaacaaatataaggtttacgagcta tgagaattggtgctatcaccattagctatttgctgtaatgtcaagaaaatgttcaccaga tgcaagaatgtaccttttctttttagaaagccaaatgtactttagacatgaatgcaacta tttaaagaatagcttcatcaatgttattccttacatgtcataagattcttacttaaactt ggtcttctttcaaattgtttgtatgaagatgctgtacccacttgaacagtcctcaggtgt ttacataaatactatgttttacagttttcatattttaaaatattaataaagttaaatcac aatagttcaaaaaaaaaaaaaaaa -Ted =================================== Ted Chiang, Analyst Centre for Computational Biology Hospital for Sick Children, Toronto t: 416.813.7028 e: tchiang at sickkids.ca =================================== From gbottu at ben.vub.ac.be Thu May 27 07:52:19 2004 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Thu, 27 May 2004 09:52:19 +0200 Subject: [EMBOSS] getorf question.. In-Reply-To: References: Message-ID: <20040527075219.GA22818@bigben.ulb.ac.be> Dear Ted, It is the "logic" of the algorithm. getorf defines an ORF as a region that : - begins with a start codon - ends with a stop codon - has inside no stop codon (but can have start codons) In translation it will give an as long as possible protein. It does not give a set of proteins that overlap at the COOH-end and where the start methionine of one is an internal methionine of another. Guy Bottu, Belgian EMBnet Node From akira.onozuka at shionogi.co.jp Fri May 28 02:15:05 2004 From: akira.onozuka at shionogi.co.jp (Akira Onozuka) Date: Fri, 28 May 2004 11:15:05 +0900 Subject: [EMBOSS] Can't connect internal SRSWWW ver7 Message-ID: Dear EMBOSS users I would like to ask a very primitive question. I installed EMBOSS 2.8 on linux environment and we have SRSWWW internally on other host machine without proxy configuration. Our emboss.default file is vary simple as follows. ############## DB GENBANK [ type: N method: srswww format: genbank url: http://hostname:8080/srs71bin/cgi-bin/wgetz dbalias: GENBANK fields: "sv des org key" comment: "Genbank IDs" ] ############# But, when I typed seqret -sequence DDBJ:AB001611 -outseq AB001611.fasta -osformat fasta machine returns Reads and writes (returns) sequences Error: failed to open filename 'DDBJ' Error: Unable to read sequence 'DDBJ:AB001611' Died: seqret terminated: Bad value for '-sequence' and no prompt I can't specify which process has the issue for connecting with SRS. If we tried to jump to internet SRSWWW , we need proxy with user authentication, so it is difficult to verify with other outer resources in current EMBOSS version. The possibility could be (1)EMBOSS can't recognize SRS7?? (2)Some configuration trouble in emboss.default file and others....... But anyway, I would like to know which process has the issue for retrieving sequence from SRSWWW. How can I see that?? Any suggestions will be highly welcomed. Regards, Akira Onozuka ##################################################### Shionogi & Co., Ltd 12-4, Sagisu 5-chome, Fukushima-ku, Osaka 553-0002, Japan Sr.Research Scientist TEL:+81-6-6455-2015??FAX :+81-6-6455-2066 E-mail akira.onozuka at shionogi.co.jp ##################################################### From David.Bauer at schering.de Fri May 28 07:45:23 2004 From: David.Bauer at schering.de (David.Bauer at schering.de) Date: Fri, 28 May 2004 09:45:23 +0200 Subject: Antwort: [EMBOSS] Can't connect internal SRSWWW ver7 Message-ID: Hello Akira, one answer and one more question (I guess Peter is listening :-) In your emboss.default the database name is GENBANK. (DB GENBANK) So you must use GENBANK:AB001611 to get the sequence. The dbalias specifies the name of the database within SRS. This is used to formulate the wgetz request. If you want to query more than one database you can put the list in this place. In SRS GenBank and RefSeq are separate databases. So I use dbalias: "{genbank%20refseq}" If it still does not work use -debug. Seqret (like all other emboss programs) then writes a file seqret.dbg which contains the complete communication log of seqret with the srs server. Hope this helps, David. And now my question to Peter: I would like to use in fields also the GI number. In ajsrsdb I see queries for sv, org, des etc. But even if I specify this in fields of emboss.default the SRS request is only for ID and ACC. So what to do, if I want to be able to retrieve by SV ? Dear EMBOSS users I would like to ask a very primitive question. I installed EMBOSS 2.8 on linux environment and we have SRSWWW internally on other host machine without proxy configuration. Our emboss.default file is vary simple as follows. ############## DB GENBANK [ type: N method: srswww format: genbank url: http://hostname:8080/srs71bin/cgi-bin/wgetz dbalias: GENBANK fields: "sv des org key" comment: "Genbank IDs" ] ############# But, when I typed seqret -sequence DDBJ:AB001611 -outseq AB001611.fasta -osformat fasta machine returns Reads and writes (returns) sequences Error: failed to open filename 'DDBJ' Error: Unable to read sequence 'DDBJ:AB001611' Died: seqret terminated: Bad value for '-sequence' and no prompt I can't specify which process has the issue for connecting with SRS. If we tried to jump to internet SRSWWW , we need proxy with user authentication, so it is difficult to verify with other outer resources in current EMBOSS version. The possibility could be (1)EMBOSS can't recognize SRS7?? (2)Some configuration trouble in emboss.default file and others....... But anyway, I would like to know which process has the issue for retrieving sequence from SRSWWW. How can I see that?? Any suggestions will be highly welcomed. Regards, Akira Onozuka ##################################################### Shionogi & Co., Ltd 12-4, Sagisu 5-chome, Fukushima-ku, Osaka 553-0002, Japan Sr.Research Scientist TEL:+81-6-6455-2015??FAX :+81-6-6455-2066 E-mail akira.onozuka at shionogi.co.jp ##################################################### From idrummon at receptor.mgh.harvard.edu Fri May 28 19:58:18 2004 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Fri, 28 May 2004 15:58:18 -0400 Subject: [EMBOSS] size limits on extractseq? Message-ID: Is there an upper limit on the file size that extractseq can handle? I run into a problem using extractseq to get segments out of mouse chromosome files. It will only access the first 19.7 MB or so of a 185 MB file. The files are fasta files of the mouse genome build 32 from NCBI. Here is what the problem looks like: (real file sizes are ls'd below) $ extractseq Extract regions from a sequence Input sequence: mm_chr1.fa Regions to extract (eg: 4-57,78-94) [1-19589943]: $ extractseq Extract regions from a sequence Input sequence: mm_chr2.fa Regions to extract (eg: 4-57,78-94) [1-19704910]: $ ls -l total 3782918 -rw-r--r-- 1 nobody nobody 200460727 May 25 23:56 mm_chr1.fa -rw-r--r-- 1 nobody nobody 135604265 May 26 15:16 mm_chr10.fa -rw-r--r-- 1 nobody nobody 123799904 May 26 15:17 mm_chr11.fa -rw-r--r-- 1 nobody nobody 120032577 May 26 15:19 mm_chr12.fa -rw-r--r-- 1 nobody nobody 119608375 May 26 15:20 mm_chr13.fa -rw-r--r-- 1 nobody nobody 185168052 May 26 14:28 mm_chr2.fa -- Iain Drummond, Ph.D. Assistant Professor Department of Medicine, Harvard Medical School and Renal Unit, Massachusetts General Hospital Mailing address: Renal Unit / MGH 149-8000 149 13th St. Charlestown, MA 02129 Tel: 617 726 5647 Fax: 617 726 5669 idrummond at partners.org idrummon at receptor.mgh.harvard.edu Lab Home Page: http://danio.mgh.harvard.edu From w2hgcg at netscape.net Mon May 31 10:49:37 2004 From: w2hgcg at netscape.net (w2hgcg at netscape.net) Date: Mon, 31 May 2004 06:49:37 -0400 Subject: [EMBOSS] ontology for emboss Message-ID: <6AD3D204.3BCDE0D5.000665E2@netscape.net> >From reading the Project meeting file corresponding to the 12th of December I noticed a mention to an ontology for emboss, I would like to know if there is such an ontology, and if so from where can I download it, cheers. __________________________________________________________________ Introducing the New Netscape Internet Service. Only $9.95 a month -- Sign up today at http://isp.netscape.com/register Netscape. Just the Net You Need. New! Netscape Toolbar for Internet Explorer Search from anywhere on the Web and block those annoying pop-ups. Download now at http://channels.netscape.com/ns/search/install.jsp From idrummon at receptor.mgh.harvard.edu Mon May 31 12:18:50 2004 From: idrummon at receptor.mgh.harvard.edu (Iain Drummond) Date: Mon, 31 May 2004 08:18:50 -0400 Subject: [EMBOSS] SUMMARY: size limits on extractseq? In-Reply-To: <1085978250.40bab68a704f1@webmail.utm.utoronto.ca> Message-ID: This turned out to be operator error. extractseq works fine on large files. The NCBI mouse chromosome files are actually a collection of contigs; extractseq looks only at the first file. Both comments from Clinton and Peter are on the mark; the problem was the sequence file. -- Iain Drummond, Ph.D. Assistant Professor Department of Medicine, Harvard Medical School and Renal Unit, Massachusetts General Hospital Mailing address: Renal Unit / MGH 149-8000 149 13th St. Charlestown, MA 02129 Tel: 617 726 5647 Fax: 617 726 5669 idrummond at partners.org idrummon at receptor.mgh.harvard.edu Lab Home Page: http://danio.mgh.harvard.edu > From: Clinton Fernandes > Reply-To: clintonf at interchange.ubc.ca > Date: Sun, 30 May 2004 21:37:30 -0700 > To: Iain Drummond > Subject: Re: [EMBOSS] size limits on extractseq? > > It may be the source of the file. > > I have experienced difficulty sometimes saving a file in a Windows environment > and working with the file in a Linux environment. While I obviously don't know > the specifics of your environment, this may be something you haven't > considered. > > I never had a problem with extractseq, but what I was experiencing seemed > somewhat similar to your problem. A sequence I downloaded from the internet > had > invisible characters that dos2unix did not remove. This resulted in some very > quirky behaviour in an extraction program that I had coded. I had to copy the > sequence to the clipboard and paste it into a text editor in my Linux machine. > > Again, what I have described may be completely left-field to what you are > experiencing, but it may bear looking into if the situations are similar. > > -- > Clinton Fernandes > Bioinformatician > UBC, Dept. of Microbiology > Wesbrook Bldg, Room 224 > 6174 University Blvd, > Vancouver, BC, Canada > > (604) 827-5160 > e-mail: clintonf at interchange.ubc.ca > > > Quoting Iain Drummond : > >> Is there an upper limit on the file size that extractseq can handle? >> >> I run into a problem using extractseq to get segments out of mouse >> chromosome files. It will only access the first 19.7 MB or so of a 185 MB >> file. The files are fasta files of the mouse genome build 32 from NCBI. Here >> is what the problem looks like: (real file sizes are ls'd below) >> >> $ extractseq >> Extract regions from a sequence >> Input sequence: mm_chr1.fa >> Regions to extract (eg: 4-57,78-94) [1-19589943]: >> >> $ extractseq >> Extract regions from a sequence >> Input sequence: mm_chr2.fa >> Regions to extract (eg: 4-57,78-94) [1-19704910]: >> >> $ ls -l >> total 3782918 >> -rw-r--r-- 1 nobody nobody 200460727 May 25 23:56 mm_chr1.fa >> -rw-r--r-- 1 nobody nobody 135604265 May 26 15:16 mm_chr10.fa >> -rw-r--r-- 1 nobody nobody 123799904 May 26 15:17 mm_chr11.fa >> -rw-r--r-- 1 nobody nobody 120032577 May 26 15:19 mm_chr12.fa >> -rw-r--r-- 1 nobody nobody 119608375 May 26 15:20 mm_chr13.fa >> -rw-r--r-- 1 nobody nobody 185168052 May 26 14:28 mm_chr2.fa >> >> -- >> >> Iain Drummond, Ph.D. >> Assistant Professor >> Department of Medicine, Harvard Medical School and >> Renal Unit, Massachusetts General Hospital >> >> Mailing address: >> Renal Unit / MGH 149-8000 >> 149 13th St. >> Charlestown, MA 02129 >> >> Tel: 617 726 5647 >> Fax: 617 726 5669 >> >> idrummond at partners.org >> idrummon at receptor.mgh.harvard.edu >> >> Lab Home Page: >> http://danio.mgh.harvard.edu >> >> >> >