From a.garcia at imb.uq.edu.au Mon Apr 5 10:37:59 2004 From: a.garcia at imb.uq.edu.au (a.garcia at imb.uq.edu.au) Date: Tue, 06 Apr 2004 00:37:59 +1000 Subject: [EMBOSS] workflows/emboss Message-ID: We would like to present G-PIPE; is a tool for building work flows. It wraps analysis methods available in EMBOSS (all of them). G-PIPE is built on top of PISE; including new analysis methods is possible. Once the user defines the work flow he/she can monitor its execution. It is possible to dispatch jobs over different servers. The work flows once defined are stored as an XML file that can later be loaded and replicated. G-PIPE is now installed in a better server, we have tested it running some analysis work flows, so far so good. http://130.102.113.135/gpipe.htm In order to access GPIPE JAVA must be enabled; the user is presented with two frames, one on which a menu with different methods is presented, and another frame where the corresponding GUI for the selected analysis method is displayed. The user selects the first analysis method, decides which is the next step in the work flow, selects this next step and so on. A more detailed (not as much as we would like to offer) description of the process to build and share a work flow is available together with an example of a work flow at http://130.102.113.135/gpipe.htm the tool is available at http://kun.homelinux.com/Pise/5.a/gpipe.html Gpipe exports the workflows as XML files and also as perl scripts. If the user wants it is possible to load, run and modify the scripts using a command line interface. G-PIPE uses BioPerl. We advise those who are interested to read the few documentation available and run the example we provide. Thanks in advance. From cfernand at utm.utoronto.ca Mon Apr 5 15:05:04 2004 From: cfernand at utm.utoronto.ca (Clinton Fernandes) Date: Mon, 5 Apr 2004 12:05:04 -0700 Subject: [EMBOSS] Problems installing on Enterprise Message-ID: <1081191904.4071ade094ee6@webmail.utm.utoronto.ca> Hello, I am having problems installing EMBOSS on my Enterprise workstation and was hoping someone may have a suggestion to help. I have recently upgraded my RedHat 9.0 workstation to Enterprise. Under RH 9.0 EMBOSS installed without problems. However, on Enterprise I get to following errors when issuing the "make" command: /usr/bin/ld: cannot find -lX11 collect2: ld returned 1 exit status make[2]: *** [aaindexextract] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all-recursive] Error 1 There is no /etc/X11 directory. I have been told that this is now /etc/X11R6, and I made a symbolic link to that directory (/etc/X11) but get the same error. /usr/bin/ld does exist and no errors arise under "configure". Does anyone have any suggestions? Thanks a lot. -- 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 From mccarthy at cs.usask.ca Mon Apr 5 15:20:55 2004 From: mccarthy at cs.usask.ca (Luke McCarthy) Date: Mon, 05 Apr 2004 13:20:55 -0600 Subject: [EMBOSS] Problems installing on Enterprise In-Reply-To: <1081191904.4071ade094ee6@webmail.utm.utoronto.ca> References: <1081191904.4071ade094ee6@webmail.utm.utoronto.ca> Message-ID: <1081192855.18649.45.camel@crazyharry.bioinfo-group.usask.ca> On Mon, 2004-04-05 at 13:05, Clinton Fernandes wrote: > I have recently upgraded my RedHat 9.0 workstation to Enterprise. Under RH 9.0 > EMBOSS installed without problems. However, on Enterprise I get to following > errors when issuing the "make" command: > > /usr/bin/ld: cannot find -lX11 > collect2: ld returned 1 exit status > make[2]: *** [aaindexextract] Error 1 > make[1]: *** [all-recursive] Error 1 > make: *** [all-recursive] Error 1 You need to install the XFree86-devel rpm. This rpm contains /usr/X11R6/lib/libX11.a, which is the file that -lX11 translates to (a static version of the X11 library...) > There is no /etc/X11 directory. I have been told that this is now /etc/X11R6, > and I made a symbolic link to that directory (/etc/X11) but get the same error. > /usr/bin/ld does exist and no errors arise under "configure". Remove the link you created. Nothing in /etc has anything to do with this problem. Cheers, Luke McCarthy -- Luke McCarthy Research Officer, Bioinformatics Department of Computer Science University of Saskatchewan mccarthy at cs.usask.ca From billthebrute at yahoo.fr Tue Apr 6 09:35:46 2004 From: billthebrute at yahoo.fr (=?iso-8859-1?q?william=20ritchie?=) Date: Tue, 6 Apr 2004 15:35:46 +0200 (CEST) Subject: [EMBOSS] EMBOSS on redhat9 In-Reply-To: <1081192855.18649.45.camel@crazyharry.bioinfo-group.usask.ca> Message-ID: <20040406133546.32128.qmail@web25203.mail.ukl.yahoo.com> Hi , I merrily installed emboss on redhat8 a while ago without difficulty, but now we ve gone to redhat9 I m having trouble getting the install to work. Here are the last lines of the ./make . . collect2: ld returned 1 exit status make[2]: *** [aaindexextract] Erreur 1 make[2]: Quitte le r?pertoire `/usr/local/EMBOSS-2.8.0/emboss' make[1]: *** [all-recursive] Erreur 1 make[1]: Quitte le r?pertoire `/usr/local/EMBOSS-2.8.0/emboss' make: *** [all-recursive] Erreur 1 and ./make install (under su) . . collect2: ld returned 1 exit status make[2]: *** [aaindexextract] Erreur 1 make[2]: Quitte le r?pertoire `/usr/local/EMBOSS-2.8.0/emboss' make[1]: *** [install-recursive] Erreur 1 make[1]: Quitte le r?pertoire `/usr/local/EMBOSS-2.8.0/emboss' make: *** [install-recursive] Erreur 1 I don t know if this can help...sorry some of it is in french. Cheers Yahoo! Mail : votre e-mail personnel et gratuit qui vous suit partout ! Cr?ez votre Yahoo! Mail sur http://fr.benefits.yahoo.com/ Dialoguez en direct avec vos amis gr?ce ? Yahoo! Messenger !T?l?chargez Yahoo! Messenger sur http://fr.messenger.yahoo.com From billthebrute at yahoo.fr Tue Apr 6 11:18:02 2004 From: billthebrute at yahoo.fr (=?iso-8859-1?q?william=20ritchie?=) Date: Tue, 6 Apr 2004 17:18:02 +0200 (CEST) Subject: [EMBOSS] Problems installing on Enterprise In-Reply-To: <1081191904.4071ade094ee6@webmail.utm.utoronto.ca> Message-ID: <20040406151802.51222.qmail@web25209.mail.ukl.yahoo.com> had the same problem. I used the rpm installer and all went smoothly.... http://www.biolinux.org/emboss.html Yahoo! Mail : votre e-mail personnel et gratuit qui vous suit partout ! Cr?ez votre Yahoo! Mail sur http://fr.benefits.yahoo.com/ Dialoguez en direct avec vos amis gr?ce ? Yahoo! Messenger !T?l?chargez Yahoo! Messenger sur http://fr.messenger.yahoo.com From postmaster at ebi.ac.uk Thu Apr 8 00:05:24 2004 From: postmaster at ebi.ac.uk (MailScanner) Date: Thu, 8 Apr 2004 05:05:24 +0100 (BST) Subject: [EMBOSS] Warning: E-mail containing attachment(s) blocked Message-ID: <200404080405.i3845OL28349@maui.ebi.ac.uk> Our MailScanner has blocked a message that you sent:- To: pmr at ebi.ac.uk Subject: here, the introduction Date: Thu Apr 8 05:05:24 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: Executable DOS/Windows programs are dangerous in email (freaky_number_phone.doc.exe) -- MailScanner Email Virus Scanner www.mailscanner.info From postmaster at ioroot.tld Thu Apr 8 01:14:11 2004 From: postmaster at ioroot.tld (postmaster at ioroot.tld) Date: Thu, 8 Apr 2004 00:14:11 -0500 Subject: [EMBOSS] Delivery Status Notification (Failure) Message-ID: This is an automatically generated Delivery Status Notification. Delivery to the following recipients failed. rick_mehalick at i-o.com -------------- next part -------------- An embedded message was scrubbed... From: emboss at embnet.org Subject: is that your porn pic? Date: Thu, 8 Apr 2004 13:14:13 +0800 Size: 1394 Url: http://lists.open-bio.org/pipermail/emboss/attachments/20040408/e8060c1f/attachment.mht From salzberg at cs.jhu.edu Fri Apr 9 13:51:00 2004 From: salzberg at cs.jhu.edu (via the vacation program) Date: Fri, 9 Apr 2004 13:51:00 -0400 (EDT) Subject: [EMBOSS] This is not my email address any longer Message-ID: <200404091751.i39Hp0DM029373@blaze.cs.jhu.edu> This message is being sent to you automatically by the vacation program. Steven Salzberg did NOT receive your email and will not get it; email sent to this account is automatically deleted. Steven Salzberg's primary appointment is at The Institute for Genomic Research (TIGR), where he has been since 1998. Please check our website there (or my home page) to get my correct email. This message does not contain any email addresses to prevent spammers from filling my inbox with even more junk than they already send. 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Your request for support has been recieved and will be processed as soon as possible. If you did not submitt your request using: http://www.ebi.ac.uk/support/ please do so now. Requests that have not been submitted using the URL above will take longer to process or will be ignored. Your request number is: 90287 ######################################################################### From imf at allcore.co.uk Sat Apr 17 08:48:15 2004 From: imf at allcore.co.uk (imf at allcore.co.uk) Date: Sat, 17 Apr 2004 13:48:15 +0100 Subject: [EMBOSS] IMF - the Internet Merchants Federation Message-ID: Your Invitation to Join. . . . . The Internet Merchants Federation - IMF = = = = = = = = = = = = = = = = = = = = Absolutely NO COST - NO joining fee, NO subscriptions, NO obligations. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The IMF is a Non-Profit organisation specifically designed to help all businesses, large and small, to promote themselves via the Internet or by E-mail. O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O + + + FOR MORE INFORMATION, SIMPLY REPLY TO THIS EMAIL + + + + + + + or visit our web site -just click this link - http://www.allcore.co.uk + + + + O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O MEMBERSHIP BENEFITS INCLUDE:- ** Directory entry in List of member's Approved User Friendly and Safe web-sites ** Visitors to one member's site tend to visit other member's sites - MORE hits for you! ** Promotion to Internet Users of fair trade and confidence in your web-site ** IMF Logo for display on your web-site - increase your credibility ** Code of Practice - promoting industry self-regulation ** Privacy Policy template - download and incude within your web-site ** Representation with regulators, government and trade bodies ** Arbitration Scheme - a service without costs to you or your customers ** Simple on-line registration OPTIONAL BENEFITS INCLUDE:- * Enhanced Directory entry in Members Listings * Real-time, unique web-site verification logo * Customer and Visitor Rating Service - with performance feedback O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O + + + FOR MORE INFORMATION, SIMPLY REPLY TO THIS EMAIL + + + + + + + or visit our web site -just click this link - http://www.allcore.co.uk + + + + O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O This project has been made possible through part funding from the UK Government DTI initiative, Business Insight for Broadband Access UNSUBSCRIBE? There is no need - THIS IS A ONE-TIME mailing We shall not contact you again, unless you request us to do so. SPAM MAIL? ** This is not an indiscriminate bulk email - ** Information has only been sent to selected domains. ** We believe your web-site qualifies for membership of the IMF. ** We are NOT trying to sell you anything - There is NO COST. ** This email is for advice and information purely of benefit to you. Thank you for taking your time to read this email. We look forward to hearing from you O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O + + + FOR MORE INFORMATION, SIMPLY REPLY TO THIS EMAIL + + + + + + + or visit our web site -just click this link - http://www.allcore.co.uk + + + + O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O From postmaster at ebi.ac.uk Sun Apr 18 06:36:44 2004 From: postmaster at ebi.ac.uk (MailScanner) Date: Sun, 18 Apr 2004 11:36:44 +0100 (BST) Subject: [EMBOSS] Warning: E-mail containing attachment(s) blocked Message-ID: <200404181036.i3IAaim27323@maui.ebi.ac.uk> Our MailScanner has blocked a message that you sent:- To: ebisrs at ebi.ac.uk Subject: stolen Date: Sun Apr 18 11:36:44 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 (material.rtf.scr) -- MailScanner Email Virus Scanner www.mailscanner.info From Mailer-Daemon at mailgw1.cityu.edu.hk Sun Apr 18 21:44:30 2004 From: Mailer-Daemon at mailgw1.cityu.edu.hk (Mail Delivery System) Date: Mon, 19 Apr 2004 09:44:30 +0800 (CST) Subject: [EMBOSS] Delivery Notification: Delivery has failed Message-ID: <0HWE001S9A66GL@mailgw1.cityu.edu.hk> This report relates to a message you sent with the following header fields: Return-path: Received: from conversion-daemon.mailgw1.cityu.edu.hk by mailgw1.cityu.edu.hk (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) id <0HWE001019XCGL at mailgw1.cityu.edu.hk> (original mail from emboss at embnet.org); Mon, 19 Apr 2004 09:44:30 +0800 (CST) Received: from mail.cityu.edu.hk ([202.57.101.253]) by mailgw1.cityu.edu.hk (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) with ESMTP id <0HWE00D79A5CIC at mailgw1.cityu.edu.hk> for sckevin at mail.cityu.edu.hk; Mon, 19 Apr 2004 09:44:29 +0800 (CST) Date: Mon, 19 Apr 2004 09:46:38 +0800 From: emboss at embnet.org Subject: Re: Hi To: sckevin at mail.cityu.edu.hk Message-id: <0HWE00D7FA5EIC at mailgw1.cityu.edu.hk> MIME-version: 1.0 Content-type: multipart/mixed; boundary="Boundary_(ID_eJMPONTNX1R4kDuq1Ne+UQ)" X-Priority: 3 X-MSMail-priority: Normal Your message cannot be delivered to the following recipients: Recipient address: sckevin at mail.cityu.edu.hk Reason: This email is rejected because an unsafe file is found: your_file.pif -------------- next part -------------- Return-path: Received: from conversion-daemon.mailgw1.cityu.edu.hk by mailgw1.cityu.edu.hk (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) id <0HWE001019XCGL at mailgw1.cityu.edu.hk> (original mail from emboss at embnet.org); Mon, 19 Apr 2004 09:44:30 +0800 (CST) Received: from mail.cityu.edu.hk ([202.57.101.253]) by mailgw1.cityu.edu.hk (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) with ESMTP id <0HWE00D79A5CIC at mailgw1.cityu.edu.hk> for sckevin at mail.cityu.edu.hk; Mon, 19 Apr 2004 09:44:29 +0800 (CST) Date: Mon, 19 Apr 2004 09:46:38 +0800 From: emboss at embnet.org Subject: Re: Hi To: sckevin at mail.cityu.edu.hk Message-id: <0HWE00D7FA5EIC at mailgw1.cityu.edu.hk> MIME-version: 1.0 Content-type: multipart/mixed; boundary="Boundary_(ID_eJMPONTNX1R4kDuq1Ne+UQ)" X-Priority: 3 X-MSMail-priority: Normal This is a multi-part message in MIME format. --Boundary_(ID_eJMPONTNX1R4kDuq1Ne+UQ) Content-type: text/plain; charset=Windows-1252 Content-transfer-encoding: 7BIT Your file is attached. --Boundary_(ID_eJMPONTNX1R4kDuq1Ne+UQ) Content-type: text/plain; Name=UnsafeFile.txt Content-transfer-encoding: 7BIT Content-disposition: inline Content-description: Unsafe file is rejected: your_file.pif ********* UNSAFE FILE IS REJECTED! ********* This email is bounced back to the sender because an unsafe file is found. * Name of the unsafe file: your_file.pif Postmaster (Mail Administrator), City University of Hong Kong Email: postmaster at cityu.edu.hk (Reference number: 20040419_094429_19108) ******************************************** --Boundary_(ID_eJMPONTNX1R4kDuq1Ne+UQ)-- From MAILER-DAEMON at hol.gr Mon Apr 19 12:45:40 2004 From: MAILER-DAEMON at hol.gr (MAILER-DAEMON at hol.gr) Date: 19 Apr 2004 16:45:40 -0000 Subject: [EMBOSS] failure notice Message-ID: <20040419164728.634C77D2A2@mercury.hgmp.mrc.ac.uk> Hi. This is the qmail-send program at hol.gr. 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. -------------------- Postmaster postmaster at hol.gr Hellas On Line SA : Sorry, no mailbox here by that name. (#5.1.1) --- Below this line is a copy of the message. Return-Path: Received: (qmail 22482 invoked from network); 19 Apr 2004 16:45:40 -0000 Received: from unknown (HELO MX.hol.gr) ([192.168.20.23]) (envelope-sender ) by maildir1.mail.dc.hol.net (qmail-ldap-1.03) with SMTP for ; 19 Apr 2004 16:45:40 -0000 Received: from hol.gr ([195.251.21.104]) by MX.hol.gr (8.12.8/8.12.8) with ESMTP id i3JGlMUS029117 for ; Mon, 19 Apr 2004 19:47:23 +0300 Message-Id: <200404191647.i3JGlMUS029117 at MX.hol.gr> From: emboss at embnet.org To: domalisk at hol.gr Subject: [] Re: Your picture Date: Mon, 19 Apr 2004 19:45:32 +0300 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0008_0000442C.00004BFD" X-Priority: 3 X-MSMail-Priority: Normal X-MailScanner: Found to be infected This is a multi-part message in MIME format. ------=_NextPart_000_0008_0000442C.00004BFD Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit See the attached file for details. ------=_NextPart_000_0008_0000442C.00004BFD Content-Type: text/plain; charset=""ISO-8859-7""; name="VirusWarning.txt" Content-Disposition: attachment; filename="VirusWarning.txt" Content-Transfer-Encoding: quoted-printable This is a message from HOLscanner =0D =0D The original e-mail attachment "your_picture.pif" is on the list of unacce= ptable=0D attachments for this site and has been replaced by this warning message. W= e =0D were unable to keep a copy of the original attachment. =0D =0D At Mon Apr 19 19:47:27 2004 the virus scanner said:=0D Shortcuts to MS-Dos programs are very dangerous in email (your_picture.p= if) =0D -- =0D Postmaster=0D =0D =0D =0D ********************************=0D =0D =C1=F5=F4=FC =F4=EF =EC=DE=ED=F5=EC=E1 =E5=DF=ED=E1=E9 =E1=F0=FC =F4=E7=ED = HOLscanner=0D =0D =D4=EF =E1=F1=F7=E9=EA=FC =F3=F5=ED=E7=EC=EC=DD=ED=EF =E1=F1=F7=E5=DF=EF "= your_picture.pif" =F3=F5=E3=EA=E1=F4=E1=EB=DD=E3=E5=F4=E1=E9 =F3=F4=E1 =EC= =E7 =E1=F0=EF=E4=E5=EA=F4=DC =F3=F5=ED=E7=EC=EC=DD=ED=E1=0D =E1=F1=F7=E5=DF=E1 =E3=E9 =E1=F5=F4=E7 =F4=E7 =F3=E5=EB=DF=E4=E1 =EA=E1=E9= =E1=ED=F4=E9=EA=E1=F4=E1=F3=F4=DC=E8=E7=EA=E5 =EC=E5 =E1=F5=F4=FC =F4=EF = =F0=F1=EF=E5=E9=E4=EF=F0=EF=E9=E7=F4=E9=EA=FC =EC=DE=ED=F5=EC=E1.=0D =C4=E5=ED =DE=F4=E1=ED =E4=F5=ED=E1=F4=FC =ED=E1 =EA=F1=E1=F4=DE=F3=EF=F5= =EC=E5 =E1=ED=F4=DF=E3=F1=E1=F6=EF =E1=F0=FC =F4=EF =E1=F1=F7=E9=EA=FC =F3= =F5=ED=E7=EC=EC=DD=ED=EF =E1=F1=F7=E5=DF=EF.=0D =0D =D3=F4=E9=F2 Mon Apr 19 19:47:27 2004 =EF =E1=ED=E9=F7=ED=E5=F5=F4=DE=F2 = =E9=FE=ED =E5=DF=F0=E5:=0D Shortcuts to MS-Dos programs are very dangerous in email (your_picture.p= if) =0D -- =0D Postmaster=0D =0D =0D =0D =0D ------=_NextPart_000_0008_0000442C.00004BFD-- From service at ibank.barclays.co.uk Wed Apr 21 04:13:30 2004 From: service at ibank.barclays.co.uk (Barclays IBank service) Date: Wed, 21 Apr 2004 08:13:30 +0000 Subject: [EMBOSS] Urgent information from Barclays IBank In-Reply-To: <22C3192DL6LJB2LL@embnet.org> References: <22C3192DL6LJB2LL@embnet.org> Message-ID: <1C40D6LACIF06K98@ibank.barclays.co.uk> An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss/attachments/20040421/6c60fd98/attachment.html From MAILER-DAEMON at umsmed.edu Thu Apr 22 18:20:17 2004 From: MAILER-DAEMON at umsmed.edu (Mail Delivery System) Date: Thu, 22 Apr 2004 17:20:17 -0500 (CDT) Subject: [EMBOSS] Undelivered Mail Returned to Sender Message-ID: <20040422222017.C791A1735E2@unix04.umsmed.edu> This is the Postfix program at host unix04.umsmed.edu. I'm sorry to have to inform you that the message returned below could not be delivered to one or more destinations. For further assistance, please send mail to If you do so, please include this problem report. You can delete your own text from the message returned below. The Postfix program : host 172.17.66.203[172.17.66.203] said: 554 Transaction failed (too many hops) -------------- next part -------------- An embedded message was scrubbed... From: emboss at embnet.org Subject: hello Date: Fri, 23 Apr 2004 06:20:07 +0800 Size: 7000 Url: http://lists.open-bio.org/pipermail/emboss/attachments/20040422/feac89d8/attachment.mht From kellert at ohsu.edu Fri Apr 23 14:21:49 2004 From: kellert at ohsu.edu (Thomas J Keller) Date: Fri, 23 Apr 2004 11:21:49 -0700 Subject: [EMBOSS] abiview and X11 on Mac 10.3.3 Message-ID: <161FABC8-9553-11D8-B4C4-0003930405E2@ohsu.edu> Greetings, Any updates on how to get Xll to work with abiview. It used to work with 10.2. But fails now after a clean install of 10.3 (updated to 10.3.3). Graph type [x11]: Can't open display If I give ps as the graph type, it generates a proper ps file. Graph type [x11]: ps Created abiview.ps But Graph type [x11]: xterm EMBOSS An error in abiview.c at line 132: //. not an ABI file I'd like to be able to edit abi files, suggestions? Thanks, Tom K. Tom Keller, Ph.D. http://www.ohsu.edu/research/core kellert at ohsu.edu 503-494-2442 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 610 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss/attachments/20040423/3f5c9c48/attachment.bin From postmaster at ebi.ac.uk Tue Apr 27 09:31:58 2004 From: postmaster at ebi.ac.uk (MailScanner) Date: Tue, 27 Apr 2004 14:31:58 +0100 (BST) Subject: [EMBOSS] Warning: E-mail containing attachment(s) blocked Message-ID: <200404271331.i3RDVwu19633@maui.ebi.ac.uk> Our MailScanner has blocked a message that you sent:- To: higgins at ebi.ac.uk Subject: Date: Tue Apr 27 14:31:58 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: Shortcuts to MS-Dos programs are very dangerous in email (disco.rtf.pif) -- MailScanner Email Virus Scanner www.mailscanner.info From henrikki.almusa at helsinki.fi Fri Apr 30 04:29:48 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Fri, 30 Apr 2004 11:29:48 +0300 Subject: [EMBOSS] Embassy: Domainatrix Message-ID: <200404301129.48306.henrikki.almusa@helsinki.fi> Hello, Domainatrix seems to have quite a lot of programs. However there is no indication about them in the emboss web pages. Shouldn't they be listed in the embassy section of the application page? Thanks, -- Henrikki Almusa From jison at hgmp.mrc.ac.uk Fri Apr 30 08:15:16 2004 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Fri, 30 Apr 2004 13:15:16 +0100 Subject: [EMBOSS] Embassy: Domainatrix References: <200404301129.48306.henrikki.almusa@helsinki.fi> Message-ID: <40924353.93855EC6@hgmp.mrc.ac.uk> Hi Henrikki Its in hand - the documentation was taken down for updating in light of changes to the library code and other improvements. I'll get it all back on-line asap and if there's anything I can help with in the meantime, feel free to get in touch directly. Cheers Jon Henrikki Almusa wrote: > Hello, > > Domainatrix seems to have quite a lot of programs. However there is no > indication about them in the emboss web pages. Shouldn't they be listed in > the embassy section of the application page? > > Thanks, > -- > Henrikki Almusa -- Jon C. Ison, PhD Proteomics Applications Group MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494500 Fax: +44 1223 494512 E-mail: jison at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk From a.garcia at imb.uq.edu.au Mon Apr 5 14:37:59 2004 From: a.garcia at imb.uq.edu.au (a.garcia at imb.uq.edu.au) Date: Tue, 06 Apr 2004 00:37:59 +1000 Subject: [EMBOSS] workflows/emboss Message-ID: We would like to present G-PIPE; is a tool for building work flows. It wraps analysis methods available in EMBOSS (all of them). G-PIPE is built on top of PISE; including new analysis methods is possible. Once the user defines the work flow he/she can monitor its execution. It is possible to dispatch jobs over different servers. The work flows once defined are stored as an XML file that can later be loaded and replicated. G-PIPE is now installed in a better server, we have tested it running some analysis work flows, so far so good. http://130.102.113.135/gpipe.htm In order to access GPIPE JAVA must be enabled; the user is presented with two frames, one on which a menu with different methods is presented, and another frame where the corresponding GUI for the selected analysis method is displayed. The user selects the first analysis method, decides which is the next step in the work flow, selects this next step and so on. A more detailed (not as much as we would like to offer) description of the process to build and share a work flow is available together with an example of a work flow at http://130.102.113.135/gpipe.htm the tool is available at http://kun.homelinux.com/Pise/5.a/gpipe.html Gpipe exports the workflows as XML files and also as perl scripts. If the user wants it is possible to load, run and modify the scripts using a command line interface. G-PIPE uses BioPerl. We advise those who are interested to read the few documentation available and run the example we provide. Thanks in advance. From cfernand at utm.utoronto.ca Mon Apr 5 19:05:04 2004 From: cfernand at utm.utoronto.ca (Clinton Fernandes) Date: Mon, 5 Apr 2004 12:05:04 -0700 Subject: [EMBOSS] Problems installing on Enterprise Message-ID: <1081191904.4071ade094ee6@webmail.utm.utoronto.ca> Hello, I am having problems installing EMBOSS on my Enterprise workstation and was hoping someone may have a suggestion to help. I have recently upgraded my RedHat 9.0 workstation to Enterprise. Under RH 9.0 EMBOSS installed without problems. However, on Enterprise I get to following errors when issuing the "make" command: /usr/bin/ld: cannot find -lX11 collect2: ld returned 1 exit status make[2]: *** [aaindexextract] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all-recursive] Error 1 There is no /etc/X11 directory. I have been told that this is now /etc/X11R6, and I made a symbolic link to that directory (/etc/X11) but get the same error. /usr/bin/ld does exist and no errors arise under "configure". Does anyone have any suggestions? Thanks a lot. -- 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 From mccarthy at cs.usask.ca Mon Apr 5 19:20:55 2004 From: mccarthy at cs.usask.ca (Luke McCarthy) Date: Mon, 05 Apr 2004 13:20:55 -0600 Subject: [EMBOSS] Problems installing on Enterprise In-Reply-To: <1081191904.4071ade094ee6@webmail.utm.utoronto.ca> References: <1081191904.4071ade094ee6@webmail.utm.utoronto.ca> Message-ID: <1081192855.18649.45.camel@crazyharry.bioinfo-group.usask.ca> On Mon, 2004-04-05 at 13:05, Clinton Fernandes wrote: > I have recently upgraded my RedHat 9.0 workstation to Enterprise. Under RH 9.0 > EMBOSS installed without problems. However, on Enterprise I get to following > errors when issuing the "make" command: > > /usr/bin/ld: cannot find -lX11 > collect2: ld returned 1 exit status > make[2]: *** [aaindexextract] Error 1 > make[1]: *** [all-recursive] Error 1 > make: *** [all-recursive] Error 1 You need to install the XFree86-devel rpm. This rpm contains /usr/X11R6/lib/libX11.a, which is the file that -lX11 translates to (a static version of the X11 library...) > There is no /etc/X11 directory. I have been told that this is now /etc/X11R6, > and I made a symbolic link to that directory (/etc/X11) but get the same error. > /usr/bin/ld does exist and no errors arise under "configure". Remove the link you created. Nothing in /etc has anything to do with this problem. Cheers, Luke McCarthy -- Luke McCarthy Research Officer, Bioinformatics Department of Computer Science University of Saskatchewan mccarthy at cs.usask.ca From billthebrute at yahoo.fr Tue Apr 6 13:35:46 2004 From: billthebrute at yahoo.fr (=?iso-8859-1?q?william=20ritchie?=) Date: Tue, 6 Apr 2004 15:35:46 +0200 (CEST) Subject: [EMBOSS] EMBOSS on redhat9 In-Reply-To: <1081192855.18649.45.camel@crazyharry.bioinfo-group.usask.ca> Message-ID: <20040406133546.32128.qmail@web25203.mail.ukl.yahoo.com> Hi , I merrily installed emboss on redhat8 a while ago without difficulty, but now we ve gone to redhat9 I m having trouble getting the install to work. Here are the last lines of the ./make . . collect2: ld returned 1 exit status make[2]: *** [aaindexextract] Erreur 1 make[2]: Quitte le r?pertoire `/usr/local/EMBOSS-2.8.0/emboss' make[1]: *** [all-recursive] Erreur 1 make[1]: Quitte le r?pertoire `/usr/local/EMBOSS-2.8.0/emboss' make: *** [all-recursive] Erreur 1 and ./make install (under su) . . collect2: ld returned 1 exit status make[2]: *** [aaindexextract] Erreur 1 make[2]: Quitte le r?pertoire `/usr/local/EMBOSS-2.8.0/emboss' make[1]: *** [install-recursive] Erreur 1 make[1]: Quitte le r?pertoire `/usr/local/EMBOSS-2.8.0/emboss' make: *** [install-recursive] Erreur 1 I don t know if this can help...sorry some of it is in french. Cheers Yahoo! Mail : votre e-mail personnel et gratuit qui vous suit partout ! Cr?ez votre Yahoo! Mail sur http://fr.benefits.yahoo.com/ Dialoguez en direct avec vos amis gr?ce ? Yahoo! Messenger !T?l?chargez Yahoo! Messenger sur http://fr.messenger.yahoo.com From billthebrute at yahoo.fr Tue Apr 6 15:18:02 2004 From: billthebrute at yahoo.fr (=?iso-8859-1?q?william=20ritchie?=) Date: Tue, 6 Apr 2004 17:18:02 +0200 (CEST) Subject: [EMBOSS] Problems installing on Enterprise In-Reply-To: <1081191904.4071ade094ee6@webmail.utm.utoronto.ca> Message-ID: <20040406151802.51222.qmail@web25209.mail.ukl.yahoo.com> had the same problem. I used the rpm installer and all went smoothly.... http://www.biolinux.org/emboss.html Yahoo! Mail : votre e-mail personnel et gratuit qui vous suit partout ! Cr?ez votre Yahoo! Mail sur http://fr.benefits.yahoo.com/ Dialoguez en direct avec vos amis gr?ce ? Yahoo! Messenger !T?l?chargez Yahoo! Messenger sur http://fr.messenger.yahoo.com From postmaster at ebi.ac.uk Thu Apr 8 04:05:24 2004 From: postmaster at ebi.ac.uk (MailScanner) Date: Thu, 8 Apr 2004 05:05:24 +0100 (BST) Subject: [EMBOSS] Warning: E-mail containing attachment(s) blocked Message-ID: <200404080405.i3845OL28349@maui.ebi.ac.uk> Our MailScanner has blocked a message that you sent:- To: pmr at ebi.ac.uk Subject: here, the introduction Date: Thu Apr 8 05:05:24 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: Executable DOS/Windows programs are dangerous in email (freaky_number_phone.doc.exe) -- MailScanner Email Virus Scanner www.mailscanner.info From postmaster at ioroot.tld Thu Apr 8 05:14:11 2004 From: postmaster at ioroot.tld (postmaster at ioroot.tld) Date: Thu, 8 Apr 2004 00:14:11 -0500 Subject: [EMBOSS] Delivery Status Notification (Failure) Message-ID: This is an automatically generated Delivery Status Notification. Delivery to the following recipients failed. rick_mehalick at i-o.com -------------- next part -------------- An embedded message was scrubbed... From: emboss at embnet.org Subject: is that your porn pic? Date: Thu, 8 Apr 2004 13:14:13 +0800 Size: 1394 URL: From salzberg at cs.jhu.edu Fri Apr 9 17:51:00 2004 From: salzberg at cs.jhu.edu (via the vacation program) Date: Fri, 9 Apr 2004 13:51:00 -0400 (EDT) Subject: [EMBOSS] This is not my email address any longer Message-ID: <200404091751.i39Hp0DM029373@blaze.cs.jhu.edu> This message is being sent to you automatically by the vacation program. Steven Salzberg did NOT receive your email and will not get it; email sent to this account is automatically deleted. Steven Salzberg's primary appointment is at The Institute for Genomic Research (TIGR), where he has been since 1998. Please check our website there (or my home page) to get my correct email. This message does not contain any email addresses to prevent spammers from filling my inbox with even more junk than they already send. 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Your request for support has been recieved and will be processed as soon as possible. If you did not submitt your request using: http://www.ebi.ac.uk/support/ please do so now. Requests that have not been submitted using the URL above will take longer to process or will be ignored. Your request number is: 90287 ######################################################################### From imf at allcore.co.uk Sat Apr 17 12:48:15 2004 From: imf at allcore.co.uk (imf at allcore.co.uk) Date: Sat, 17 Apr 2004 13:48:15 +0100 Subject: [EMBOSS] IMF - the Internet Merchants Federation Message-ID: Your Invitation to Join. . . . . 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There is no need - THIS IS A ONE-TIME mailing We shall not contact you again, unless you request us to do so. SPAM MAIL? ** This is not an indiscriminate bulk email - ** Information has only been sent to selected domains. ** We believe your web-site qualifies for membership of the IMF. ** We are NOT trying to sell you anything - There is NO COST. ** This email is for advice and information purely of benefit to you. Thank you for taking your time to read this email. We look forward to hearing from you O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O + + + FOR MORE INFORMATION, SIMPLY REPLY TO THIS EMAIL + + + + + + + or visit our web site -just click this link - http://www.allcore.co.uk + + + + O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O-O From postmaster at ebi.ac.uk Sun Apr 18 10:36:44 2004 From: postmaster at ebi.ac.uk (MailScanner) Date: Sun, 18 Apr 2004 11:36:44 +0100 (BST) Subject: [EMBOSS] Warning: E-mail containing attachment(s) blocked Message-ID: <200404181036.i3IAaim27323@maui.ebi.ac.uk> Our MailScanner has blocked a message that you sent:- To: ebisrs at ebi.ac.uk Subject: stolen Date: Sun Apr 18 11:36:44 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 (material.rtf.scr) -- MailScanner Email Virus Scanner www.mailscanner.info From Mailer-Daemon at mailgw1.cityu.edu.hk Mon Apr 19 01:44:30 2004 From: Mailer-Daemon at mailgw1.cityu.edu.hk (Mail Delivery System) Date: Mon, 19 Apr 2004 09:44:30 +0800 (CST) Subject: [EMBOSS] Delivery Notification: Delivery has failed Message-ID: <0HWE001S9A66GL@mailgw1.cityu.edu.hk> This report relates to a message you sent with the following header fields: Return-path: Received: from conversion-daemon.mailgw1.cityu.edu.hk by mailgw1.cityu.edu.hk (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) id <0HWE001019XCGL at mailgw1.cityu.edu.hk> (original mail from emboss at embnet.org); Mon, 19 Apr 2004 09:44:30 +0800 (CST) Received: from mail.cityu.edu.hk ([202.57.101.253]) by mailgw1.cityu.edu.hk (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) with ESMTP id <0HWE00D79A5CIC at mailgw1.cityu.edu.hk> for sckevin at mail.cityu.edu.hk; Mon, 19 Apr 2004 09:44:29 +0800 (CST) Date: Mon, 19 Apr 2004 09:46:38 +0800 From: emboss at embnet.org Subject: Re: Hi To: sckevin at mail.cityu.edu.hk Message-id: <0HWE00D7FA5EIC at mailgw1.cityu.edu.hk> MIME-version: 1.0 Content-type: multipart/mixed; boundary="Boundary_(ID_eJMPONTNX1R4kDuq1Ne+UQ)" X-Priority: 3 X-MSMail-priority: Normal Your message cannot be delivered to the following recipients: Recipient address: sckevin at mail.cityu.edu.hk Reason: This email is rejected because an unsafe file is found: your_file.pif -------------- next part -------------- Return-path: Received: from conversion-daemon.mailgw1.cityu.edu.hk by mailgw1.cityu.edu.hk (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) id <0HWE001019XCGL at mailgw1.cityu.edu.hk> (original mail from emboss at embnet.org); Mon, 19 Apr 2004 09:44:30 +0800 (CST) Received: from mail.cityu.edu.hk ([202.57.101.253]) by mailgw1.cityu.edu.hk (iPlanet Messaging Server 5.2 HotFix 1.21 (built Sep 8 2003)) with ESMTP id <0HWE00D79A5CIC at mailgw1.cityu.edu.hk> for sckevin at mail.cityu.edu.hk; Mon, 19 Apr 2004 09:44:29 +0800 (CST) Date: Mon, 19 Apr 2004 09:46:38 +0800 From: emboss at embnet.org Subject: Re: Hi To: sckevin at mail.cityu.edu.hk Message-id: <0HWE00D7FA5EIC at mailgw1.cityu.edu.hk> MIME-version: 1.0 Content-type: multipart/mixed; boundary="Boundary_(ID_eJMPONTNX1R4kDuq1Ne+UQ)" X-Priority: 3 X-MSMail-priority: Normal This is a multi-part message in MIME format. --Boundary_(ID_eJMPONTNX1R4kDuq1Ne+UQ) Content-type: text/plain; charset=Windows-1252 Content-transfer-encoding: 7BIT Your file is attached. --Boundary_(ID_eJMPONTNX1R4kDuq1Ne+UQ) Content-type: text/plain; Name=UnsafeFile.txt Content-transfer-encoding: 7BIT Content-disposition: inline Content-description: Unsafe file is rejected: your_file.pif ********* UNSAFE FILE IS REJECTED! ********* This email is bounced back to the sender because an unsafe file is found. * Name of the unsafe file: your_file.pif Postmaster (Mail Administrator), City University of Hong Kong Email: postmaster at cityu.edu.hk (Reference number: 20040419_094429_19108) ******************************************** --Boundary_(ID_eJMPONTNX1R4kDuq1Ne+UQ)-- From MAILER-DAEMON at hol.gr Mon Apr 19 16:45:40 2004 From: MAILER-DAEMON at hol.gr (MAILER-DAEMON at hol.gr) Date: 19 Apr 2004 16:45:40 -0000 Subject: [EMBOSS] failure notice Message-ID: <20040419164728.634C77D2A2@mercury.hgmp.mrc.ac.uk> Hi. This is the qmail-send program at hol.gr. 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. -------------------- Postmaster postmaster at hol.gr Hellas On Line SA : Sorry, no mailbox here by that name. (#5.1.1) --- Below this line is a copy of the message. Return-Path: Received: (qmail 22482 invoked from network); 19 Apr 2004 16:45:40 -0000 Received: from unknown (HELO MX.hol.gr) ([192.168.20.23]) (envelope-sender ) by maildir1.mail.dc.hol.net (qmail-ldap-1.03) with SMTP for ; 19 Apr 2004 16:45:40 -0000 Received: from hol.gr ([195.251.21.104]) by MX.hol.gr (8.12.8/8.12.8) with ESMTP id i3JGlMUS029117 for ; Mon, 19 Apr 2004 19:47:23 +0300 Message-Id: <200404191647.i3JGlMUS029117 at MX.hol.gr> From: emboss at embnet.org To: domalisk at hol.gr Subject: [] Re: Your picture Date: Mon, 19 Apr 2004 19:45:32 +0300 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0008_0000442C.00004BFD" X-Priority: 3 X-MSMail-Priority: Normal X-MailScanner: Found to be infected This is a multi-part message in MIME format. ------=_NextPart_000_0008_0000442C.00004BFD Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit See the attached file for details. ------=_NextPart_000_0008_0000442C.00004BFD Content-Type: text/plain; charset=""ISO-8859-7""; name="VirusWarning.txt" Content-Disposition: attachment; filename="VirusWarning.txt" Content-Transfer-Encoding: quoted-printable This is a message from HOLscanner =0D =0D The original e-mail attachment "your_picture.pif" is on the list of unacce= ptable=0D attachments for this site and has been replaced by this warning message. W= e =0D were unable to keep a copy of the original attachment. =0D =0D At Mon Apr 19 19:47:27 2004 the virus scanner said:=0D Shortcuts to MS-Dos programs are very dangerous in email (your_picture.p= if) =0D -- =0D Postmaster=0D =0D =0D =0D ********************************=0D =0D =C1=F5=F4=FC =F4=EF =EC=DE=ED=F5=EC=E1 =E5=DF=ED=E1=E9 =E1=F0=FC =F4=E7=ED = HOLscanner=0D =0D =D4=EF =E1=F1=F7=E9=EA=FC =F3=F5=ED=E7=EC=EC=DD=ED=EF =E1=F1=F7=E5=DF=EF "= your_picture.pif" =F3=F5=E3=EA=E1=F4=E1=EB=DD=E3=E5=F4=E1=E9 =F3=F4=E1 =EC= =E7 =E1=F0=EF=E4=E5=EA=F4=DC =F3=F5=ED=E7=EC=EC=DD=ED=E1=0D =E1=F1=F7=E5=DF=E1 =E3=E9 =E1=F5=F4=E7 =F4=E7 =F3=E5=EB=DF=E4=E1 =EA=E1=E9= =E1=ED=F4=E9=EA=E1=F4=E1=F3=F4=DC=E8=E7=EA=E5 =EC=E5 =E1=F5=F4=FC =F4=EF = =F0=F1=EF=E5=E9=E4=EF=F0=EF=E9=E7=F4=E9=EA=FC =EC=DE=ED=F5=EC=E1.=0D =C4=E5=ED =DE=F4=E1=ED =E4=F5=ED=E1=F4=FC =ED=E1 =EA=F1=E1=F4=DE=F3=EF=F5= =EC=E5 =E1=ED=F4=DF=E3=F1=E1=F6=EF =E1=F0=FC =F4=EF =E1=F1=F7=E9=EA=FC =F3= =F5=ED=E7=EC=EC=DD=ED=EF =E1=F1=F7=E5=DF=EF.=0D =0D =D3=F4=E9=F2 Mon Apr 19 19:47:27 2004 =EF =E1=ED=E9=F7=ED=E5=F5=F4=DE=F2 = =E9=FE=ED =E5=DF=F0=E5:=0D Shortcuts to MS-Dos programs are very dangerous in email (your_picture.p= if) =0D -- =0D Postmaster=0D =0D =0D =0D =0D ------=_NextPart_000_0008_0000442C.00004BFD-- From service at ibank.barclays.co.uk Wed Apr 21 08:13:30 2004 From: service at ibank.barclays.co.uk (Barclays IBank service) Date: Wed, 21 Apr 2004 08:13:30 +0000 Subject: [EMBOSS] Urgent information from Barclays IBank In-Reply-To: <22C3192DL6LJB2LL@embnet.org> References: <22C3192DL6LJB2LL@embnet.org> Message-ID: <1C40D6LACIF06K98@ibank.barclays.co.uk> An HTML attachment was scrubbed... URL: From MAILER-DAEMON at umsmed.edu Thu Apr 22 22:20:17 2004 From: MAILER-DAEMON at umsmed.edu (Mail Delivery System) Date: Thu, 22 Apr 2004 17:20:17 -0500 (CDT) Subject: [EMBOSS] Undelivered Mail Returned to Sender Message-ID: <20040422222017.C791A1735E2@unix04.umsmed.edu> This is the Postfix program at host unix04.umsmed.edu. I'm sorry to have to inform you that the message returned below could not be delivered to one or more destinations. For further assistance, please send mail to If you do so, please include this problem report. You can delete your own text from the message returned below. The Postfix program : host 172.17.66.203[172.17.66.203] said: 554 Transaction failed (too many hops) -------------- next part -------------- An embedded message was scrubbed... From: emboss at embnet.org Subject: hello Date: Fri, 23 Apr 2004 06:20:07 +0800 Size: 7000 URL: From kellert at ohsu.edu Fri Apr 23 18:21:49 2004 From: kellert at ohsu.edu (Thomas J Keller) Date: Fri, 23 Apr 2004 11:21:49 -0700 Subject: [EMBOSS] abiview and X11 on Mac 10.3.3 Message-ID: <161FABC8-9553-11D8-B4C4-0003930405E2@ohsu.edu> Greetings, Any updates on how to get Xll to work with abiview. It used to work with 10.2. But fails now after a clean install of 10.3 (updated to 10.3.3). Graph type [x11]: Can't open display If I give ps as the graph type, it generates a proper ps file. Graph type [x11]: ps Created abiview.ps But Graph type [x11]: xterm EMBOSS An error in abiview.c at line 132: //. not an ABI file I'd like to be able to edit abi files, suggestions? Thanks, Tom K. Tom Keller, Ph.D. http://www.ohsu.edu/research/core kellert at ohsu.edu 503-494-2442 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 610 bytes Desc: not available URL: From postmaster at ebi.ac.uk Tue Apr 27 13:31:58 2004 From: postmaster at ebi.ac.uk (MailScanner) Date: Tue, 27 Apr 2004 14:31:58 +0100 (BST) Subject: [EMBOSS] Warning: E-mail containing attachment(s) blocked Message-ID: <200404271331.i3RDVwu19633@maui.ebi.ac.uk> Our MailScanner has blocked a message that you sent:- To: higgins at ebi.ac.uk Subject: Date: Tue Apr 27 14:31:58 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: Shortcuts to MS-Dos programs are very dangerous in email (disco.rtf.pif) -- MailScanner Email Virus Scanner www.mailscanner.info From henrikki.almusa at helsinki.fi Fri Apr 30 08:29:48 2004 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Fri, 30 Apr 2004 11:29:48 +0300 Subject: [EMBOSS] Embassy: Domainatrix Message-ID: <200404301129.48306.henrikki.almusa@helsinki.fi> Hello, Domainatrix seems to have quite a lot of programs. However there is no indication about them in the emboss web pages. Shouldn't they be listed in the embassy section of the application page? Thanks, -- Henrikki Almusa From jison at hgmp.mrc.ac.uk Fri Apr 30 12:15:16 2004 From: jison at hgmp.mrc.ac.uk (Dr J.C. Ison) Date: Fri, 30 Apr 2004 13:15:16 +0100 Subject: [EMBOSS] Embassy: Domainatrix References: <200404301129.48306.henrikki.almusa@helsinki.fi> Message-ID: <40924353.93855EC6@hgmp.mrc.ac.uk> Hi Henrikki Its in hand - the documentation was taken down for updating in light of changes to the library code and other improvements. I'll get it all back on-line asap and if there's anything I can help with in the meantime, feel free to get in touch directly. Cheers Jon Henrikki Almusa wrote: > Hello, > > Domainatrix seems to have quite a lot of programs. However there is no > indication about them in the emboss web pages. Shouldn't they be listed in > the embassy section of the application page? > > Thanks, > -- > Henrikki Almusa -- Jon C. Ison, PhD Proteomics Applications Group MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Tel: +44 1223 494500 Fax: +44 1223 494512 E-mail: jison at rfcgr.mrc.ac.uk Web: http://www.rfcgr.mrc.ac.uk