From njoly at pasteur.fr Mon Jan 5 05:34:05 2004 From: njoly at pasteur.fr (Nicolas Joly) Date: Mon, 5 Jan 2004 11:34:05 +0100 Subject: EMBOSS port for amd64 Message-ID: <20040105103405.GA403395@medusa.sis.pasteur.fr> Hi, I just tried EMBOSS on a bi-Opteron (amd64) machine running NetBSD (-current), and noticed that it does not work. EMBOSS 2.8.0 compilation is fine, but programs don't work : njoly at calimero [~/EMBOSS-2.8.0]> ./emboss/revseq -help zsh: segmentation fault (core dumped) ./emboss/revseq -help AMD64 platforms suffers from the `va_{start,args,end}' problem already known on PPC machines (at least with gcc). With the attached patch, all programs work as expected. njoly at calimero [~]> uname -a NetBSD calimero.sis.pasteur.fr 1.6ZG NetBSD 1.6ZG (GENERIC.MP) #13: Wed Dec 31 16:41:18 CET 2003 njoly at calimero.sis.pasteur.fr:/local/src/NetBSD/obj/amd64/sys/arch/amd64/compile/GENERIC.MP amd64 Thanks in advance. Regards. -- Nicolas Joly Biological Software and Databanks. Institut Pasteur, Paris. -------------- next part -------------- Index: ajax/ajfmt.c =================================================================== RCS file: /home/repository/emboss/emboss/emboss/ajax/ajfmt.c,v retrieving revision 1.30 diff -u -r1.30 ajfmt.c --- ajax/ajfmt.c 2003/10/16 18:06:12 1.30 +++ ajax/ajfmt.c 2003/12/31 16:58:53 @@ -1411,7 +1411,7 @@ AjPStr ajFmtStr(const char* fmt, ...) { va_list ap; -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) va_list save_ap; #endif ajint len = 32; @@ -1420,13 +1420,13 @@ fnew = ajStrNewL(len); va_start(ap, fmt); -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) __va_copy(save_ap, ap); #endif fnew->Len = ajFmtVfmtStrCL(&fnew->Ptr, 0, &fnew->Res, fmt, ap); -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) __va_copy(ap, save_ap); #endif @@ -1462,7 +1462,7 @@ AjPStr thys; va_list ap; -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) va_list save_ap; #endif @@ -1471,7 +1471,7 @@ ajStrModL(pthis, 32); thys = *pthis; -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) __va_copy(save_ap, ap); #endif @@ -1542,7 +1542,7 @@ { AjPStr thys; va_list ap; -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) va_list save_ap; #endif ajint len; @@ -1552,7 +1552,7 @@ ajStrModL(pthis, 32); thys = *pthis; -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) __va_copy(save_ap, ap); #endif @@ -2045,19 +2045,19 @@ { va_list ap; ajint n; -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) va_list save_ap; #endif va_start(ap, fmt); -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) __va_copy(save_ap,ap); #endif n = fmtVscan(thys->Ptr,fmt,ap); -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) __va_copy(ap,save_ap); #endif @@ -2086,19 +2086,19 @@ { va_list ap; ajint n; -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) va_list save_ap; #endif va_start(ap, fmt); -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) __va_copy(save_ap,ap); #endif n = fmtVscan(thys,fmt,ap); -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) __va_copy(ap,save_ap); #endif Index: ajax/ajfmt.h =================================================================== RCS file: /home/repository/emboss/emboss/emboss/ajax/ajfmt.h,v retrieving revision 1.10 diff -u -r1.10 ajfmt.h --- ajax/ajfmt.h 2003/08/07 11:07:45 1.10 +++ ajax/ajfmt.h 2003/12/31 16:58:53 @@ -10,7 +10,7 @@ #include #include "ajexcept.h" -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) #define VALIST va_list #define VA_P(x) (x) #define VA_V(x) (x) From ableasby at hgmp.mrc.ac.uk Mon Jan 5 09:11:32 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Mon, 5 Jan 2004 14:11:32 GMT Subject: EMBOSS port for amd64 Message-ID: <200401051411.i05EBWED029672@bromine.hgmp.mrc.ac.uk> Thanks for that Nicolas. We have no way of checking that here at the moment but I've made the changes you suggested in CVS. If you try the CVS version at some stage and find there are problems then please let me know. If anyone is running amd64 with a non-gcc compiler I'd be glad to hear from them too. Alan From d.counsell at rfcgr.mrc.ac.uk Fri Jan 16 09:53:48 2004 From: d.counsell at rfcgr.mrc.ac.uk (Damian Counsell) Date: Fri, 16 Jan 2004 14:53:48 +0000 Subject: Writing The Matrix Message-ID: <20040116145348.GB11486@dev4.hgmp.mrc.ac.uk> EMBOSSnians! Would it be possible to have some functions in AJAX to write scoring matrices as well as to read them ajMatrixRead --> ajMatrixWrite ajMatrixfRead --> ajMatrixfWrite ? I am going to be generating a *lot* of pair potential-based scoring matrices. all the best Damian -- MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK phone: +44 (0)1223 494585 fax: +44 (0)1223 494512 email: d.counsell at hgmp.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk/~dcounsel/ From pmr at ebi.ac.uk Fri Jan 16 12:33:52 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 16 Jan 2004 17:33:52 +0000 Subject: Writing The Matrix In-Reply-To: <20040116145348.GB11486@dev4.hgmp.mrc.ac.uk> References: <20040116145348.GB11486@dev4.hgmp.mrc.ac.uk> Message-ID: <40082080.70305@ebi.ac.uk> Damian Counsell wrote: > EMBOSSnians! > > > Would it be possible to have some functions in AJAX to write scoring > matrices as well as to read them > > ajMatrixRead --> ajMatrixWrite > ajMatrixfRead --> ajMatrixfWrite > > ? I am going to be generating a *lot* of pair potential-based scoring > matrices. Will do. It will need a new ACD output type (better than a simple outfile as then we can play with formats). I need to do something similar for Phylip 3.6 output files. I will add them at the same time. Would anyone like nexus matrix output format? Peter From emailfrom1 at yahoo.co.uk Fri Jan 16 19:09:54 2004 From: emailfrom1 at yahoo.co.uk (Email) Date: Fri, 16 Jan 2004 19:09:54 Subject: Marketing Message-ID: <20040116180838.9C4517D8A8@mercury.hgmp.mrc.ac.uk> To my family, friends & business colleagues, If you are looking to send thousands of emails to people either in the UK and abroad, in order to promote your Internet business, don't waste your time searching the net for suitable companies, as many of them are a complete waste of time and money. I have found one that does what it says it does! To find out more, go to: http://uk.geocities.com/emailmrketmd Regards John From emailfrom1 at yahoo.co.uk Wed Jan 21 19:16:25 2004 From: emailfrom1 at yahoo.co.uk (Email) Date: Wed, 21 Jan 2004 19:16:25 Subject: Addresses Message-ID: <20040121181545.543B47D1D0@mercury.hgmp.mrc.ac.uk> To my family, friends & business colleagues, If you are looking to send thousands of emails to people either in the UK and abroad, in order to promote your Internet business, don't waste your time searching the net for suitable companies, as many of them are a complete waste of time and money. I have found one that does what it says it does! To find out more, go to: http://uk.geocities.com/emailbusiness1 Regards John From hegedus at biomembrane.hu Wed Jan 21 12:54:33 2004 From: hegedus at biomembrane.hu (Tamas Hegedus) Date: Wed, 21 Jan 2004 18:54:33 +0100 (CET) Subject: ExternalMethodQuery Message-ID: Dear All, I have set up a DB in emboss.default as external, fasta format, accessing a MySQL database with my script. It is working fine if I want to retrieve one sequence (DB:feh_human). If I want to query more sequences ("DB:feh_*"), there is nothing (no sequences, no prompt). Since my program working fine if I run it 'stand alone' (connectorom feh_*; not "DB:feh_*"), I think I miss some important information for usage the methodquery, for writing external application returning with more sequences: eg. what is the separator for EMBOSS between sequences. Thanks for your help and suggetion, Tamas -- Tamas Hegedus, Research Fellow | phone: 480-301-6041 Mayo Clinic Scottsdale | fax: 480-301-7017 13000 East Shea Blvd | mailto:hegedus at biomembrane.hu Scottsdale, AZ, 85259 | http://www.biomembrane.hu/~hegedus From shay at bioinfo.sickkids.on.ca Thu Jan 22 15:40:08 2004 From: shay at bioinfo.sickkids.on.ca (Shayanthan Parameswaran) Date: Thu, 22 Jan 2004 15:40:08 -0500 Subject: Compiling a single program in EMBOSS Message-ID: <40103528.1010406@bioinfo.sickkids.on.ca> To the developers, We would like to know if it is possible to compile / recompile a single program in EMBOSS without having to recompile EMBOSS each time. The specific program is palindrome. Can this only be done by modifying the Makefile (which seems a little complex) or is there is simpler way? Thanks. Shay -- Shayanthan Parameswaran Centre for Computational Biology email: shay at bioinfo.sickkids.on.ca The Hospital for Sick Children From ableasby at hgmp.mrc.ac.uk Thu Jan 22 16:06:47 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Thu, 22 Jan 2004 21:06:47 GMT Subject: Compiling a single program in EMBOSS Message-ID: <200401222106.i0ML6lrl016936@bromine.hgmp.mrc.ac.uk> Shay, It is possible if you work from the CVS version of EMBOSS. You will need the latest versions of the GNU tools: autoconf automake libtool (unless you use MacOSX which has a modified libtool ... in that case just replace the ltmain.sh files from CVS with the OSX version) Instructions for using the CVS version are on the EMBOSS web pages. HTH Alan From d.counsell at rfcgr.mrc.ac.uk Fri Jan 23 12:18:02 2004 From: d.counsell at rfcgr.mrc.ac.uk (Damian Counsell) Date: Fri, 23 Jan 2004 17:18:02 +0000 Subject: $28K for an EMBOSS installation ;-) Message-ID: <20040123171802.GD23667@dev4.hgmp.mrc.ac.uk> http://www.apple.com/xserve/cluster/wgcluster.html -- MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK phone: +44 (0)1223 494585 fax: +44 (0)1223 494512 email: d.counsell at hgmp.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk/~dcounsel/ From Mailer-Daemon at bba.de Thu Jan 29 18:52:49 2004 From: Mailer-Daemon at bba.de (Mailer-Daemon at bba.de) Date: Fri, 30 Jan 2004 00:52:49 +0100 (CET) Subject: BENACHRICHTIGUNG ZUR MAIL ZUSTELLUNG Message-ID: <200401292352.i0TNqn410283@styx.bba.de> Sehr geehrter Internet Email Benutzer, dies ist eine automatisierte Benachrichtung zur Mailzustellung, da Ihre Email nicht auf die gewohnte Art und Weise zugestellt werden konnte. Es ist folgendes Problem aufgetreten: In dieser Mail wurde ein Virus mit folgender Kennung gefunden: >>> Virus 'W32/MyDoom-A' Mit freundlichen Gruessen, Ihr GeNUGate Mail-Gateway. =========================================================== In English =========================================================== Dear Internet Email User, this is an automated mail delivery notification, because your email has not been delivered the usual way. Your mail was not deliverd for the following reason: This mail contained a virus with the following Virus-Id: >>> Virus 'W32/MyDoom-A' Best regards, Your GeNUGate Mail Gateway ========================================================= ENVELOPE INFORMATION ========================================================= FROM = emboss-dev at embnet.org RCPT = fred at bba.de ========================================================= HEADER INFORMATION ========================================================= Received: from embnet.org (137.122.147.102) by (smtprelay) with ESMTP Fri Jan 30 00:52:38 2004. From: emboss-dev at embnet.org To: fred at bba.de Subject: Test Date: Thu, 29 Jan 2004 19:05:21 -0500 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0009_E76BBF7B.70DC1211" X-Priority: 3 X-MSMail-Priority: Normal ========================================================= From njoly at pasteur.fr Mon Jan 5 10:34:05 2004 From: njoly at pasteur.fr (Nicolas Joly) Date: Mon, 5 Jan 2004 11:34:05 +0100 Subject: EMBOSS port for amd64 Message-ID: <20040105103405.GA403395@medusa.sis.pasteur.fr> Hi, I just tried EMBOSS on a bi-Opteron (amd64) machine running NetBSD (-current), and noticed that it does not work. EMBOSS 2.8.0 compilation is fine, but programs don't work : njoly at calimero [~/EMBOSS-2.8.0]> ./emboss/revseq -help zsh: segmentation fault (core dumped) ./emboss/revseq -help AMD64 platforms suffers from the `va_{start,args,end}' problem already known on PPC machines (at least with gcc). With the attached patch, all programs work as expected. njoly at calimero [~]> uname -a NetBSD calimero.sis.pasteur.fr 1.6ZG NetBSD 1.6ZG (GENERIC.MP) #13: Wed Dec 31 16:41:18 CET 2003 njoly at calimero.sis.pasteur.fr:/local/src/NetBSD/obj/amd64/sys/arch/amd64/compile/GENERIC.MP amd64 Thanks in advance. Regards. -- Nicolas Joly Biological Software and Databanks. Institut Pasteur, Paris. -------------- next part -------------- Index: ajax/ajfmt.c =================================================================== RCS file: /home/repository/emboss/emboss/emboss/ajax/ajfmt.c,v retrieving revision 1.30 diff -u -r1.30 ajfmt.c --- ajax/ajfmt.c 2003/10/16 18:06:12 1.30 +++ ajax/ajfmt.c 2003/12/31 16:58:53 @@ -1411,7 +1411,7 @@ AjPStr ajFmtStr(const char* fmt, ...) { va_list ap; -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) va_list save_ap; #endif ajint len = 32; @@ -1420,13 +1420,13 @@ fnew = ajStrNewL(len); va_start(ap, fmt); -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) __va_copy(save_ap, ap); #endif fnew->Len = ajFmtVfmtStrCL(&fnew->Ptr, 0, &fnew->Res, fmt, ap); -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) __va_copy(ap, save_ap); #endif @@ -1462,7 +1462,7 @@ AjPStr thys; va_list ap; -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) va_list save_ap; #endif @@ -1471,7 +1471,7 @@ ajStrModL(pthis, 32); thys = *pthis; -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) __va_copy(save_ap, ap); #endif @@ -1542,7 +1542,7 @@ { AjPStr thys; va_list ap; -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) va_list save_ap; #endif ajint len; @@ -1552,7 +1552,7 @@ ajStrModL(pthis, 32); thys = *pthis; -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) __va_copy(save_ap, ap); #endif @@ -2045,19 +2045,19 @@ { va_list ap; ajint n; -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) va_list save_ap; #endif va_start(ap, fmt); -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) __va_copy(save_ap,ap); #endif n = fmtVscan(thys->Ptr,fmt,ap); -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) __va_copy(ap,save_ap); #endif @@ -2086,19 +2086,19 @@ { va_list ap; ajint n; -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) va_list save_ap; #endif va_start(ap, fmt); -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) __va_copy(save_ap,ap); #endif n = fmtVscan(thys,fmt,ap); -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) __va_copy(ap,save_ap); #endif Index: ajax/ajfmt.h =================================================================== RCS file: /home/repository/emboss/emboss/emboss/ajax/ajfmt.h,v retrieving revision 1.10 diff -u -r1.10 ajfmt.h --- ajax/ajfmt.h 2003/08/07 11:07:45 1.10 +++ ajax/ajfmt.h 2003/12/31 16:58:53 @@ -10,7 +10,7 @@ #include #include "ajexcept.h" -#if defined(__PPC__) && defined(_CALL_SYSV) +#if defined(__amd64__) || (defined(__PPC__) && defined(_CALL_SYSV)) #define VALIST va_list #define VA_P(x) (x) #define VA_V(x) (x) From ableasby at hgmp.mrc.ac.uk Mon Jan 5 14:11:32 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Mon, 5 Jan 2004 14:11:32 GMT Subject: EMBOSS port for amd64 Message-ID: <200401051411.i05EBWED029672@bromine.hgmp.mrc.ac.uk> Thanks for that Nicolas. We have no way of checking that here at the moment but I've made the changes you suggested in CVS. If you try the CVS version at some stage and find there are problems then please let me know. If anyone is running amd64 with a non-gcc compiler I'd be glad to hear from them too. Alan From d.counsell at rfcgr.mrc.ac.uk Fri Jan 16 14:53:48 2004 From: d.counsell at rfcgr.mrc.ac.uk (Damian Counsell) Date: Fri, 16 Jan 2004 14:53:48 +0000 Subject: Writing The Matrix Message-ID: <20040116145348.GB11486@dev4.hgmp.mrc.ac.uk> EMBOSSnians! Would it be possible to have some functions in AJAX to write scoring matrices as well as to read them ajMatrixRead --> ajMatrixWrite ajMatrixfRead --> ajMatrixfWrite ? I am going to be generating a *lot* of pair potential-based scoring matrices. all the best Damian -- MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK phone: +44 (0)1223 494585 fax: +44 (0)1223 494512 email: d.counsell at hgmp.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk/~dcounsel/ From pmr at ebi.ac.uk Fri Jan 16 17:33:52 2004 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 16 Jan 2004 17:33:52 +0000 Subject: Writing The Matrix In-Reply-To: <20040116145348.GB11486@dev4.hgmp.mrc.ac.uk> References: <20040116145348.GB11486@dev4.hgmp.mrc.ac.uk> Message-ID: <40082080.70305@ebi.ac.uk> Damian Counsell wrote: > EMBOSSnians! > > > Would it be possible to have some functions in AJAX to write scoring > matrices as well as to read them > > ajMatrixRead --> ajMatrixWrite > ajMatrixfRead --> ajMatrixfWrite > > ? I am going to be generating a *lot* of pair potential-based scoring > matrices. Will do. It will need a new ACD output type (better than a simple outfile as then we can play with formats). I need to do something similar for Phylip 3.6 output files. I will add them at the same time. Would anyone like nexus matrix output format? Peter From emailfrom1 at yahoo.co.uk Fri Jan 16 19:09:54 2004 From: emailfrom1 at yahoo.co.uk (Email) Date: Fri, 16 Jan 2004 19:09:54 Subject: Marketing Message-ID: <20040116180838.9C4517D8A8@mercury.hgmp.mrc.ac.uk> To my family, friends & business colleagues, If you are looking to send thousands of emails to people either in the UK and abroad, in order to promote your Internet business, don't waste your time searching the net for suitable companies, as many of them are a complete waste of time and money. I have found one that does what it says it does! To find out more, go to: http://uk.geocities.com/emailmrketmd Regards John From emailfrom1 at yahoo.co.uk Wed Jan 21 19:16:25 2004 From: emailfrom1 at yahoo.co.uk (Email) Date: Wed, 21 Jan 2004 19:16:25 Subject: Addresses Message-ID: <20040121181545.543B47D1D0@mercury.hgmp.mrc.ac.uk> To my family, friends & business colleagues, If you are looking to send thousands of emails to people either in the UK and abroad, in order to promote your Internet business, don't waste your time searching the net for suitable companies, as many of them are a complete waste of time and money. I have found one that does what it says it does! To find out more, go to: http://uk.geocities.com/emailbusiness1 Regards John From hegedus at biomembrane.hu Wed Jan 21 17:54:33 2004 From: hegedus at biomembrane.hu (Tamas Hegedus) Date: Wed, 21 Jan 2004 18:54:33 +0100 (CET) Subject: ExternalMethodQuery Message-ID: Dear All, I have set up a DB in emboss.default as external, fasta format, accessing a MySQL database with my script. It is working fine if I want to retrieve one sequence (DB:feh_human). If I want to query more sequences ("DB:feh_*"), there is nothing (no sequences, no prompt). Since my program working fine if I run it 'stand alone' (connectorom feh_*; not "DB:feh_*"), I think I miss some important information for usage the methodquery, for writing external application returning with more sequences: eg. what is the separator for EMBOSS between sequences. Thanks for your help and suggetion, Tamas -- Tamas Hegedus, Research Fellow | phone: 480-301-6041 Mayo Clinic Scottsdale | fax: 480-301-7017 13000 East Shea Blvd | mailto:hegedus at biomembrane.hu Scottsdale, AZ, 85259 | http://www.biomembrane.hu/~hegedus From shay at bioinfo.sickkids.on.ca Thu Jan 22 20:40:08 2004 From: shay at bioinfo.sickkids.on.ca (Shayanthan Parameswaran) Date: Thu, 22 Jan 2004 15:40:08 -0500 Subject: Compiling a single program in EMBOSS Message-ID: <40103528.1010406@bioinfo.sickkids.on.ca> To the developers, We would like to know if it is possible to compile / recompile a single program in EMBOSS without having to recompile EMBOSS each time. The specific program is palindrome. Can this only be done by modifying the Makefile (which seems a little complex) or is there is simpler way? Thanks. Shay -- Shayanthan Parameswaran Centre for Computational Biology email: shay at bioinfo.sickkids.on.ca The Hospital for Sick Children From ableasby at hgmp.mrc.ac.uk Thu Jan 22 21:06:47 2004 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Thu, 22 Jan 2004 21:06:47 GMT Subject: Compiling a single program in EMBOSS Message-ID: <200401222106.i0ML6lrl016936@bromine.hgmp.mrc.ac.uk> Shay, It is possible if you work from the CVS version of EMBOSS. You will need the latest versions of the GNU tools: autoconf automake libtool (unless you use MacOSX which has a modified libtool ... in that case just replace the ltmain.sh files from CVS with the OSX version) Instructions for using the CVS version are on the EMBOSS web pages. HTH Alan From d.counsell at rfcgr.mrc.ac.uk Fri Jan 23 17:18:02 2004 From: d.counsell at rfcgr.mrc.ac.uk (Damian Counsell) Date: Fri, 23 Jan 2004 17:18:02 +0000 Subject: $28K for an EMBOSS installation ;-) Message-ID: <20040123171802.GD23667@dev4.hgmp.mrc.ac.uk> http://www.apple.com/xserve/cluster/wgcluster.html -- MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK phone: +44 (0)1223 494585 fax: +44 (0)1223 494512 email: d.counsell at hgmp.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk/~dcounsel/ From Mailer-Daemon at bba.de Thu Jan 29 23:52:49 2004 From: Mailer-Daemon at bba.de (Mailer-Daemon at bba.de) Date: Fri, 30 Jan 2004 00:52:49 +0100 (CET) Subject: BENACHRICHTIGUNG ZUR MAIL ZUSTELLUNG Message-ID: <200401292352.i0TNqn410283@styx.bba.de> Sehr geehrter Internet Email Benutzer, dies ist eine automatisierte Benachrichtung zur Mailzustellung, da Ihre Email nicht auf die gewohnte Art und Weise zugestellt werden konnte. Es ist folgendes Problem aufgetreten: In dieser Mail wurde ein Virus mit folgender Kennung gefunden: >>> Virus 'W32/MyDoom-A' Mit freundlichen Gruessen, Ihr GeNUGate Mail-Gateway. =========================================================== In English =========================================================== Dear Internet Email User, this is an automated mail delivery notification, because your email has not been delivered the usual way. Your mail was not deliverd for the following reason: This mail contained a virus with the following Virus-Id: >>> Virus 'W32/MyDoom-A' Best regards, Your GeNUGate Mail Gateway ========================================================= ENVELOPE INFORMATION ========================================================= FROM = emboss-dev at embnet.org RCPT = fred at bba.de ========================================================= HEADER INFORMATION ========================================================= Received: from embnet.org (137.122.147.102) by (smtprelay) with ESMTP Fri Jan 30 00:52:38 2004. From: emboss-dev at embnet.org To: fred at bba.de Subject: Test Date: Thu, 29 Jan 2004 19:05:21 -0500 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0009_E76BBF7B.70DC1211" X-Priority: 3 X-MSMail-Priority: Normal =========================================================