From martin_artist at yahoo.com Mon Oct 6 03:14:47 2003 From: martin_artist at yahoo.com (ENRON = Swarzenegger) Date: Mon, 6 Oct 2003 03:14:47 Subject: Stealing CA $9 billions = Recall Election Message-ID: <20031006101627.5E4217D26B@mercury.hgmp.mrc.ac.uk> Bush bible PNAC Swarzeneger got money from ENRON to forgive 9 billions pay back I'm very worry, desperate PNAC may do 3rd Pearl Harbor to US. - Second is here: 1997 http://www.newamericancentury.org/RebuildingAmericasDefenses.pdf page 48 Clinton economy is good - page 51 on document or 63 / on Acrobat viewer.. - We have to have major attack on America first, to convince people OPEN YOUR MIND FOR YOURSELF AND YOUR KIDS LIFE; http://www.alternetnews.com/ Arnold or Adolph, what the different; D A N K E, will Terminate US all & California first Prescott help Adolph, George him & Enron; Gasoline $4 per gallon is just the beginning. Actor = skilled liar, how can we trust them ? I heard, his porno job is for sale; & He is ENRON BOY http://www.tarpley.net/bushb.htm http://www.bartcop.com/421102.htm http://www.bk2k.com/bushbodycount/prescott-bush/index.shtml http://hnn.us/comments/15105.html Hitler, Noriega, Hussein, bin Laden, Pinochet - did business with the Bush family. Now we do business with Bush as well; - $500 000 000 000 is gone, missing, and make US poor Perfect Taxpayers Rip Off - MONEY LAUNDRY - true Iraq repair kidding, - direct to own pocket, Isn't this a crime ?? + Lie of war reasons, and lie, and lie, and lie. Please look on this and think by yourself; where we are going ?? Or PNAC push us there, like stick to a blind sheep. - Start thinking on your own, please. http://pnac.tvnewslies.org http://www.tvnewslies.org START THINKING AGAIN !!! www.moveon.org/news/1577.html www.prisonplanet.com www.moveon.org www.votetoimpeach.com www.kgo810.com listen 810 AM; Bernie, Genie, Ray only (night time) How many Concentration Camps do they need today ? one for sure is on Cuba. If, after that news - you can't sleep too well -; get Warren book; " The Governor " try understand - how to blackmail Congress - Or movie films; " Enemy of the State" that most of us today " Spy like US " - abusing power by top managers " Air America " - how marihuana come to US It may happened, Pentagon will have to arrest White House and his own " Liar in Chief" to save USA On the base of George Washington Legacy War President & his bible "PNAC" inventing Terrorism & new Pearl Harbor: http://www.newamericancentury.org/RebuildingAmericasDefenses.pdf ) From henrikki.almusa at helsinki.fi Tue Oct 14 07:45:54 2003 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Tue, 14 Oct 2003 14:45:54 +0300 Subject: Tfscan addition Message-ID: <200310141445.54240.henrikki.almusa@helsinki.fi> Hello, I'm trying to allow a external data file being used by tfscan. It works as i'm hoping when all the info is given in command line. However i can't seem to be able to modify the acd file properly. I would want it to query the data if in the menu (list, above in acd-file) user selected custom 'C'. But it doesn't. So how can this be done? Patch attached. TIA -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: tfscan.patch Type: text/x-diff Size: 1295 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20031014/1a3f371a/attachment.bin From ronald.yang at jakru.com Tue Oct 14 11:55:12 2003 From: ronald.yang at jakru.com (H.Ronald Yang) Date: Tue, 14 Oct 2003 11:55:12 -0400 Subject: EMBOSS GUI : mwcontam : unknown datatype 'filelist' Message-ID: <008201c3926b$8dcd16d0$02020a0a@rescentris.com> Hi, I have a problem using "mwcontam" and "mwfilter" through EMBOSS Web GUI. When I click on the one of "PROTEIN COMPOSITION" tool, "mwcontam", from the left side panel, there is error. Right after "input section", it says "ERROR" and "unknown datatype 'filelist'". Is this possible to fix? Thanks in advance, Ron From ronald.yang at jakru.com Tue Oct 14 13:58:00 2003 From: ronald.yang at jakru.com (H.Ronald Yang) Date: Tue, 14 Oct 2003 13:58:00 -0400 Subject: EMBOSS GUI : mwcontam : unknown datatype 'filelist' References: <007001c39272$ceead790$862010ac@unisabanacli.unisabana.edu.co> Message-ID: <00d701c3927c$b591d820$02020a0a@rescentris.com> I am using Luke's EMBOSS-GUI. Maybe I should ask the question to Luke. If so, sorry to bother you with this. Ron ----- Original Message ----- From: "Leyla Jael Garc?a Castro" To: "'H.Ronald Yang'" Sent: Tuesday, October 14, 2003 12:47 PM Subject: RE: EMBOSS GUI : mwcontam : unknown datatype 'filelist' > Are you using JEmboss or another web GUI? > > -----Mensaje original----- > De: owner-emboss-dev at hgmp.mrc.ac.uk > [mailto:owner-emboss-dev at hgmp.mrc.ac.uk] En nombre de H.Ronald Yang > Enviado el: Martes, 14 de Octubre de 2003 10:55 a.m. > Para: emboss at embnet.org; emboss-dev at embnet.org > CC: R. Wolfgang Rumpf > Asunto: EMBOSS GUI : mwcontam : unknown datatype 'filelist' > > Hi, > > I have a problem using "mwcontam" and "mwfilter" through EMBOSS > Web GUI. > When I click on the one of "PROTEIN COMPOSITION" tool, "mwcontam", > from the > left side panel, there is error. Right after "input section", it > says > "ERROR" and "unknown datatype 'filelist'". Is this possible to > fix? > > Thanks in advance, > Ron > > From mccarthy at cs.usask.ca Tue Oct 14 16:08:39 2003 From: mccarthy at cs.usask.ca (Luke McCarthy) Date: 14 Oct 2003 14:08:39 -0600 Subject: datafile and filelist data types Message-ID: <1066162119.4912.17.camel@crazyharry.usask.ca> Hi, The mwcontam and mwfilter applications use the data types 'datafile' and 'filelist' in their respective ACD files. There is no mention of these data types in the ACD spec at http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Acd/syntax.html#Acddata11 and they don't appear to be used by any other applications in the 2.7.1 release. Is this a bug? If so, is it a bug in the ACD spec as described online, or is it a bug in the mwcontam and mwfilter applications? Cheers, Luke -- Luke McCarthy Research Officer, Bioinformatics Department of Computer Science University of Saskatchewan mccarthy at cs.usask.ca From ableasby at hgmp.mrc.ac.uk Tue Oct 14 16:26:11 2003 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Tue, 14 Oct 2003 21:26:11 +0100 (BST) Subject: datafile and filelist data types Message-ID: <200310142026.h9EKQBxc026914@bromine.hgmp.mrc.ac.uk> Hi Luke, ACD has been going through a rework for 2.8.0 . The documentation is being updated at the moment. It was said at the last meeting that the documentation was, for once, ahead of the code! The file to look at is in the CVS download and is the dco/manuals/acdsyntax-template.html one. 'filelist' still hasn't made it into those docs but other cahnges-to-come have. filelist is a comma separated list of files, dirlist is mentioned in to docs above. We'll sort out 'filelist' in the docs. It is not a bug in the mw* programs, they are both useful datatypes. HTH Alan From pmr at ebi.ac.uk Wed Oct 15 03:48:06 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 15 Oct 2003 08:48:06 +0100 Subject: datafile and filelist data types References: <200310142026.h9EKQBxc026914@bromine.hgmp.mrc.ac.uk> Message-ID: <3F8CFBB6.6020100@ebi.ac.uk> Hi Luke, Alan Bleasby wrote: > ACD has been going through a rework for 2.8.0 . The documentation > is being updated at the moment. It was said at the last meeting that > the documentation was, for once, ahead of the code! It was indeed!!! The code has now caught up. The acdsyntax documentation is now generated automatically by running (a slightly extended) entrails, parsing the results and generating the tables of ACD types and attributes. There is also a check for missing text, mainly descriptions of attributes for each ACD type. > The file to look at is in the CVS download and is the > dco/manuals/acdsyntax-template.html > one. 'filelist' still hasn't made it into those docs but other > cahnges-to-come have. filelist is a comma separated list of files, > dirlist is mentioned in to docs above. We'll sort out 'filelist' > in the docs. The working copy (we can't put it up live until 2.8.0 goes out) is at http://www.ebi.ac.uk/~pmr/acdtables.html From time to time this may refer to ACD changes I've not yet committed, but it will be the 2.8.0 version of the ACD syntax documentation. To check on the datatypes available in ACD, you should run the entrails program (built with "make check") to get a full list. There are serveral new ACD types for 2.8.0 - most are simply input files with specific types, and are reserved for phylip 3.6. Details will follow in a posting to emboss-dev when the documentation is complete. > It is not a bug in the mw* programs, they are both useful datatypes. Though there are still some datatypes that seem to be not used, they are "reserved" for places where strings are currently used. > HTH ... and, specially for Canada, OZE :-) Peter From henrikki.almusa at helsinki.fi Wed Oct 15 04:31:06 2003 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Wed, 15 Oct 2003 11:31:06 +0300 Subject: Tfscan addition In-Reply-To: <200310141445.54240.henrikki.almusa@helsinki.fi> References: <200310141445.54240.henrikki.almusa@helsinki.fi> Message-ID: <200310151131.06910.henrikki.almusa@helsinki.fi> On Tuesday 14 October 2003 14:45, Henrikki Almusa wrote: > I would want it to query the data if in the menu (list, above in acd-file) > user selected custom 'C'. But it doesn't. So how can this be done? I solved this myself. So here's a patch (attached) for tfscan that allows data file to be given from commandline. Also allows emboss to query it if missing. -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: tfscan.patch Type: text/x-diff Size: 1292 bytes Desc: not available Url : http://lists.open-bio.org/pipermail/emboss-dev/attachments/20031015/96f4a67f/attachment.bin From ableasby at hgmp.mrc.ac.uk Sun Oct 19 05:09:58 2003 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Sun, 19 Oct 2003 10:09:58 +0100 (BST) Subject: Developer 2.8.0-pre available for ftp Message-ID: <200310190909.h9J99wtE008314@bromine.hgmp.mrc.ac.uk> Dear developers, A pre-release of EMBOSS-2.8.0 is available for, primarily, GUI developers at: ftp://ftp.uk.embnet.org/pub/EMBOSS/pre/EMBOSS-2.8.0-pre.tar.gz This is not the final 2.8.0, in-house additions, additions of contributions, fixes (etc) are still in progress. The file has not been QA-tested as thoroughly as a main release. EMBASSY packages have not yet been configured for the final release. Nevertheless it will allow GUI developers to bring their parsers up to date before the main release, which we expect to happen in a couple of weeks if all goes well. As ever, check the ChangeLog file. I recommend that you use the default system compiler on systems where gcc is also installed. That is done by (e.g.) setenv CC cc before using the configure script. Doing so will ensure full optimisation for your platform. Systems which use gcc as the compiler are, of course, catered for. For SGI systems there is a new compilation flag --with-sgiabi= which can take the values n32m3, n32m4, 64m3 and 64m4 and their meanings should hopefully be clear. Compilation on all systems now has large file support switched on by default (although the current indexing system is still limited to 2Gb source files.. this will be replaced, we hope, in 2.9.0). If you need 64-bit pointers on AIX, HP-UX, Solaris (and the hardware supports them) you can use the --enable-64 configuration switch. It is highly unlikely you'll want to use that switch. If you use a system other than AIX, Linux, SGI, HP-UX, Solaris, Tru64 or MacOSX then large file support will probably not be enabled. In that case please contact me (and it might be a help if you send me your system stdio.h if you can legally do so). Alan From P.Ernst at dkfz-heidelberg.de Fri Oct 24 06:39:58 2003 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Fri, 24 Oct 2003 12:39:58 +0200 (MEST) Subject: ACD backwards compatibility In-Reply-To: <200310190909.h9J99wtE008314@bromine.hgmp.mrc.ac.uk> Message-ID: Dear Emboss developers, version: pre-release of EMBOSS-2.8.0. problem: ACD backwards compatibility I realised that the upcoming EMBOSS release does not understand the old attributes anymore (here: attribute "required"). Wouldn't it be nice to have some backwards compatibility for the cases, where the keywords simply have changed? Otherwise authors of EMBASSY programs have to provide different versions of ACD files for pre-2.8.0 and post-2.8.0 releases. The command-line option "-debug" could issue a warning, however this shouldn't be the default, because of the reason mentioned in the paragraph before. Example: ACD: from graphtest.acd: xygraph: graph [ prompt: "Graph type (? for list of types)" help: "Graphics device" parameter: "Y" required: "Y" ] With pre-release 2.8.0: % graphtest Error: File t/graphtest.acd line 6: (graph) Attribute 'required' unknown % acdvalid graphtest Error: File t/graphtest.acd line 6: (graph) Attribute 'required' unknown With release 2.7.1: % .../emboss-2.7.1/bin/acdvalid graphtest Error: File t/graphtest.acd line 6: Multiple definition of parameter/required/optional Error: File t/graphtest.acd line 6: prompt specified but no information Error: File t/graphtest.acd line 6: Unexpected information value for type 'xygraph' I this simple example, I could solve the problem by simply removing the "required" attribute, because the "parameter" attribute is still there, but I think this is a general question. Kind regards, Peter From P.Ernst at dkfz-heidelberg.de Fri Oct 24 06:51:53 2003 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Fri, 24 Oct 2003 12:51:53 +0200 (MEST) Subject: names defined in pcre_internal.h In-Reply-To: <200310190909.h9J99wtE008314@bromine.hgmp.mrc.ac.uk> Message-ID: Dear Emboss developers, version: pre-release of EMBOSS-2.8.0. problem: names defined in pcre_internal.h the new "perl compatible regular expressions" (pcre) in EMBOSS do have an include file named "pcre_internal.h". However this include file is not just used internally to compile the regular expression code in Ajax, but is also included in the "emboss.h" include chain (through ajreg.h). Because this include file contains several definitions not following the usual prefix-scheme e.g. definitions for "TRUE" and "FALSE" or names derived from Perl (e.g. OP_NOT, OP_REF or OP_REVERSE), I experienced name conflicts during compilation of my programs that are using EMBOSS. Maybe it is possible to a.) prefix the definitions in pcre_internal.h (to fight against the namespace pollution) and/or b.) remove pcre_internal.h from the include chain of emboss.h. (the name suggests that it was not supposed to be public) Kind regards, Peter -- ======================================================================= Peter Ernst Department of Molecular Biophysics - B020 Deutsches Krebsforschungszentrum (German Cancer Research Center) DKFZ Im Neuenheimer Feld 580 / Technologiepark 3 69120 Heidelberg, Germany phone: +49-6221-42-2330 http://genome.dkfz-heidelberg.de/ fax: +49-6221-42-2333 ======================================================================= From pmr at ebi.ac.uk Fri Oct 24 11:01:25 2003 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Fri, 24 Oct 2003 16:01:25 +0100 (BST) Subject: names defined in pcre_internal.h In-Reply-To: References: <200310190909.h9J99wtE008314@bromine.hgmp.mrc.ac.uk> Message-ID: <52028.194.94.44.4.1067007685.squirrel@webmail.ebi.ac.uk> Peter Ernst writes: > version: pre-release of EMBOSS-2.8.0. > problem: names defined in pcre_internal.h > > the new "perl compatible regular expressions" (pcre) in EMBOSS do have > an include file named "pcre_internal.h". However this include file is > not just used internally to compile the regular expression code in > Ajax, but is also included in the "emboss.h" include chain (through > ajreg.h). > > Because this include file contains several definitions not following > the usual prefix-scheme e.g. definitions for "TRUE" and "FALSE" or > names derived from Perl (e.g. OP_NOT, OP_REF or OP_REVERSE), I > experienced name conflicts during compilation of my programs that are > using EMBOSS. > > Maybe it is possible to > > a.) prefix the definitions in pcre_internal.h (to fight against the > namespace pollution) and/or Should be no problem. > b.) remove pcre_internal.h from the include chain of emboss.h. > (the name suggests that it was not supposed to be public) Ummmm ... I need to check on whether it is needed (and whether we can avoid needing it). PCRE is a separate regular expression library that we have included in Ajax, as a replacement for the Henry Spencer regular expression libraries. regards, Peter Rice From pmr at ebi.ac.uk Fri Oct 24 11:06:41 2003 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Fri, 24 Oct 2003 16:06:41 +0100 (BST) Subject: ACD backwards compatibility In-Reply-To: References: <200310190909.h9J99wtE008314@bromine.hgmp.mrc.ac.uk> Message-ID: <10607.194.94.44.4.1067008001.squirrel@webmail.ebi.ac.uk> Peter Ernst writes: > Dear Emboss developers, > > version: pre-release of EMBOSS-2.8.0. > problem: ACD backwards compatibility > > I realised that the upcoming EMBOSS release does not understand the > old attributes anymore (here: attribute "required"). Wouldn't it be > nice to have some backwards compatibility for the cases, where the > keywords simply have changed? Yes. I have code to do that. There was a problem with "standard" and "standardtype" which will clash if abbrevitions are used ("standardtype" is renamed "knowntype"). Assuming nobody had "standardtype" shortened to "standard" it should be OK. The existing code had to be cleaned up for acdvalid to report correctly, but now the ACD files are cleaned we can add the old "required" and "optional" attributes back as aliases ... but for a limited time. They will be gone by release 3.0.0. regards, Peter Rice From gbottu at ben.vub.ac.be Mon Oct 27 11:23:11 2003 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Mon, 27 Oct 2003 17:23:11 +0100 (CET) Subject: fastA and BLAST under EMBOSS, the DB problem Message-ID: <200310271623.h9RGNBVp1335193@black.vub.ac.be> from : BEN Dear colleagues, Recently the discussion about integrating BLAST and fastA under EMBOSS has flared up again. At the BEN site we have BLAST, fastA and some other programs installed under an EMBOSS "wrapper" program. In their present form these programs are however not readily installable elsewhere. When a year ago we dropped GCG I rushed to replace the lost functionality for our users and did not consider portability. I think it would be a good idea to distribute our BLAST and fastA wrappers as an "Embassadir". Therefore I would like to co-operate with the developement team of EMBOSS as well as with the developers of GUI's to see what is necessary. The most serious problem is databank access. The fastA programs need a databank in fastA format. If we choose the option of editing the original code there must be a way to retrieve the sequences and feed them serially to the algorithm. If we however choose the option of making a "wrapper" (like emma), as I did, the question is how to provide the sequences. Saving the complete EMBL databank in /tmp/xxx each time you want to search it is evidently not convenient. Therefore my idea was to access directly already installed databanks in fastA format. In the current version of our wrappers the names of the available databanks are written in the ACD files. This is of course not convenient at all. A way of getting around thi hurdle is, I think, the following : the local manager must anyway have the "native" fastA installed and properly configured. The available databanks must be listed in a configuration file. The name of the file is pointed at with the environment variable FASTLIBS or is put on the command line as -l xxx . The file contains lines of type : EMBL (general nucleic acid databank)$1+em+@/dbfb/fastalibs/embl.lib SwissProt (general protein databank)$0+sw+/dbfb/swissprot/sw So, it contains as well a text to be displayed by the interface as a short name (em) to be put on the command line as the actual location of the databank (singe file or "library"). Evidently EMBOSS could parse this file. Maybe a new ACD object of type "fastalib" could be implemented. Then the ACD files would need to contain just : fastalib: fastalib [ required: "@.... type: "@....nucleotide.....protein.... ] The local manager would have to put in emboss.defaults a line of type FASTADB [ file: configfile_xxx ] or EMBOSS could just read the environment variable FASTLIBS. For BLAST you need databanks in BLAST format, so editing the original code will not circumvent the problem. A similar approach is however possible : if all the databanks are put in a single directory (environment variable BLASTDB). A problem is how to obtain a long text with the databank description to be displayed in the interface. If all the databanks have a *.nal or *.pal file the TITLE attribute could be used, although letting EMBOSS parse all those files each time you start the program is maybe not a good idea. What do you think about it. Regards, Guy Bottu From pmr at ebi.ac.uk Mon Oct 27 13:29:20 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 27 Oct 2003 18:29:20 +0000 Subject: fastA and BLAST under EMBOSS, the DB problem In-Reply-To: <200310271623.h9RGNBVp1335193@black.vub.ac.be> References: <200310271623.h9RGNBVp1335193@black.vub.ac.be> Message-ID: <3F9D6400.9000403@ebi.ac.uk> Guy Bottu wrote: > I think it would be a good idea to distribute our > BLAST and fastA wrappers as an "Embassadir". Therefore I would like to > co-operate with the developement team of EMBOSS as well as with the developers > of GUI's to see what is necessary. > > The most serious problem is databank access. EMBOSS database definitions now include the concept of "resource" which can be used to define databases for FASTA and BLAST and any otehr resources. We only need to write some resource definitions (you can invent attributes) and implement them as valid values for a "resource" acd type (which would be very easy to add in ACD). regards, Peter Rice From jeopm.finnlotto00 at laposte.net Thu Oct 30 12:11:12 2003 From: jeopm.finnlotto00 at laposte.net (=?iso-8859-1?Q?jeopm.finnlotto00@laposte.net?=) Date: Thu, 30 Oct 2003 18:11:12 +0100 Subject: =?iso-8859-1?Q?CONGRATULATIONS!!!?= Message-ID: FROM: THE PRIZE AWARD DEPARTMENT WORLDWIDE PREMIER LOTTO, UK Congratulations Category A prize winner! You have been selected as one of two winners of the Worldwide Premier Lotto UK computer ballot draws and thus will be a privileged recipient of the grand draw prize of? 7,500,000 (Seven million five hundred thousand Great Britain Pounds only). Winning File Reference number for your prize is WWPL/UK/ 61-812087; ticket number 003-214-39/A. 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URL: http://lists.open-bio.org/pipermail/emboss-dev/attachments/20031030/bb763107/attachment.html From martin_artist at yahoo.com Mon Oct 6 03:14:47 2003 From: martin_artist at yahoo.com (ENRON = Swarzenegger) Date: Mon, 6 Oct 2003 03:14:47 Subject: Stealing CA $9 billions = Recall Election Message-ID: <20031006101627.5E4217D26B@mercury.hgmp.mrc.ac.uk> Bush bible PNAC Swarzeneger got money from ENRON to forgive 9 billions pay back I'm very worry, desperate PNAC may do 3rd Pearl Harbor to US. - Second is here: 1997 http://www.newamericancentury.org/RebuildingAmericasDefenses.pdf page 48 Clinton economy is good - page 51 on document or 63 / on Acrobat viewer.. - We have to have major attack on America first, to convince people OPEN YOUR MIND FOR YOURSELF AND YOUR KIDS LIFE; http://www.alternetnews.com/ Arnold or Adolph, what the different; D A N K E, will Terminate US all & California first Prescott help Adolph, George him & Enron; Gasoline $4 per gallon is just the beginning. Actor = skilled liar, how can we trust them ? I heard, his porno job is for sale; & He is ENRON BOY http://www.tarpley.net/bushb.htm http://www.bartcop.com/421102.htm http://www.bk2k.com/bushbodycount/prescott-bush/index.shtml http://hnn.us/comments/15105.html Hitler, Noriega, Hussein, bin Laden, Pinochet - did business with the Bush family. Now we do business with Bush as well; - $500 000 000 000 is gone, missing, and make US poor Perfect Taxpayers Rip Off - MONEY LAUNDRY - true Iraq repair kidding, - direct to own pocket, Isn't this a crime ?? + Lie of war reasons, and lie, and lie, and lie. Please look on this and think by yourself; where we are going ?? Or PNAC push us there, like stick to a blind sheep. - Start thinking on your own, please. http://pnac.tvnewslies.org http://www.tvnewslies.org START THINKING AGAIN !!! www.moveon.org/news/1577.html www.prisonplanet.com www.moveon.org www.votetoimpeach.com www.kgo810.com listen 810 AM; Bernie, Genie, Ray only (night time) How many Concentration Camps do they need today ? one for sure is on Cuba. If, after that news - you can't sleep too well -; get Warren book; " The Governor " try understand - how to blackmail Congress - Or movie films; " Enemy of the State" that most of us today " Spy like US " - abusing power by top managers " Air America " - how marihuana come to US It may happened, Pentagon will have to arrest White House and his own " Liar in Chief" to save USA On the base of George Washington Legacy War President & his bible "PNAC" inventing Terrorism & new Pearl Harbor: http://www.newamericancentury.org/RebuildingAmericasDefenses.pdf ) From henrikki.almusa at helsinki.fi Tue Oct 14 11:45:54 2003 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Tue, 14 Oct 2003 14:45:54 +0300 Subject: Tfscan addition Message-ID: <200310141445.54240.henrikki.almusa@helsinki.fi> Hello, I'm trying to allow a external data file being used by tfscan. It works as i'm hoping when all the info is given in command line. However i can't seem to be able to modify the acd file properly. I would want it to query the data if in the menu (list, above in acd-file) user selected custom 'C'. But it doesn't. So how can this be done? Patch attached. TIA -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: tfscan.patch Type: text/x-diff Size: 1295 bytes Desc: not available URL: From ronald.yang at jakru.com Tue Oct 14 15:55:12 2003 From: ronald.yang at jakru.com (H.Ronald Yang) Date: Tue, 14 Oct 2003 11:55:12 -0400 Subject: EMBOSS GUI : mwcontam : unknown datatype 'filelist' Message-ID: <008201c3926b$8dcd16d0$02020a0a@rescentris.com> Hi, I have a problem using "mwcontam" and "mwfilter" through EMBOSS Web GUI. When I click on the one of "PROTEIN COMPOSITION" tool, "mwcontam", from the left side panel, there is error. Right after "input section", it says "ERROR" and "unknown datatype 'filelist'". Is this possible to fix? Thanks in advance, Ron From ronald.yang at jakru.com Tue Oct 14 17:58:00 2003 From: ronald.yang at jakru.com (H.Ronald Yang) Date: Tue, 14 Oct 2003 13:58:00 -0400 Subject: EMBOSS GUI : mwcontam : unknown datatype 'filelist' References: <007001c39272$ceead790$862010ac@unisabanacli.unisabana.edu.co> Message-ID: <00d701c3927c$b591d820$02020a0a@rescentris.com> I am using Luke's EMBOSS-GUI. Maybe I should ask the question to Luke. If so, sorry to bother you with this. Ron ----- Original Message ----- From: "Leyla Jael Garc?a Castro" To: "'H.Ronald Yang'" Sent: Tuesday, October 14, 2003 12:47 PM Subject: RE: EMBOSS GUI : mwcontam : unknown datatype 'filelist' > Are you using JEmboss or another web GUI? > > -----Mensaje original----- > De: owner-emboss-dev at hgmp.mrc.ac.uk > [mailto:owner-emboss-dev at hgmp.mrc.ac.uk] En nombre de H.Ronald Yang > Enviado el: Martes, 14 de Octubre de 2003 10:55 a.m. > Para: emboss at embnet.org; emboss-dev at embnet.org > CC: R. Wolfgang Rumpf > Asunto: EMBOSS GUI : mwcontam : unknown datatype 'filelist' > > Hi, > > I have a problem using "mwcontam" and "mwfilter" through EMBOSS > Web GUI. > When I click on the one of "PROTEIN COMPOSITION" tool, "mwcontam", > from the > left side panel, there is error. Right after "input section", it > says > "ERROR" and "unknown datatype 'filelist'". Is this possible to > fix? > > Thanks in advance, > Ron > > From mccarthy at cs.usask.ca Tue Oct 14 20:08:39 2003 From: mccarthy at cs.usask.ca (Luke McCarthy) Date: 14 Oct 2003 14:08:39 -0600 Subject: datafile and filelist data types Message-ID: <1066162119.4912.17.camel@crazyharry.usask.ca> Hi, The mwcontam and mwfilter applications use the data types 'datafile' and 'filelist' in their respective ACD files. There is no mention of these data types in the ACD spec at http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Acd/syntax.html#Acddata11 and they don't appear to be used by any other applications in the 2.7.1 release. Is this a bug? If so, is it a bug in the ACD spec as described online, or is it a bug in the mwcontam and mwfilter applications? Cheers, Luke -- Luke McCarthy Research Officer, Bioinformatics Department of Computer Science University of Saskatchewan mccarthy at cs.usask.ca From ableasby at hgmp.mrc.ac.uk Tue Oct 14 20:26:11 2003 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Tue, 14 Oct 2003 21:26:11 +0100 (BST) Subject: datafile and filelist data types Message-ID: <200310142026.h9EKQBxc026914@bromine.hgmp.mrc.ac.uk> Hi Luke, ACD has been going through a rework for 2.8.0 . The documentation is being updated at the moment. It was said at the last meeting that the documentation was, for once, ahead of the code! The file to look at is in the CVS download and is the dco/manuals/acdsyntax-template.html one. 'filelist' still hasn't made it into those docs but other cahnges-to-come have. filelist is a comma separated list of files, dirlist is mentioned in to docs above. We'll sort out 'filelist' in the docs. It is not a bug in the mw* programs, they are both useful datatypes. HTH Alan From pmr at ebi.ac.uk Wed Oct 15 07:48:06 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 15 Oct 2003 08:48:06 +0100 Subject: datafile and filelist data types References: <200310142026.h9EKQBxc026914@bromine.hgmp.mrc.ac.uk> Message-ID: <3F8CFBB6.6020100@ebi.ac.uk> Hi Luke, Alan Bleasby wrote: > ACD has been going through a rework for 2.8.0 . The documentation > is being updated at the moment. It was said at the last meeting that > the documentation was, for once, ahead of the code! It was indeed!!! The code has now caught up. The acdsyntax documentation is now generated automatically by running (a slightly extended) entrails, parsing the results and generating the tables of ACD types and attributes. There is also a check for missing text, mainly descriptions of attributes for each ACD type. > The file to look at is in the CVS download and is the > dco/manuals/acdsyntax-template.html > one. 'filelist' still hasn't made it into those docs but other > cahnges-to-come have. filelist is a comma separated list of files, > dirlist is mentioned in to docs above. We'll sort out 'filelist' > in the docs. The working copy (we can't put it up live until 2.8.0 goes out) is at http://www.ebi.ac.uk/~pmr/acdtables.html From time to time this may refer to ACD changes I've not yet committed, but it will be the 2.8.0 version of the ACD syntax documentation. To check on the datatypes available in ACD, you should run the entrails program (built with "make check") to get a full list. There are serveral new ACD types for 2.8.0 - most are simply input files with specific types, and are reserved for phylip 3.6. Details will follow in a posting to emboss-dev when the documentation is complete. > It is not a bug in the mw* programs, they are both useful datatypes. Though there are still some datatypes that seem to be not used, they are "reserved" for places where strings are currently used. > HTH ... and, specially for Canada, OZE :-) Peter From henrikki.almusa at helsinki.fi Wed Oct 15 08:31:06 2003 From: henrikki.almusa at helsinki.fi (Henrikki Almusa) Date: Wed, 15 Oct 2003 11:31:06 +0300 Subject: Tfscan addition In-Reply-To: <200310141445.54240.henrikki.almusa@helsinki.fi> References: <200310141445.54240.henrikki.almusa@helsinki.fi> Message-ID: <200310151131.06910.henrikki.almusa@helsinki.fi> On Tuesday 14 October 2003 14:45, Henrikki Almusa wrote: > I would want it to query the data if in the menu (list, above in acd-file) > user selected custom 'C'. But it doesn't. So how can this be done? I solved this myself. So here's a patch (attached) for tfscan that allows data file to be given from commandline. Also allows emboss to query it if missing. -- Henrikki Almusa -------------- next part -------------- A non-text attachment was scrubbed... Name: tfscan.patch Type: text/x-diff Size: 1292 bytes Desc: not available URL: From ableasby at hgmp.mrc.ac.uk Sun Oct 19 09:09:58 2003 From: ableasby at hgmp.mrc.ac.uk (Alan Bleasby) Date: Sun, 19 Oct 2003 10:09:58 +0100 (BST) Subject: Developer 2.8.0-pre available for ftp Message-ID: <200310190909.h9J99wtE008314@bromine.hgmp.mrc.ac.uk> Dear developers, A pre-release of EMBOSS-2.8.0 is available for, primarily, GUI developers at: ftp://ftp.uk.embnet.org/pub/EMBOSS/pre/EMBOSS-2.8.0-pre.tar.gz This is not the final 2.8.0, in-house additions, additions of contributions, fixes (etc) are still in progress. The file has not been QA-tested as thoroughly as a main release. EMBASSY packages have not yet been configured for the final release. Nevertheless it will allow GUI developers to bring their parsers up to date before the main release, which we expect to happen in a couple of weeks if all goes well. As ever, check the ChangeLog file. I recommend that you use the default system compiler on systems where gcc is also installed. That is done by (e.g.) setenv CC cc before using the configure script. Doing so will ensure full optimisation for your platform. Systems which use gcc as the compiler are, of course, catered for. For SGI systems there is a new compilation flag --with-sgiabi= which can take the values n32m3, n32m4, 64m3 and 64m4 and their meanings should hopefully be clear. Compilation on all systems now has large file support switched on by default (although the current indexing system is still limited to 2Gb source files.. this will be replaced, we hope, in 2.9.0). If you need 64-bit pointers on AIX, HP-UX, Solaris (and the hardware supports them) you can use the --enable-64 configuration switch. It is highly unlikely you'll want to use that switch. If you use a system other than AIX, Linux, SGI, HP-UX, Solaris, Tru64 or MacOSX then large file support will probably not be enabled. In that case please contact me (and it might be a help if you send me your system stdio.h if you can legally do so). Alan From P.Ernst at dkfz-heidelberg.de Fri Oct 24 10:39:58 2003 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Fri, 24 Oct 2003 12:39:58 +0200 (MEST) Subject: ACD backwards compatibility In-Reply-To: <200310190909.h9J99wtE008314@bromine.hgmp.mrc.ac.uk> Message-ID: Dear Emboss developers, version: pre-release of EMBOSS-2.8.0. problem: ACD backwards compatibility I realised that the upcoming EMBOSS release does not understand the old attributes anymore (here: attribute "required"). Wouldn't it be nice to have some backwards compatibility for the cases, where the keywords simply have changed? Otherwise authors of EMBASSY programs have to provide different versions of ACD files for pre-2.8.0 and post-2.8.0 releases. The command-line option "-debug" could issue a warning, however this shouldn't be the default, because of the reason mentioned in the paragraph before. Example: ACD: from graphtest.acd: xygraph: graph [ prompt: "Graph type (? for list of types)" help: "Graphics device" parameter: "Y" required: "Y" ] With pre-release 2.8.0: % graphtest Error: File t/graphtest.acd line 6: (graph) Attribute 'required' unknown % acdvalid graphtest Error: File t/graphtest.acd line 6: (graph) Attribute 'required' unknown With release 2.7.1: % .../emboss-2.7.1/bin/acdvalid graphtest Error: File t/graphtest.acd line 6: Multiple definition of parameter/required/optional Error: File t/graphtest.acd line 6: prompt specified but no information Error: File t/graphtest.acd line 6: Unexpected information value for type 'xygraph' I this simple example, I could solve the problem by simply removing the "required" attribute, because the "parameter" attribute is still there, but I think this is a general question. Kind regards, Peter From P.Ernst at dkfz-heidelberg.de Fri Oct 24 10:51:53 2003 From: P.Ernst at dkfz-heidelberg.de (Peter Ernst) Date: Fri, 24 Oct 2003 12:51:53 +0200 (MEST) Subject: names defined in pcre_internal.h In-Reply-To: <200310190909.h9J99wtE008314@bromine.hgmp.mrc.ac.uk> Message-ID: Dear Emboss developers, version: pre-release of EMBOSS-2.8.0. problem: names defined in pcre_internal.h the new "perl compatible regular expressions" (pcre) in EMBOSS do have an include file named "pcre_internal.h". However this include file is not just used internally to compile the regular expression code in Ajax, but is also included in the "emboss.h" include chain (through ajreg.h). Because this include file contains several definitions not following the usual prefix-scheme e.g. definitions for "TRUE" and "FALSE" or names derived from Perl (e.g. OP_NOT, OP_REF or OP_REVERSE), I experienced name conflicts during compilation of my programs that are using EMBOSS. Maybe it is possible to a.) prefix the definitions in pcre_internal.h (to fight against the namespace pollution) and/or b.) remove pcre_internal.h from the include chain of emboss.h. (the name suggests that it was not supposed to be public) Kind regards, Peter -- ======================================================================= Peter Ernst Department of Molecular Biophysics - B020 Deutsches Krebsforschungszentrum (German Cancer Research Center) DKFZ Im Neuenheimer Feld 580 / Technologiepark 3 69120 Heidelberg, Germany phone: +49-6221-42-2330 http://genome.dkfz-heidelberg.de/ fax: +49-6221-42-2333 ======================================================================= From pmr at ebi.ac.uk Fri Oct 24 15:01:25 2003 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Fri, 24 Oct 2003 16:01:25 +0100 (BST) Subject: names defined in pcre_internal.h In-Reply-To: References: <200310190909.h9J99wtE008314@bromine.hgmp.mrc.ac.uk> Message-ID: <52028.194.94.44.4.1067007685.squirrel@webmail.ebi.ac.uk> Peter Ernst writes: > version: pre-release of EMBOSS-2.8.0. > problem: names defined in pcre_internal.h > > the new "perl compatible regular expressions" (pcre) in EMBOSS do have > an include file named "pcre_internal.h". However this include file is > not just used internally to compile the regular expression code in > Ajax, but is also included in the "emboss.h" include chain (through > ajreg.h). > > Because this include file contains several definitions not following > the usual prefix-scheme e.g. definitions for "TRUE" and "FALSE" or > names derived from Perl (e.g. OP_NOT, OP_REF or OP_REVERSE), I > experienced name conflicts during compilation of my programs that are > using EMBOSS. > > Maybe it is possible to > > a.) prefix the definitions in pcre_internal.h (to fight against the > namespace pollution) and/or Should be no problem. > b.) remove pcre_internal.h from the include chain of emboss.h. > (the name suggests that it was not supposed to be public) Ummmm ... I need to check on whether it is needed (and whether we can avoid needing it). PCRE is a separate regular expression library that we have included in Ajax, as a replacement for the Henry Spencer regular expression libraries. regards, Peter Rice From pmr at ebi.ac.uk Fri Oct 24 15:06:41 2003 From: pmr at ebi.ac.uk (pmr at ebi.ac.uk) Date: Fri, 24 Oct 2003 16:06:41 +0100 (BST) Subject: ACD backwards compatibility In-Reply-To: References: <200310190909.h9J99wtE008314@bromine.hgmp.mrc.ac.uk> Message-ID: <10607.194.94.44.4.1067008001.squirrel@webmail.ebi.ac.uk> Peter Ernst writes: > Dear Emboss developers, > > version: pre-release of EMBOSS-2.8.0. > problem: ACD backwards compatibility > > I realised that the upcoming EMBOSS release does not understand the > old attributes anymore (here: attribute "required"). Wouldn't it be > nice to have some backwards compatibility for the cases, where the > keywords simply have changed? Yes. I have code to do that. There was a problem with "standard" and "standardtype" which will clash if abbrevitions are used ("standardtype" is renamed "knowntype"). Assuming nobody had "standardtype" shortened to "standard" it should be OK. The existing code had to be cleaned up for acdvalid to report correctly, but now the ACD files are cleaned we can add the old "required" and "optional" attributes back as aliases ... but for a limited time. They will be gone by release 3.0.0. regards, Peter Rice From gbottu at ben.vub.ac.be Mon Oct 27 16:23:11 2003 From: gbottu at ben.vub.ac.be (Guy Bottu) Date: Mon, 27 Oct 2003 17:23:11 +0100 (CET) Subject: fastA and BLAST under EMBOSS, the DB problem Message-ID: <200310271623.h9RGNBVp1335193@black.vub.ac.be> from : BEN Dear colleagues, Recently the discussion about integrating BLAST and fastA under EMBOSS has flared up again. At the BEN site we have BLAST, fastA and some other programs installed under an EMBOSS "wrapper" program. In their present form these programs are however not readily installable elsewhere. When a year ago we dropped GCG I rushed to replace the lost functionality for our users and did not consider portability. I think it would be a good idea to distribute our BLAST and fastA wrappers as an "Embassadir". Therefore I would like to co-operate with the developement team of EMBOSS as well as with the developers of GUI's to see what is necessary. The most serious problem is databank access. The fastA programs need a databank in fastA format. If we choose the option of editing the original code there must be a way to retrieve the sequences and feed them serially to the algorithm. If we however choose the option of making a "wrapper" (like emma), as I did, the question is how to provide the sequences. Saving the complete EMBL databank in /tmp/xxx each time you want to search it is evidently not convenient. Therefore my idea was to access directly already installed databanks in fastA format. In the current version of our wrappers the names of the available databanks are written in the ACD files. This is of course not convenient at all. A way of getting around thi hurdle is, I think, the following : the local manager must anyway have the "native" fastA installed and properly configured. The available databanks must be listed in a configuration file. The name of the file is pointed at with the environment variable FASTLIBS or is put on the command line as -l xxx . The file contains lines of type : EMBL (general nucleic acid databank)$1+em+@/dbfb/fastalibs/embl.lib SwissProt (general protein databank)$0+sw+/dbfb/swissprot/sw So, it contains as well a text to be displayed by the interface as a short name (em) to be put on the command line as the actual location of the databank (singe file or "library"). Evidently EMBOSS could parse this file. Maybe a new ACD object of type "fastalib" could be implemented. Then the ACD files would need to contain just : fastalib: fastalib [ required: "@.... type: "@....nucleotide.....protein.... ] The local manager would have to put in emboss.defaults a line of type FASTADB [ file: configfile_xxx ] or EMBOSS could just read the environment variable FASTLIBS. For BLAST you need databanks in BLAST format, so editing the original code will not circumvent the problem. A similar approach is however possible : if all the databanks are put in a single directory (environment variable BLASTDB). A problem is how to obtain a long text with the databank description to be displayed in the interface. If all the databanks have a *.nal or *.pal file the TITLE attribute could be used, although letting EMBOSS parse all those files each time you start the program is maybe not a good idea. What do you think about it. Regards, Guy Bottu From pmr at ebi.ac.uk Mon Oct 27 18:29:20 2003 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 27 Oct 2003 18:29:20 +0000 Subject: fastA and BLAST under EMBOSS, the DB problem In-Reply-To: <200310271623.h9RGNBVp1335193@black.vub.ac.be> References: <200310271623.h9RGNBVp1335193@black.vub.ac.be> Message-ID: <3F9D6400.9000403@ebi.ac.uk> Guy Bottu wrote: > I think it would be a good idea to distribute our > BLAST and fastA wrappers as an "Embassadir". Therefore I would like to > co-operate with the developement team of EMBOSS as well as with the developers > of GUI's to see what is necessary. > > The most serious problem is databank access. EMBOSS database definitions now include the concept of "resource" which can be used to define databases for FASTA and BLAST and any otehr resources. 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