From tcarver at hgmp.mrc.ac.uk Mon Nov 5 13:23:12 2001 From: tcarver at hgmp.mrc.ac.uk (Tim Carver) Date: Mon, 05 Nov 2001 18:23:12 +0000 Subject: Jemboss v.alpha1.0 Release Message-ID: <3BE6D910.FC55832@hgmp.mrc.ac.uk> Announcing Jemboss v.alpha1.0 Release ============================== Jemboss is a graphical user interface to EMBOSS, written in Java. It is currently being developed at the HGMP-RC by Tim Carver in the EMBOSS developement team. It is now part of the EMBOSS distribution. Jemboss is being written to be run either as (i) a client-server interface or (ii) standalone and using a local EMBOSS installation. However, most of the development has been on building a client-server, to enable access to EMBOSS from remote sites and on PC workstations. A server has been setup at the a HGMP which is available to registered users of the HGMP. This enables the user to download the client onto a PC or unix platform and connect to the HGMP server which runs the applications. This webpage is currently available at: http://www.uk.embnet.org/Software/EMBOSS/Jemboss/ Jemboss presents you with a form to assign the input parameters for each program. Given a sequence, it will work out the values of the input parameters that are dependent on the sequence attributes. This is done by a JNI (Java Native Interface) call to the EMBOSS ajax libraries. It is also being designed to cope with all the inter-dependencies of other input parameters. (See the note below for compiling EMBOSS to use JNI). Results are stored on the server and can be re-called. Also, run information is stored on the server (date of run, command line). If the application is run interactively then the results are automatically displayed on the screen. Otherwise a job manager keeps track of all programs submitted to a batch queue in a Jemboss session. File system management is provided, both on the users machine locally and on the server. The files can be dragged from the file tree into the form. Files can also be opened and displayed from the file manager. More work is being carried out in this area, to add additional functionality (e.g. file transfer between local and remote file systems). Downloading from the CVS: ==================== This is currently only available from the HGMP CVS server. See: http://www.uk.embnet.org/Software/EMBOSS/Doc/cvs.html NB: In downloading from the CVS server, as well as downloading Jemboss, you are also downloading an inter-release version of EMBOSS which has not yet been put through the testing procedures. To configure EMBOSS to use the Java Native Interface in Jemboss a "--with-java" and "--with-javaos" need to be used, and pointed at the java1.3 installation. For example: ./configure --enable-warnings --with-pngdriver=/packages/emboss/png --with-java=/packages/java/jdk1.3/include --with-javaos=/packages/java/jdk1.3/include/solaris and must not be configured using the --disable-shared configure option. Known CVS problem: ================ The xerces.jar file appears to get currupted when added to the server. So a copy of this jar file has been made available on via anonymous ftp: ftp://ftp.uk.embnet.org/pub/EMBOSS/jemboss/xerces.jar which needs to be put in $EMBOSS_ROOT/jemboss/lib. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss-dev/attachments/20011105/c4e9fe77/attachment.html From dmartin at bioinformatics.msiwtb.dundee.ac.uk Fri Nov 16 09:28:13 2001 From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin) Date: Fri, 16 Nov 2001 14:28:13 +0000 (GMT) Subject: Number of division files in emblcd indices.. Message-ID: I am ploughing through the code for a number of things trying to work out why my EMBL indexing isn't working. I notice that there is a limit on the number of files in a division.. with EMBL now being 254 files, is this a problem? ..d ---------------------------------- David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, Dundee ---------------------------------- From gd168 at sparqnet.net Tue Nov 27 22:42:30 2001 From: gd168 at sparqnet.net (gd168 at sparqnet.net) Date: Wed, 28 Nov 2001 03:42:30 +0000 (GMT) Subject: =?big5?Q?=A8=E7=BD=D0=A5=FE=B0=EA=A6U=AF=C5=BE=C7=AE=D5=C5T=C0=B3=C0=F4=ABO=A5=FE=AD=B1=A6^=A6=AC=AA=C5=A7X,=A8=C3=BD=D0=B1=C4=A5=CE=A6=B3=C0=F4=ABO=BC=D0=B3=B9=BB{=C3=D2=A4=A7=C0=F4=ABO=B9p=AEg=BA=D2=AF=BB=A7X=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@?= ctVsw2llcKGbjNE Message-ID: An HTML attachment was scrubbed... URL: http://lists.open-bio.org/pipermail/emboss-dev/attachments/20011128/2878fc42/attachment.html From tcarver at hgmp.mrc.ac.uk Mon Nov 5 18:23:12 2001 From: tcarver at hgmp.mrc.ac.uk (Tim Carver) Date: Mon, 05 Nov 2001 18:23:12 +0000 Subject: Jemboss v.alpha1.0 Release Message-ID: <3BE6D910.FC55832@hgmp.mrc.ac.uk> Announcing Jemboss v.alpha1.0 Release ============================== Jemboss is a graphical user interface to EMBOSS, written in Java. It is currently being developed at the HGMP-RC by Tim Carver in the EMBOSS developement team. It is now part of the EMBOSS distribution. Jemboss is being written to be run either as (i) a client-server interface or (ii) standalone and using a local EMBOSS installation. However, most of the development has been on building a client-server, to enable access to EMBOSS from remote sites and on PC workstations. A server has been setup at the a HGMP which is available to registered users of the HGMP. This enables the user to download the client onto a PC or unix platform and connect to the HGMP server which runs the applications. This webpage is currently available at: http://www.uk.embnet.org/Software/EMBOSS/Jemboss/ Jemboss presents you with a form to assign the input parameters for each program. Given a sequence, it will work out the values of the input parameters that are dependent on the sequence attributes. This is done by a JNI (Java Native Interface) call to the EMBOSS ajax libraries. It is also being designed to cope with all the inter-dependencies of other input parameters. (See the note below for compiling EMBOSS to use JNI). Results are stored on the server and can be re-called. Also, run information is stored on the server (date of run, command line). If the application is run interactively then the results are automatically displayed on the screen. Otherwise a job manager keeps track of all programs submitted to a batch queue in a Jemboss session. File system management is provided, both on the users machine locally and on the server. The files can be dragged from the file tree into the form. Files can also be opened and displayed from the file manager. More work is being carried out in this area, to add additional functionality (e.g. file transfer between local and remote file systems). Downloading from the CVS: ==================== This is currently only available from the HGMP CVS server. See: http://www.uk.embnet.org/Software/EMBOSS/Doc/cvs.html NB: In downloading from the CVS server, as well as downloading Jemboss, you are also downloading an inter-release version of EMBOSS which has not yet been put through the testing procedures. To configure EMBOSS to use the Java Native Interface in Jemboss a "--with-java" and "--with-javaos" need to be used, and pointed at the java1.3 installation. For example: ./configure --enable-warnings --with-pngdriver=/packages/emboss/png --with-java=/packages/java/jdk1.3/include --with-javaos=/packages/java/jdk1.3/include/solaris and must not be configured using the --disable-shared configure option. Known CVS problem: ================ The xerces.jar file appears to get currupted when added to the server. So a copy of this jar file has been made available on via anonymous ftp: ftp://ftp.uk.embnet.org/pub/EMBOSS/jemboss/xerces.jar which needs to be put in $EMBOSS_ROOT/jemboss/lib. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmartin at bioinformatics.msiwtb.dundee.ac.uk Fri Nov 16 14:28:13 2001 From: dmartin at bioinformatics.msiwtb.dundee.ac.uk (David Martin) Date: Fri, 16 Nov 2001 14:28:13 +0000 (GMT) Subject: Number of division files in emblcd indices.. Message-ID: I am ploughing through the code for a number of things trying to work out why my EMBL indexing isn't working. I notice that there is a limit on the number of files in a division.. with EMBL now being 254 files, is this a problem? ..d ---------------------------------- David Martin PhD Bioinformatics Scientific Officer Wellcome Trust Biocentre, Dundee ---------------------------------- From gd168 at sparqnet.net Wed Nov 28 03:42:30 2001 From: gd168 at sparqnet.net (gd168 at sparqnet.net) Date: Wed, 28 Nov 2001 03:42:30 +0000 (GMT) Subject: =?big5?Q?=A8=E7=BD=D0=A5=FE=B0=EA=A6U=AF=C5=BE=C7=AE=D5=C5T=C0=B3=C0=F4=ABO=A5=FE=AD=B1=A6^=A6=AC=AA=C5=A7X,=A8=C3=BD=D0=B1=C4=A5=CE=A6=B3=C0=F4=ABO=BC=D0=B3=B9=BB{=C3=D2=A4=A7=C0=F4=ABO=B9p=AEg=BA=D2=AF=BB=A7X=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@=A1@?= ctVsw2llcKGbjNE Message-ID: An HTML attachment was scrubbed... URL: