From mail at tobias-schwarz.net Sat Jun 6 12:41:16 2009 From: mail at tobias-schwarz.net (Tobias Schwarz) Date: Sat, 06 Jun 2009 18:41:16 +0200 Subject: [EMBOSS] kemboss GUI for EMBOSS 6.0.1 Message-ID: <4A2A9C2C.3020403@tobias-schwarz.net> Dear all, I am happy to announce kemboss, a graphical user interface for EMBOSS 6.0.1, based on the Kaptain scripts by Thomas Siegmund. In contrast to the scripts, kemboss is a compiled binary, and is therefore not dependent on kaptain. It thus offers some advantages, for example the possibility to save and load individual settings, print the program output, an integrated editor, etc. Kemboss 0.9 is based on Qt4 and thus is available for Linux, Windows, MacOS and many other Unix systems. Some screenshots, the source code, as well as binaries for the above-mentioned operating systems are available at: http://www.tobias-schwarz.net/kemboss.html Please report all problems, bugs and suggestions to kemboss at tobias-schwarz.net Have fun, Tobias -- Tobias Schwarz University of Wuerzburg Children's Hospital Josef-Schneider-Str. 2 97090 Wuerzburg, Germany www.tobias-schwarz.net From pmr at ebi.ac.uk Mon Jun 8 09:41:19 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 08 Jun 2009 14:41:19 +0100 Subject: [EMBOSS] EMBOSS Funding and New developments Message-ID: <4A2D14FF.9000109@ebi.ac.uk> Dear EMBOSS Users and Developers We bring you great news - EMBOSS is funded in full by the BBSRC "Bioinformatics and Biological Resources" Fund. We now have money for Alan Bleasby and 2 other positions (Jon Ison and Mahmut Uludag) from 1st May until the end of 2011. The core aims of the funding proposal were to continue support, maintenance and development of EMBOSS, and to provide extensive online training materials for users, developers and system administrators using text from a series of books to be published by Cambridge University Press. We are also explicitly targeting areas where we see EMBOSS can be expanded: * Richer data content in EMBOSS outputs leading to major improvements in the integration and visualisation of results in browsers. * Processing many more data fields in EMBOSS inputs (taxonomy, genes, GO terms, cross-references, keywords. * Extending and improving database access: better indexing, query language support and combining searches across multiple databases, support for non-sequence data resources and new data access methods * Scaling up the libraries and adding new applications to support the data volumes generated by next-generation sequencing runs. We anticipate many more users will be working with short read data mapped to reference sequences over the next few years. * We aim to add at least 100 new applications in these 3 years. Suggestions for new applications are very welcome. * Release 6.1.0 will appear, as usual, on 15th July. * Major work on new developments and new library code will start from August. We hope to meet many of you at BOSC/ISMB/ECCB in Stockholm at the end of this month, We will arrange a lunchtime "Birds of a Feather" session at ISMB to discuss the needs of users over the next 3 years. regards, Peter Rice From georgios at biotek.uio.no Tue Jun 9 04:40:17 2009 From: georgios at biotek.uio.no (George Magklaras) Date: Tue, 09 Jun 2009 10:40:17 +0200 Subject: [EMBOSS] [emboss-dev] EMBOSS Funding and New developments In-Reply-To: <4A2D14FF.9000109@ebi.ac.uk> References: <4A2D14FF.9000109@ebi.ac.uk> Message-ID: <4A2E1FF1.4030902@biotek.uio.no> That's very good news Peter. I would add to the list the production of documentation for the EMBOSS admins. In terms of improving the indexing, may node managers (including myself) have created scripts to automate the formatting of large databases. Maybe it might be an idea to include them in some sort of add-on section, so that people can have error-free formatted dbs with the click of a button or a script call. GM -- George Magklaras BSc Hons MPhil RHCE:805008309135525 Senior Computer Systems Engineer/EMBnet node manager EMBnet Technical Management Board The Biotechnology Centre of Oslo, University of Oslo http://www.no.embnet.org Tel: +47-22840535 -- Peter Rice wrote: > Dear EMBOSS Users and Developers > > We bring you great news - EMBOSS is funded in full by the BBSRC > "Bioinformatics and Biological Resources" Fund. We now have money for > Alan Bleasby and 2 other positions (Jon Ison and Mahmut Uludag) from 1st > May until the end of 2011. > > The core aims of the funding proposal were to continue support, > maintenance and development of EMBOSS, and to provide extensive online > training materials for users, developers and system administrators using > text from a series of books to be published by Cambridge University Press. > > We are also explicitly targeting areas where we see EMBOSS can be > expanded: > > * Richer data content in EMBOSS outputs leading to major improvements > in the integration and visualisation of results in browsers. > > * Processing many more data fields in EMBOSS inputs (taxonomy, > genes, GO terms, cross-references, keywords. > > * Extending and improving database access: better indexing, query > language support and combining searches across multiple databases, > support for non-sequence data resources and new data access methods > > * Scaling up the libraries and adding new applications to support the > data volumes generated by next-generation sequencing runs. We > anticipate many more users will be working with short read data > mapped to reference sequences over the next few years. > > * We aim to add at least 100 new applications in these 3 years. > Suggestions for new applications are very welcome. > > * Release 6.1.0 will appear, as usual, on 15th July. > > * Major work on new developments and new library code will start from > August. > > We hope to meet many of you at BOSC/ISMB/ECCB in Stockholm at the end of > this month, We will arrange a lunchtime "Birds of a Feather" session > at ISMB to discuss the needs of users over the next 3 years. > > regards, > > Peter Rice > _______________________________________________ > emboss-dev mailing list > emboss-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss-dev > From pmr at ebi.ac.uk Tue Jun 9 11:11:58 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 09 Jun 2009 16:11:58 +0100 Subject: [EMBOSS] [emboss-dev] EMBOSS Funding and New developments In-Reply-To: <4A2E1FF1.4030902@biotek.uio.no> References: <4A2D14FF.9000109@ebi.ac.uk> <4A2E1FF1.4030902@biotek.uio.no> Message-ID: <4A2E7BBE.8030500@ebi.ac.uk> George Magklaras wrote: > That's very good news Peter. > > I would add to the list the production of documentation for the EMBOSS > admins. In terms of improving the indexing, may node managers (including > myself) have created scripts to automate the formatting of large > databases. Maybe it might be an idea to include them in some sort of > add-on section, so that people can have error-free formatted dbs with > the click of a button or a script call. Documentation is on the way in the form of an Administrators Guide ... long promised but we are now adding the final touches to the text. The book will be open source and the text will also appear on the EMBOSS website. As to the scripts ... yes, and excellent suggestion. We could make a directory adminscripts in the distribution for these. Please contribute useful scripts for use to include. We would like to include some documentation on what the script is intended to do and how to modify it. As the target users are administrators, we can expect them to be able to make their own modifications. regards, Peter Rice From dalloliogm at gmail.com Tue Jun 9 11:44:54 2009 From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio) Date: Tue, 9 Jun 2009 17:44:54 +0200 Subject: [EMBOSS] EMBOSS Funding and New developments In-Reply-To: <4A2D14FF.9000109@ebi.ac.uk> References: <4A2D14FF.9000109@ebi.ac.uk> Message-ID: <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> On Mon, Jun 8, 2009 at 3:41 PM, Peter Rice wrote: > Dear EMBOSS Users and Developers > > Suggestions for new applications are very welcome. > I think EMBOSS is highly effective when combined with Makefiles or tools to describe pipelines. Maybe in the future you could add some recipe or example in the documentation, it would be useful. In any case, it would be good to add to the tutorials some references on methods to describe pipelines. Another need that people have asked me several times (I am administrator of a web forum on bioinformatics) is to have a standard and official web interface to the emboss tools, since the list at http://emboss.sourceforge.net/interfaces/#web is outdated and google doesn't return clear results. > > > We hope to meet many of you at BOSC/ISMB/ECCB in Stockholm at the end of > this month, We will arrange a lunchtime "Birds of a Feather" session > at ISMB to discuss the needs of users over the next 3 years. > > regards, > > Peter Rice > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- Giovanni Dall'Olio, phd student Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain) My blog on bioinformatics: http://bioinfoblog.it From pmr at ebi.ac.uk Tue Jun 9 11:59:45 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 09 Jun 2009 16:59:45 +0100 Subject: [EMBOSS] EMBOSS Funding and New developments In-Reply-To: <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> References: <4A2D14FF.9000109@ebi.ac.uk> <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> Message-ID: <4A2E86F1.2050507@ebi.ac.uk> Giovanni Marco Dall'Olio wrote: > I think EMBOSS is highly effective when combined with Makefiles or tools to > describe pipelines. > Maybe in the future you could add some recipe or example in the > documentation, it would be useful. In any case, it would be good to add to > the tutorials some references on methods to describe pipelines. What pipelines so users prefer? We have experience with Taverna and with SoapLab web services. We have also worked with Accelrys/Scitegic's Pipeline Pilot. These all include EMBOSS examples in their documentation. > Another need that people have asked me several times (I am administrator of > a web forum on bioinformatics) is to have a standard and official web > interface to the emboss tools, since the list at > http://emboss.sourceforge.net/interfaces/#web is outdated and google doesn't > return clear results. We have long hoped that one interface would become the standard. Our usual recommendation for web-based users is the wEMBOSS interface but when ever we ask which interfaces users prefer we get many different replies. So, please let us know which interfaces you like best and we will try to work with the developers to make sure it keeps up with changes to EMBOSS ... and we can try to help them by adding new features or by automatically building their interface to a new EMBOSS release. regards, Peter Rice From dalloliogm at gmail.com Tue Jun 9 13:11:11 2009 From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio) Date: Tue, 9 Jun 2009 19:11:11 +0200 Subject: [EMBOSS] EMBOSS Funding and New developments In-Reply-To: <4A2E86F1.2050507@ebi.ac.uk> References: <4A2D14FF.9000109@ebi.ac.uk> <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> <4A2E86F1.2050507@ebi.ac.uk> Message-ID: <5aa3b3570906091011v16ea5f89h55c14928e4b4361d@mail.gmail.com> On Tue, Jun 9, 2009 at 5:59 PM, Peter Rice wrote: > Giovanni Marco Dall'Olio wrote: > > I think EMBOSS is highly effective when combined with Makefiles or tools > to > > describe pipelines. > > Maybe in the future you could add some recipe or example in the > > documentation, it would be useful. In any case, it would be good to add > to > > the tutorials some references on methods to describe pipelines. > > What pipelines so users prefer? > > We have experience with Taverna and with SoapLab web services. We have > also worked with Accelrys/Scitegic's Pipeline Pilot. These all include > EMBOSS examples in their documentation. Yes, taverna and soaplab services are very good but they are more oriented to write applications that connect to Internet and execute tools which are also web services. Sometimes you need much simpler tools, e.g. organize a workflow of command line tools to be run in local on an unix shell, and this is something for which emboss is very good, since it resembles many unix tools like grep and similar. My favorite introduction to Makefiles is the one on the Software Carpentry manual: - http://swc.scipy.org/lec/build.html I could write some example for you if you want, but actually I haven't been using emboss for a while, so.. let me re-read the documentation first :-) > Another need that people have asked me several times (I am administrator > of > > a web forum on bioinformatics) is to have a standard and official web > > interface to the emboss tools, since the list at > > http://emboss.sourceforge.net/interfaces/#web is outdated and google > doesn't > > return clear results. > > We have long hoped that one interface would become the standard. Our > usual recommendation for web-based users is the wEMBOSS interface but > when ever we ask which interfaces users prefer we get many different > replies. > > So, please let us know which interfaces you like best and we will try to > work with the developers to make sure it keeps up with changes to EMBOSS > ... and we can try to help them by adding new features or by > automatically building their interface to a new EMBOSS release. > the web forum is this one (in Italian): - http://www.molecularlab.it/forum/default.asp usually, people ask questions like 'how to I translate a sequence to protein?', 'how to create a dotplot', etc.. - there is not always a good answer to these questions, but in the past I have suggested the emboss tools because they seemed a kind of standard. (by the way, it would be good to know which tests have being applied to verify emboss code. I don't like telling people to use a command line tool, if there is no way to tell that it has been proved to work fine). I used to like very much this interface: - http://embossgui.sourceforge.net/demo/ which is very clear and has a list of all the tools, but is still running the 3.0 version. I also like the ebi interface, because it is hosted on an well-known server (people don't like using servers they don't know) but it supports very few tools; galaxy has also a nice web interface to emboss, but sometimes you just need to link a paste&submit interface to execute simple tasks like translating a sequence, and I haven't found anything like that yet. > regards, > > Peter Rice > -- Giovanni Dall'Olio, phd student Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain) My blog on bioinformatics: http://bioinfoblog.it From gbottu at vub.ac.be Thu Jun 11 10:41:10 2009 From: gbottu at vub.ac.be (Guy Bottu) Date: Thu, 11 Jun 2009 16:41:10 +0200 Subject: [EMBOSS] EMBOSS Funding and New developments In-Reply-To: <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> References: <4A2D14FF.9000109@ebi.ac.uk> <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> Message-ID: <4A311786.6000504@vub.ac.be> Giovanni Marco Dall'Olio wrote: > Another need that people have asked me several times (I am administrator of > a web forum on bioinformatics) is to have a standard and official web > interface to the emboss tools, since the list at > http://emboss.sourceforge.net/interfaces/#web is outdated and google doesn't > return clear results. Now that we are at it, could the hyperlink not be changed ? It is http://wemboss.sourceforge.net and not anymore http://www.wemboss.org Guy Bottu From belegdol at gmail.com Fri Jun 12 16:40:08 2009 From: belegdol at gmail.com (Julian Sikorski) Date: Fri, 12 Jun 2009 22:40:08 +0200 Subject: [EMBOSS] Packaging EMBOSS for Fedora Message-ID: Hi, a while ago I made an attempt to create an EMBOSS package for Fedora [1]. The progress was stalled for a while due to my MSc having higher priority, but I have recently picked up the work again. I have one crucial question: is it worth to package jemboss? It seems it didn't see development since 2005, and I have experienced some important issues when trying to use it (mainly not working with files with spaces in filenames). What do you think? Kind regards, Julian [1] https://bugzilla.redhat.com/show_bug.cgi?id=496133 From uludag at ebi.ac.uk Fri Jun 12 19:49:16 2009 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Sat, 13 Jun 2009 00:49:16 +0100 Subject: [EMBOSS] Packaging EMBOSS for Fedora In-Reply-To: References: Message-ID: <1244850556.8999.7.camel@login-svr1.ebi.ac.uk> Hi Julian, > I have one crucial question: is it worth to package jemboss? It seems it > didn't see development since 2005, and I have experienced some important > issues when trying to use it (mainly not working with files with spaces > in filenames). What do you think? I had a quick look into the files with spaces in filenames problem, we can include a fix in the coming release (6.1) for this problem. Previous release of EMBOSS (6.0) included some fixes of similar nature, as well as some small gui improvements. We recently have updated EMBOSS/Jemboss make/install machinery to make standalone Jemboss come out of box when users install EMBOSS, i think we were successful and this will be a new feature in EMBOSS 6.1. Regards, Mahmut From koenvanderdrift at gmail.com Mon Jun 15 13:30:47 2009 From: koenvanderdrift at gmail.com (Koen van der Drift) Date: Mon, 15 Jun 2009 13:30:47 -0400 Subject: [EMBOSS] Mac OS X instructions Message-ID: <5cba6b9f0906151030k1725891fmfd3f3e4faad746c@mail.gmail.com> Hi, Unless I missed it, I noticed that the EMBOSS website has some very outdated instructions on how to install EMBOSS on Mac OS X, eg here http://emboss.sourceforge.net/download/macosx.html and here (outside link from EMBOSS website): http://gnu-darwin.sourceforge.net/gdc/emboss.txt As most of you probably know there has been also the possibility for a while to use the fink package manager for this. I am the maintainer of that package, and try to keep it updated, version 6.0.1 is available including most of the patches. Fink is a very convenient means to install packages, and will take care of installing all the necessary third party packages and proper configuration. Is it possible to update the website to include this possibility, and maybe remove the older and outdated links? Thanks, - Koen. From hmenager at pasteur.fr Tue Jun 16 05:06:23 2009 From: hmenager at pasteur.fr (hmenager at pasteur.fr) Date: Tue, 16 Jun 2009 11:06:23 +0200 (CEST) Subject: [EMBOSS] EMBOSS Funding and New developments In-Reply-To: References: Message-ID: <56720.157.99.64.103.1245143183.squirrel@php.pasteur.fr> Hi, > I used to like very much this interface: > - http://embossgui.sourceforge.net/demo/ > which is very clear and has a list of all the tools, but is still running > the 3.0 version. > > I also like the ebi interface, because it is hosted on an well-known > server > (people don't like using servers they don't know) but it supports very few > tools; > > galaxy has also a nice web interface to emboss, but sometimes you just > need > to link a paste&submit interface to execute simple tasks like translating > a > sequence, and I haven't found anything like that yet. You could also give a try to Mobyle, which is the successor to Pise, mentionned on the EMBOSS web interfaces page, but not maintained anymore. Although it is not specific to EMBOSS, most of the package is supported by Mobyle, as well as some others (Phylip, Vienna RNA, BLASTs ...). You can try it for instance at: http://mobyle.pasteur.fr If you want information about the system, or to download it, refer to: http://bioweb2.pasteur.fr/projects/mobyle/ Regards, Herv? M?nager From hmenager at pasteur.fr Tue Jun 16 05:20:32 2009 From: hmenager at pasteur.fr (hmenager at pasteur.fr) Date: Tue, 16 Jun 2009 11:20:32 +0200 (CEST) Subject: [EMBOSS] EMBOSS Digest, Vol 48, Issue 2 In-Reply-To: References: Message-ID: <59215.157.99.64.103.1245144032.squirrel@php.pasteur.fr> > Send EMBOSS mailing list submissions to > emboss at lists.open-bio.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/emboss > or, via email, send a message with subject or body 'help' to > emboss-request at lists.open-bio.org > > You can reach the person managing the list at > emboss-owner at lists.open-bio.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of EMBOSS digest..." > > > Today's Topics: > > 1. Re: [emboss-dev] EMBOSS Funding and New developments (Peter Rice) > 2. Re: EMBOSS Funding and New developments (Giovanni Marco Dall'Olio) > 3. Re: EMBOSS Funding and New developments (Peter Rice) > 4. Re: EMBOSS Funding and New developments (Giovanni Marco Dall'Olio) > 5. Re: EMBOSS Funding and New developments (Guy Bottu) > 6. Packaging EMBOSS for Fedora (Julian Sikorski) > 7. Re: Packaging EMBOSS for Fedora (Mahmut Uludag) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 09 Jun 2009 16:11:58 +0100 > From: Peter Rice > Subject: Re: [EMBOSS] [emboss-dev] EMBOSS Funding and New developments > To: George Magklaras > Cc: emboss > Message-ID: <4A2E7BBE.8030500 at ebi.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1 > > George Magklaras wrote: >> That's very good news Peter. >> >> I would add to the list the production of documentation for the EMBOSS >> admins. In terms of improving the indexing, may node managers (including >> myself) have created scripts to automate the formatting of large >> databases. Maybe it might be an idea to include them in some sort of >> add-on section, so that people can have error-free formatted dbs with >> the click of a button or a script call. > > Documentation is on the way in the form of an Administrators Guide ... > long promised but we are now adding the final touches to the text. > > The book will be open source and the text will also appear on the EMBOSS > website. > > As to the scripts ... yes, and excellent suggestion. We could make a > directory adminscripts in the distribution for these. > > Please contribute useful scripts for use to include. We would like to > include some documentation on what the script is intended to do and how > to modify it. As the target users are administrators, we can expect them > to be able to make their own modifications. > > regards, > > Peter Rice > > > ------------------------------ > > Message: 2 > Date: Tue, 9 Jun 2009 17:44:54 +0200 > From: "Giovanni Marco Dall'Olio" > Subject: Re: [EMBOSS] EMBOSS Funding and New developments > To: Peter Rice > Cc: emboss-announce at emboss.open-bio.org, > emboss-dev at emboss.open-bio.org, emboss > Message-ID: > <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > On Mon, Jun 8, 2009 at 3:41 PM, Peter Rice wrote: > >> Dear EMBOSS Users and Developers >> > > >> Suggestions for new applications are very welcome. >> > > I think EMBOSS is highly effective when combined with Makefiles or tools > to > describe pipelines. > Maybe in the future you could add some recipe or example in the > documentation, it would be useful. In any case, it would be good to add to > the tutorials some references on methods to describe pipelines. > > Another need that people have asked me several times (I am administrator > of > a web forum on bioinformatics) is to have a standard and official web > interface to the emboss tools, since the list at > http://emboss.sourceforge.net/interfaces/#web is outdated and google > doesn't > return clear results. > > > > >> >> >> We hope to meet many of you at BOSC/ISMB/ECCB in Stockholm at the end of >> this month, We will arrange a lunchtime "Birds of a Feather" session >> at ISMB to discuss the needs of users over the next 3 years. >> >> regards, >> >> Peter Rice >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss >> > > > > -- > Giovanni Dall'Olio, phd student > Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain) > > My blog on bioinformatics: http://bioinfoblog.it > > > ------------------------------ > > Message: 3 > Date: Tue, 09 Jun 2009 16:59:45 +0100 > From: Peter Rice > Subject: Re: [EMBOSS] EMBOSS Funding and New developments > To: dalloliogm at gmail.com > Cc: emboss-dev at emboss.open-bio.org, emboss > > Message-ID: <4A2E86F1.2050507 at ebi.ac.uk> > Content-Type: text/plain; charset=UTF-8 > > Giovanni Marco Dall'Olio wrote: >> I think EMBOSS is highly effective when combined with Makefiles or tools >> to >> describe pipelines. >> Maybe in the future you could add some recipe or example in the >> documentation, it would be useful. In any case, it would be good to add >> to >> the tutorials some references on methods to describe pipelines. > > What pipelines so users prefer? > > We have experience with Taverna and with SoapLab web services. We have > also worked with Accelrys/Scitegic's Pipeline Pilot. These all include > EMBOSS examples in their documentation. > >> Another need that people have asked me several times (I am administrator >> of >> a web forum on bioinformatics) is to have a standard and official web >> interface to the emboss tools, since the list at >> http://emboss.sourceforge.net/interfaces/#web is outdated and google >> doesn't >> return clear results. > > We have long hoped that one interface would become the standard. Our > usual recommendation for web-based users is the wEMBOSS interface but > when ever we ask which interfaces users prefer we get many different > replies. > > So, please let us know which interfaces you like best and we will try to > work with the developers to make sure it keeps up with changes to EMBOSS > ... and we can try to help them by adding new features or by > automatically building their interface to a new EMBOSS release. > > regards, > > Peter Rice > > > ------------------------------ > > Message: 4 > Date: Tue, 9 Jun 2009 19:11:11 +0200 > From: "Giovanni Marco Dall'Olio" > Subject: Re: [EMBOSS] EMBOSS Funding and New developments > To: Peter Rice > Cc: emboss-dev at emboss.open-bio.org, emboss > > Message-ID: > <5aa3b3570906091011v16ea5f89h55c14928e4b4361d at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > On Tue, Jun 9, 2009 at 5:59 PM, Peter Rice wrote: > >> Giovanni Marco Dall'Olio wrote: >> > I think EMBOSS is highly effective when combined with Makefiles or >> tools >> to >> > describe pipelines. >> > Maybe in the future you could add some recipe or example in the >> > documentation, it would be useful. In any case, it would be good to >> add >> to >> > the tutorials some references on methods to describe pipelines. >> >> What pipelines so users prefer? >> >> We have experience with Taverna and with SoapLab web services. We have >> also worked with Accelrys/Scitegic's Pipeline Pilot. These all include >> EMBOSS examples in their documentation. > > > Yes, taverna and soaplab services are very good but they are more oriented > to write applications that connect to Internet and execute tools which are > also web services. > > Sometimes you need much simpler tools, e.g. organize a workflow of command > line tools to be run in local on an unix shell, and this is something for > which emboss is very good, since it resembles many unix tools like grep > and > similar. > > My favorite introduction to Makefiles is the one on the Software Carpentry > manual: > - http://swc.scipy.org/lec/build.html > > I could write some example for you if you want, but actually I haven't > been > using emboss for a while, so.. let me re-read the documentation first :-) > > > > > Another need that people have asked me several times (I am > administrator >> of >> > a web forum on bioinformatics) is to have a standard and official web >> > interface to the emboss tools, since the list at >> > http://emboss.sourceforge.net/interfaces/#web is outdated and google >> doesn't >> > return clear results. >> >> We have long hoped that one interface would become the standard. Our >> usual recommendation for web-based users is the wEMBOSS interface but >> when ever we ask which interfaces users prefer we get many different >> replies. >> >> So, please let us know which interfaces you like best and we will try to >> work with the developers to make sure it keeps up with changes to EMBOSS >> ... and we can try to help them by adding new features or by >> automatically building their interface to a new EMBOSS release. >> > > the web forum is this one (in Italian): > - http://www.molecularlab.it/forum/default.asp > usually, people ask questions like 'how to I translate a sequence to > protein?', 'how to create a dotplot', etc.. - there is not always a good > answer to these questions, but in the past I have suggested the emboss > tools > because they seemed a kind of standard. > (by the way, it would be good to know which tests have being applied to > verify emboss code. I don't like telling people to use a command line > tool, > if there is no way to tell that it has been proved to work fine). > > I used to like very much this interface: > - http://embossgui.sourceforge.net/demo/ > which is very clear and has a list of all the tools, but is still running > the 3.0 version. > > I also like the ebi interface, because it is hosted on an well-known > server > (people don't like using servers they don't know) but it supports very few > tools; > > galaxy has also a nice web interface to emboss, but sometimes you just > need > to link a paste&submit interface to execute simple tasks like translating > a > sequence, and I haven't found anything like that yet. > > > >> regards, >> >> Peter Rice >> > > > > -- > Giovanni Dall'Olio, phd student > Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain) > > My blog on bioinformatics: http://bioinfoblog.it > > > ------------------------------ > > Message: 5 > Date: Thu, 11 Jun 2009 16:41:10 +0200 > From: Guy Bottu > Subject: Re: [EMBOSS] EMBOSS Funding and New developments > To: Peter Rice > Cc: emboss-dev at emboss.open-bio.org, emboss > > Message-ID: <4A311786.6000504 at vub.ac.be> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Giovanni Marco Dall'Olio wrote: >> Another need that people have asked me several times (I am administrator >> of >> a web forum on bioinformatics) is to have a standard and official web >> interface to the emboss tools, since the list at >> http://emboss.sourceforge.net/interfaces/#web is outdated and google >> doesn't >> return clear results. > > Now that we are at it, could the hyperlink not be changed ? It is > http://wemboss.sourceforge.net and not anymore http://www.wemboss.org > > Guy Bottu > > > > > ------------------------------ > > Message: 6 > Date: Fri, 12 Jun 2009 22:40:08 +0200 > From: Julian Sikorski > Subject: [EMBOSS] Packaging EMBOSS for Fedora > To: emboss at emboss.open-bio.org > Message-ID: > Content-Type: text/plain; charset=UTF-8 > > Hi, > > a while ago I made an attempt to create an EMBOSS package for Fedora > [1]. The progress was stalled for a while due to my MSc having higher > priority, but I have recently picked up the work again. > I have one crucial question: is it worth to package jemboss? It seems it > didn't see development since 2005, and I have experienced some important > issues when trying to use it (mainly not working with files with spaces > in filenames). What do you think? > > Kind regards, > Julian > > [1] https://bugzilla.redhat.com/show_bug.cgi?id=496133 > > > > ------------------------------ > > Message: 7 > Date: Sat, 13 Jun 2009 00:49:16 +0100 > From: Mahmut Uludag > Subject: Re: [EMBOSS] Packaging EMBOSS for Fedora > To: Julian Sikorski > Cc: emboss at emboss.open-bio.org > Message-ID: <1244850556.8999.7.camel at login-svr1.ebi.ac.uk> > Content-Type: text/plain > > Hi Julian, > >> I have one crucial question: is it worth to package jemboss? It seems it >> didn't see development since 2005, and I have experienced some important >> issues when trying to use it (mainly not working with files with spaces >> in filenames). What do you think? > > I had a quick look into the files with spaces in filenames problem, we > can include a fix in the coming release (6.1) for this problem. Previous > release of EMBOSS (6.0) included some fixes of similar nature, as well > as some small gui improvements. We recently have updated EMBOSS/Jemboss > make/install machinery to make standalone Jemboss come out of box when > users install EMBOSS, i think we were successful and this will be a new > feature in EMBOSS 6.1. > > Regards, > Mahmut > > > > > ------------------------------ > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > > > End of EMBOSS Digest, Vol 48, Issue 2 > ************************************* > From hmenager at pasteur.fr Tue Jun 16 05:57:36 2009 From: hmenager at pasteur.fr (=?ISO-8859-1?Q?Herv=E9_M=E9nager?=) Date: Tue, 16 Jun 2009 11:57:36 +0200 Subject: [EMBOSS] EMBOSS Funding and New developments In-Reply-To: References: Message-ID: <4A376C90.4020801@pasteur.fr> Hi, > Another need that people have asked me several times (I am administrator of > a web forum on bioinformatics) is to have a standard and official web > interface to the emboss tools, since the list at > http://emboss.sourceforge.net/interfaces/#web is outdated and google doesn't > return clear results. You can also give a try to Mobyle. Mobyle is the successor to the Pise system which is listed on the above page but not maintained anymore. Although it is not specific to EMBOSS, most of the package is interfaced, and it also supports other popular packages (ViennaRNA, Phylip...). You can try it at http://mobyle.pasteur.fr/cgi-bin/portal.py, and get further information at http://bioweb2.pasteur.fr/projects/mobyle/. Regards, Herv? M?nager From hmenager at pasteur.fr Tue Jun 16 15:55:44 2009 From: hmenager at pasteur.fr (hmenager at pasteur.fr) Date: Tue, 16 Jun 2009 21:55:44 +0200 (CEST) Subject: [EMBOSS] EMBOSS Funding and New developments In-Reply-To: References: Message-ID: <56269.157.99.64.103.1245182144.squirrel@php.pasteur.fr> To all: sorry about my previous repeated replies. It seems my webmail is completely messed up. Herv? M?nager From andrespinzon at gmail.com Mon Jun 22 10:32:52 2009 From: andrespinzon at gmail.com (Andres Pinzon) Date: Mon, 22 Jun 2009 10:32:52 -0400 Subject: [EMBOSS] extractfeat and "-join" option Message-ID: <8968fc7e0906220732r7b53117cq2e2cc3551f15b91b@mail.gmail.com> Hi everyone, The following line, should return a single fasta file with all the CDS in a single sequence: extractfeat environmental:DP000238 -type CDS -join stdout Instead it is returning each of them as a separate entry. Am I doing something wrong? Best, -- Andr?s Pinz?n http://bioinf.ibun.unal.edu.co/~apinzon/ Bioinformatics Center, Colombia EMBnet node http://bioinf.ibun.unal.edu.co Tel +57 3165000 ext 16961 Fax +571 3165415 Micology and Phytopathology Laboratory - Los Andes University. http://bioinf.uniandes.edu.co Tel +571 3394949 ext. 2768 From pmr at ebi.ac.uk Mon Jun 22 11:44:16 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 22 Jun 2009 16:44:16 +0100 Subject: [EMBOSS] extractfeat and "-join" option In-Reply-To: <8968fc7e0906220732r7b53117cq2e2cc3551f15b91b@mail.gmail.com> References: <8968fc7e0906220732r7b53117cq2e2cc3551f15b91b@mail.gmail.com> Message-ID: <4A3FA6D0.2030202@ebi.ac.uk> Andres Pinzon wrote: > Hi everyone, > The following line, should return a single fasta file with all the CDS > in a single sequence: > > extractfeat environmental:DP000238 -type CDS -join stdout > > Instead it is returning each of them as a separate entry. Am I doing > something wrong? The -join option combines all exons for one CDS (so that it can be translated as a complete reading frame). It is not intended to join all CDSs into one. for environmental:DP000238 I get 10 CDSs with -join set and 52 (one per exon) without -join. Hope this helps, Peter From andrespinzon at gmail.com Mon Jun 22 11:56:05 2009 From: andrespinzon at gmail.com (Andres Pinzon) Date: Mon, 22 Jun 2009 11:56:05 -0400 Subject: [EMBOSS] extractfeat and "-join" option In-Reply-To: <4A3FA6D0.2030202@ebi.ac.uk> References: <8968fc7e0906220732r7b53117cq2e2cc3551f15b91b@mail.gmail.com> <4A3FA6D0.2030202@ebi.ac.uk> Message-ID: <8968fc7e0906220856o5bf7f75fr545dfef536ec838b@mail.gmail.com> That's perfect, thank you. On Mon, Jun 22, 2009 at 11:44 AM, Peter Rice wrote: > Andres Pinzon wrote:' >> Hi everyone, >> The following line, should return a single fasta file with all the CDS >> in a single sequence: >> >> ?extractfeat environmental:DP000238 -type CDS -join stdout >> >> Instead it is returning each of them as a separate entry. Am I doing >> something wrong? > > The -join option combines all exons for one CDS (so that it can be > translated as a complete reading frame). > > It is not intended to join all CDSs into one. > > for environmental:DP000238 I get 10 CDSs with -join set and 52 (one per > exon) without -join. > > Hope this helps, > > Peter > > -- Andr?s Pinz?n http://bioinf.ibun.unal.edu.co/~apinzon/ Bioinformatics Center, Colombia EMBnet node http://bioinf.ibun.unal.edu.co Tel +57 3165000 ext 16961 Fax +571 3165415 Micology and Phytopathology Laboratory - Los Andes University. http://bioinf.uniandes.edu.co Tel +571 3394949 ext. 2768 From stephen.taylor at imm.ox.ac.uk Wed Jun 24 06:04:17 2009 From: stephen.taylor at imm.ox.ac.uk (Steve Taylor) Date: Wed, 24 Jun 2009 11:04:17 +0100 Subject: [EMBOSS] Seqret fetch by URL Message-ID: <4A41FA21.4030101@imm.ox.ac.uk> Hi, I am trying to fetch a sequence using seqret. In my EMBOSS defaults I have the following entry set up. I am using EMBOSS 6.0.1 both on Linux and Solaris. DB NCBI_prot [ method: url format: fasta type: P url: "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=%s&uids=&dopt=fasta&dispmax=5&sendto=t&fr om=begin&to=end" comment: "NCBI protein - FASTA seqs only" ] If I try: seqret NCBI_prot:ACA69081 I get: Reads and writes (returns) sequences Error: Unable to read sequence 'NCBI_prot:ACA69081' Died: seqret terminated: Bad value for '-sequence' and no prompt However, if I try http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=ACA69081&uids=&dopt=fasta&dispmax=5&sendto=t&from=begin&to=end I get >gi|169751563|gb|ACA69081.1| glycoside hydrolase family 1 [Yersinia pseudotuberculosis YPIII] MSYQQLPKDFLWGGAVAAHQVEGGWDKGGKGVSIADVLSGGSHGVDRVMTDGVLEGYRYPNHEAVDFYSH YKEDIALFAEMGFKCFRTSIAWTRIFPHGDEQQPNEAGLQFYDDMFDELLKYGIEPVITLSHFEMPWHLV KEYGGWKNRKVVDFFVKFSEVVMARYKSKVKYWMTFNEINNQRNWKYPLFGYCCSGVVFTEQENPEETLY QVLHHQFVASAKVVKLGHAINPEFKIGCMVAMVPLYPFSCHPDDMMYSVEAMRERYLFGDVHMRGYYPSY ILQEWARRGFNIHMEEGDLETLRDGCADYMGLSYYMSNAVSAINPGSGNSLSGFEGSVPNPHVKASDWGW QIDPVGLRYSLSVLYERYQKPLFIVENGFGAIDKVAADGMVHDDYRIAYLKAHIEQMKKAVFEDGVDLMG YTPWGCIDCVSFTTGEYSKRYGFIYVDKNDDGTGTMARSRKLSFDWYKKVIASNGEVL Any ideas why or is there a way I can get more verbose information about what is going on? Thanks, Steve From pmr at ebi.ac.uk Wed Jun 24 07:14:19 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 24 Jun 2009 12:14:19 +0100 Subject: [EMBOSS] Seqret fetch by URL In-Reply-To: <4A41FA21.4030101@imm.ox.ac.uk> References: <4A41FA21.4030101@imm.ox.ac.uk> Message-ID: <4A420A8B.3020900@ebi.ac.uk> Steve Taylor wrote: > > Hi, > > I am trying to fetch a sequence using seqret. In my EMBOSS defaults I > have the following entry set up. I am using EMBOSS 6.0.1 both on Linux > and Solaris. > > DB NCBI_prot [ method: url format: fasta type: P > url: > "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=%s&uids=&dopt=fasta&dispmax=5&sendto=t&fr > > om=begin&to=end" > comment: "NCBI protein - FASTA seqs only" > ] > > If I try: > > seqret NCBI_prot:ACA69081 > > I get: > Reads and writes (returns) sequences > Error: Unable to read sequence 'NCBI_prot:ACA69081' > Died: seqret terminated: Bad value for '-sequence' and no prompt They have gone away .... but not very far. seqret -debug gives the actual HTML returned in the seqret.dbg file > === File Buffer: Before ajFileBuffStripHtml === > * 952daa0 HTTP/1.1 301 Moved permanently > 951b540 Date: Wed, 24 Jun 2009 11:07:02 GMT > 951b570 Server: Apache > 951b358 Location: /sviewer/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=AC > A69081&uids=&dopt=fasta&dispmax=5&sendto=t&fr > 951b388 Content-Type: text/plain > 952fd10 Vary: Accept-Encoding > 952fd40 Content-Length: 0 > 952fd70 Connection: close > 951c2e8 If you change /entrez to /sviewer in your URL it should work. Your web browser is able to follow these HTML redirects, EMBOSS is a little more basic. We gave up on trying to interpret HTML error messages in the very early days when one site responded to failed requests with a nice picture of a flower (for those new to the net ... it was EBI :-) Thanks for letting us know, Peter From ajb at ebi.ac.uk Wed Jun 24 07:15:45 2009 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 24 Jun 2009 12:15:45 +0100 (BST) Subject: [EMBOSS] Seqret fetch by URL In-Reply-To: <4A41FA21.4030101@imm.ox.ac.uk> References: <4A41FA21.4030101@imm.ox.ac.uk> Message-ID: <38786.86.26.12.63.1245842145.squirrel@webmail.ebi.ac.uk> Hi Steve, NCBI added an extra line in their entrez output. We put a patch file on the ftp server a while ago that should fix this. ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/ If it doesn't then if you add '-debug' to any EMBOSS application you'll get an 'applicationname'.dbg file which gives verbose information on the workings (or not) of the application. HTH Alan > > Hi, > > I am trying to fetch a sequence using seqret. In my EMBOSS defaults I have > the following entry set up. I am using EMBOSS 6.0.1 both on Linux and > Solaris. > > DB NCBI_prot [ method: url format: fasta type: P > url: > "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=%s&uids=&dopt=fasta&dispmax=5&sendto=t&fr > om=begin&to=end" > comment: "NCBI protein - FASTA seqs only" > ] > > If I try: > > seqret NCBI_prot:ACA69081 > > I get: > Reads and writes (returns) sequences > Error: Unable to read sequence 'NCBI_prot:ACA69081' > Died: seqret terminated: Bad value for '-sequence' and no prompt > > However, if I try > > http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=ACA69081&uids=&dopt=fasta&dispmax=5&sendto=t&from=begin&to=end > > I get > >>gi|169751563|gb|ACA69081.1| glycoside hydrolase family 1 [Yersinia >> pseudotuberculosis YPIII] > MSYQQLPKDFLWGGAVAAHQVEGGWDKGGKGVSIADVLSGGSHGVDRVMTDGVLEGYRYPNHEAVDFYSH > YKEDIALFAEMGFKCFRTSIAWTRIFPHGDEQQPNEAGLQFYDDMFDELLKYGIEPVITLSHFEMPWHLV > KEYGGWKNRKVVDFFVKFSEVVMARYKSKVKYWMTFNEINNQRNWKYPLFGYCCSGVVFTEQENPEETLY > QVLHHQFVASAKVVKLGHAINPEFKIGCMVAMVPLYPFSCHPDDMMYSVEAMRERYLFGDVHMRGYYPSY > ILQEWARRGFNIHMEEGDLETLRDGCADYMGLSYYMSNAVSAINPGSGNSLSGFEGSVPNPHVKASDWGW > QIDPVGLRYSLSVLYERYQKPLFIVENGFGAIDKVAADGMVHDDYRIAYLKAHIEQMKKAVFEDGVDLMG > YTPWGCIDCVSFTTGEYSKRYGFIYVDKNDDGTGTMARSRKLSFDWYKKVIASNGEVL > > > Any ideas why or is there a way I can get more verbose information about > what is going on? > > Thanks, > > Steve > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From stephen.taylor at imm.ox.ac.uk Wed Jun 24 08:18:18 2009 From: stephen.taylor at imm.ox.ac.uk (Steve Taylor) Date: Wed, 24 Jun 2009 13:18:18 +0100 Subject: [EMBOSS] Seqret fetch by URL In-Reply-To: <38786.86.26.12.63.1245842145.squirrel@webmail.ebi.ac.uk> References: <4A41FA21.4030101@imm.ox.ac.uk> <38786.86.26.12.63.1245842145.squirrel@webmail.ebi.ac.uk> Message-ID: <4A42198A.2050902@imm.ox.ac.uk> Hi Peter/Alan, Thanks - I changed to entrez to sviewer and it all works fine now. Steve > > NCBI added an extra line in their entrez output. We put a patch file on > the ftp server a while ago that should fix this. > > ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/ > > If it doesn't then if you add '-debug' to any EMBOSS application > you'll get an 'applicationname'.dbg file which gives verbose information > on the workings (or not) of the application. > > HTH > > Alan > > >> Hi, >> >> I am trying to fetch a sequence using seqret. In my EMBOSS defaults I have >> the following entry set up. I am using EMBOSS 6.0.1 both on Linux and >> Solaris. >> >> DB NCBI_prot [ method: url format: fasta type: P >> url: >> "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=%s&uids=&dopt=fasta&dispmax=5&sendto=t&fr >> om=begin&to=end" >> comment: "NCBI protein - FASTA seqs only" >> ] >> >> If I try: >> >> seqret NCBI_prot:ACA69081 >> >> I get: >> Reads and writes (returns) sequences >> Error: Unable to read sequence 'NCBI_prot:ACA69081' >> Died: seqret terminated: Bad value for '-sequence' and no prompt >> >> However, if I try >> >> http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=ACA69081&uids=&dopt=fasta&dispmax=5&sendto=t&from=begin&to=end >> >> I get >> >>> gi|169751563|gb|ACA69081.1| glycoside hydrolase family 1 [Yersinia >>> pseudotuberculosis YPIII] >> MSYQQLPKDFLWGGAVAAHQVEGGWDKGGKGVSIADVLSGGSHGVDRVMTDGVLEGYRYPNHEAVDFYSH >> YKEDIALFAEMGFKCFRTSIAWTRIFPHGDEQQPNEAGLQFYDDMFDELLKYGIEPVITLSHFEMPWHLV >> KEYGGWKNRKVVDFFVKFSEVVMARYKSKVKYWMTFNEINNQRNWKYPLFGYCCSGVVFTEQENPEETLY >> QVLHHQFVASAKVVKLGHAINPEFKIGCMVAMVPLYPFSCHPDDMMYSVEAMRERYLFGDVHMRGYYPSY >> ILQEWARRGFNIHMEEGDLETLRDGCADYMGLSYYMSNAVSAINPGSGNSLSGFEGSVPNPHVKASDWGW >> QIDPVGLRYSLSVLYERYQKPLFIVENGFGAIDKVAADGMVHDDYRIAYLKAHIEQMKKAVFEDGVDLMG >> YTPWGCIDCVSFTTGEYSKRYGFIYVDKNDDGTGTMARSRKLSFDWYKKVIASNGEVL >> >> >> Any ideas why or is there a way I can get more verbose information about >> what is going on? >> >> Thanks, >> >> Steve >> >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss >> > > From jasonzhang2002 at gmail.com Fri Jun 26 13:53:31 2009 From: jasonzhang2002 at gmail.com (jason zhang) Date: Fri, 26 Jun 2009 10:53:31 -0700 Subject: [EMBOSS] ehmmbuild does not support -o and -hmmfile together In-Reply-To: <4A41FA21.4030101@imm.ox.ac.uk> References: <4A41FA21.4030101@imm.ox.ac.uk> Message-ID: <4A450B1B.7010800@gmail.com> An HTML attachment was scrubbed... URL: From jasonzhang2002 at gmail.com Fri Jun 26 13:54:26 2009 From: jasonzhang2002 at gmail.com (jason zhang) Date: Fri, 26 Jun 2009 10:54:26 -0700 Subject: [EMBOSS] please support HMMERDB environment variable like HMMER Message-ID: <4A450B52.9020805@gmail.com> An HTML attachment was scrubbed... URL: From jasonzhang2002 at gmail.com Fri Jun 26 13:55:19 2009 From: jasonzhang2002 at gmail.com (jason zhang) Date: Fri, 26 Jun 2009 10:55:19 -0700 Subject: [EMBOSS] please modify two acd files for hmmer package Message-ID: <4A450B87.30802@gmail.com> please modify : default: 100 to default: "100" in ehmmsearch and ehmmpfam. I have a java parser for acd files. my parser choke for these acd files. From pmr at ebi.ac.uk Fri Jun 26 15:40:07 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 26 Jun 2009 20:40:07 +0100 Subject: [EMBOSS] ehmmbuild does not support -o and -hmmfile together In-Reply-To: <4A450B1B.7010800@gmail.com> References: <4A41FA21.4030101@imm.ox.ac.uk> <4A450B1B.7010800@gmail.com> Message-ID: <4A452417.9060501@ebi.ac.uk> jason zhang wrote: > >ehmmbuild -auto -stdout -alignfile globins50.msf -nhmm globins50 > -hmmfile globin.hmm -o out > Error: Unable to open file 'out/globin.hmm' for output > Died: ehmmbuild terminated: Bad value for '-hmmfile' with -auto defined > > It seems that -o is treated as a directory. But the document/acd lists it > as outfile. It will work with a different commandline order. With -o after -hmmfile it is incorrectly assumed to be -odirectory (it should be an ambiguous qualifier). This is fixed in the July 15th release of EMBOSS. regards, Peter Rice From pmr at ebi.ac.uk Fri Jun 26 15:41:13 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 26 Jun 2009 20:41:13 +0100 Subject: [EMBOSS] please support HMMERDB environment variable like HMMER In-Reply-To: <4A450B52.9020805@gmail.com> References: <4A450B52.9020805@gmail.com> Message-ID: <4A452459.50002@ebi.ac.uk> jason zhang wrote: > ehmmpfam does not recognize HMMERDB environment variable as hmmpfam does. > Could this be supported? Yes .. we have added the ability to specify an input file directory, and the ability to specify an environment variable as an ACD value. This will be in the 15th July release of EMBOSS. regards, Peter Rice From pmr at ebi.ac.uk Fri Jun 26 15:42:22 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 26 Jun 2009 20:42:22 +0100 Subject: [EMBOSS] please modify two acd files for hmmer package In-Reply-To: <4A450B87.30802@gmail.com> References: <4A450B87.30802@gmail.com> Message-ID: <4A45249E.50100@ebi.ac.uk> jason zhang wrote: > please modify : default: 100 to default: "100" in ehmmsearch and > ehmmpfam. I have a java parser for acd files. my parser choke for these acd > files. Fixed in the new release. I am curious ... what does your parser do? We have a few changes in the new release (extra attributes). regards, Peter From jasonzhang2002 at gmail.com Fri Jun 26 16:36:54 2009 From: jasonzhang2002 at gmail.com (jason zhang) Date: Fri, 26 Jun 2009 13:36:54 -0700 Subject: [EMBOSS] please modify two acd files for hmmer package In-Reply-To: <4A45249E.50100@ebi.ac.uk> References: <4A450B87.30802@gmail.com> <4A45249E.50100@ebi.ac.uk> Message-ID: <4A453166.50603@gmail.com> Hi, peter Peter Rice wrote: > jason zhang wrote: >> please modify : default: 100 to default: "100" in ehmmsearch and >> ehmmpfam. I have a java parser for acd files. my parser choke for >> these acd >> files. > > Fixed in the new release. > > I am curious ... what does your parser do? We have a few changes in > the new release (extra attributes). > I am coding an application which provides web interface and web service interface to a set of applications including EMBOSS. If you are interested, the web interface is here: http://174.129.249.18:8080/appweb. You can login in with testtest/123456 as the username/password. The application is currently at beta stage. The application parses ACD file and generates Web interface and Web Service (WSDL). Are the extra attributes in the new release documented somewhere? I will support them in my parser if web interface or Web Service are impacted. > regards, > > Peter > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > Regards -jason From pmr at ebi.ac.uk Fri Jun 26 16:55:12 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 26 Jun 2009 21:55:12 +0100 Subject: [EMBOSS] please modify two acd files for hmmer package In-Reply-To: <4A453166.50603@gmail.com> References: <4A450B87.30802@gmail.com> <4A45249E.50100@ebi.ac.uk> <4A453166.50603@gmail.com> Message-ID: <4A4535B0.7040500@ebi.ac.uk> jason zhang wrote: > Hi, peter > Peter Rice wrote: >> I am curious ... what does your parser do? We have a few changes in >> the new release (extra attributes). >> > I am coding an application which provides web interface and web service > interface to a set of applications including EMBOSS. If you are > interested, the web interface is here: > http://174.129.249.18:8080/appweb. Thanks. I gave it a try. looks like a good start. > The application is currently at beta stage. The application parses ACD > file and generates Web interface and Web Service (WSDL). Are the extra > attributes in the new release documented somewhere? I will support them > in my parser if web interface or Web Service are impacted. There is updated documentation at http://emboss.sourceforge.net/developers/acd/syntax.html which we automatically update with new datatypes and attributes (though I now notice it says version 3.0.0 - I will fix that!) I see your web interface includes every option ... rather like we do with the SoapLab web services. A few are not valid in all cases ... for example, when I run "antigenic" which only accepts protein sequences the -snucleotide option will break the run and -sprotein is unnecessary. On balance I find users are happiest when the options are always the same ... but you could consider hiding the less useful ones (sequence input options, anything in the "advanced" section of ACD ... with some way for the user to find them and use them. This is in line with the command line philosophy - even with -option on the command line these are never prompted for, but they can be used if the user reads the documentation or studies the -help options. Let us know if there is anything we can do to help ... for example, could we run your parser on each new release and send you the results (that implies running it aftre significant ACD changes and informing you if we see any problems at that stage). We can do the same for other ACD parsers if there is interest. regards, Peter Rice From jasonzhang2002 at gmail.com Fri Jun 26 17:31:45 2009 From: jasonzhang2002 at gmail.com (jason zhang) Date: Fri, 26 Jun 2009 14:31:45 -0700 Subject: [EMBOSS] please modify two acd files for hmmer package In-Reply-To: <4A4535B0.7040500@ebi.ac.uk> References: <4A450B87.30802@gmail.com> <4A45249E.50100@ebi.ac.uk> <4A453166.50603@gmail.com> <4A4535B0.7040500@ebi.ac.uk> Message-ID: <4A453E41.407@gmail.com> Hi, Peter Thank you for the suggestion. > I see your web interface includes every option ... rather like we do > with the SoapLab web services. A few are not valid in all cases ... > for example, when I run "antigenic" which only accepts protein > sequences the -snucleotide option will break the run and -sprotein is > unnecessary. On balance I find users are happiest when the options are > always the same ... but you could consider hiding the less useful ones > (sequence input options, anything in the "advanced" section of ACD ... > with some way for the user to find them and use them. This is in line > with the command line philosophy - even with -option on the command > line these are never prompted for, but they can be used if the user > reads the documentation or studies the -help options. I planned to hide those advanced options and they are visible only if the end users choose to. But due to the limitation in the web toolkit I used, I can not do that easily. With regards to -sprotein/-snucleotide for antigenic, the web interface can not tell that since there is no such information in ACD. I expect the end user has some basic knowledge about the program and will not make such mistake. Not all information in ACD is used. Some information such as variable, pattern can not be easily translated to javascript in web page. Again, I expect the end user can work it out. Otherwise error will occur at execution time. > > Let us know if there is anything we can do to help ... for example, > could we run your parser on each new release and send you the results > (that implies running it aftre significant ACD changes and informing > you if we see any problems at that stage). This is definitely helpful. I will discuss this with my boss and package a parser if he is ok. > > We can do the same for other ACD parsers if there is interest. > > regards, -jason From pmr at ebi.ac.uk Fri Jun 26 17:41:48 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 26 Jun 2009 22:41:48 +0100 Subject: [EMBOSS] please modify two acd files for hmmer package In-Reply-To: <4A453E41.407@gmail.com> References: <4A450B87.30802@gmail.com> <4A45249E.50100@ebi.ac.uk> <4A453166.50603@gmail.com> <4A4535B0.7040500@ebi.ac.uk> <4A453E41.407@gmail.com> Message-ID: <4A45409C.7090804@ebi.ac.uk> jason zhang wrote: > With regards to -sprotein/-snucleotide for antigenic, the web interface > can not tell that since there is no such information in ACD. I expect > the end user has some basic knowledge about the program and will not > make such mistake. Indeed, it is often best to trust the users. The information is in ACD, but it is in the sequence "type" which you would have to interpret as nucleotide, protein, or both. Some ACD files that allow both types also use a variable "ACDPROTEIN" that is set to the type of the first sequence - this allows you to make protein or nucleotide specific versions with appropriate default values - the alignment progams are common examples of this. > Not all information in ACD is used. Some information such as variable, > pattern can not be easily translated to javascript in web page. Again, I > expect the end user can work it out. Otherwise error will occur at > execution time. We try to avoid these. If you run "acdvalid " you may see warnings for things that can be difficult for parsers. Let us know if any of these give you major problems - or if there are problems we fail to detect. We try to reduce the number of acdvalid warnings for all emboss applications before each release. regards, Peter From gbottu at vub.ac.be Mon Jun 29 05:41:50 2009 From: gbottu at vub.ac.be (Guy Bottu) Date: Mon, 29 Jun 2009 11:41:50 +0200 Subject: [EMBOSS] announcing wEMBOSS version 2 Message-ID: <4A488C5E.9010301@vub.ac.be> Dear users of wEMBOSS, wEMBOSS has reached version 2. It has not much changed from the user's point of view but has changed substantially from the developer's and manager's point of view. In order to make further development easier, the code has been refreshed and is now maintained as a project under Eclipse with Epic plug-in. The development version is called wEMBOSSDEV and from this releases for distribution with name wEMBOSSDIST-x.x.x are regularly drawn. The new version does not anymore install its Perl libraries in the Perl system libraries. There was indeed no reason to do this, since the wEMBOSS libraries are not used by any other program. Storing them in a separate location makes it much easier to get rid of old versions, making sure they cannot interfere with newer versions. We have stopped the habit of distributing wrappers4EMBOSS inside wEMBOSS, since there was little to be gained by doing so. The 2 packages are now simply presented as separate tar archives for download. For the end user the main difference by now is that the included applets (Jalview for viewing multiple sequence alignments and ATV for viewing phylogenetic trees) have been upgraded to the latest version. Also, with the new version of wEMBOSS the Web Browser windows open in predetermined positions, making them better spread over the computer screen. Guy Bottu, wEMBOSS development team P.S. For those who already downloaded version 2.1 : it turned out to contain a number of bugs. These have been fixed with version 2.1.1 of 23 June, which you should definitively download. From ellis at biochem.dental.upenn.edu Mon Jun 29 14:23:59 2009 From: ellis at biochem.dental.upenn.edu (Ellis Golub) Date: Mon, 29 Jun 2009 14:23:59 -0400 Subject: [EMBOSS] HPGL driver Message-ID: <1090629142359.ZM606423@biochem.dental.upenn.edu> Hello -- I've just upgraded to version 6.0.1 from 3.0.0, and I've run into a problem with the hpgl plot driver. When I try to use it, I get a large number of Invalid pen selection errors, and the resulting hpgl file is monochrome. In the docs, the plotter pens are supposed to be preconfigured. How do I configure them correctly? Ellis Golub -- ============================================================= Ellis Golub Phone: (215) 898-4629 Biochemistry Department FAX: (215) 898-3695 School of Dental Medicine ellis at biochem.dental.upenn.edu University of Pennsylvania 240 South 40th Street Philadelphia, PA 19104-6030 Home: http://biochem.dental.upenn.edu/~ellis/ PGP: http://biochem.dental.upenn.edu/~ellis/public_key.html ============================================================== From ajb at ebi.ac.uk Tue Jun 30 08:02:08 2009 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 30 Jun 2009 13:02:08 +0100 (BST) Subject: [EMBOSS] HPGL driver In-Reply-To: <1090629142359.ZM606423@biochem.dental.upenn.edu> References: <1090629142359.ZM606423@biochem.dental.upenn.edu> Message-ID: <50168.86.26.12.63.1246363328.squirrel@webmail.ebi.ac.uk> Dear Ellis, Thanks for pointing this out. We're currently discussing the problem and hope to have a fix in place before the next release (Jul 15th). ATB Alan > Hello -- > > I've just upgraded to version 6.0.1 from 3.0.0, and I've run into a > problem > with the hpgl plot driver. When I try to use it, I get a large number of > Invalid pen selection errors, and the resulting hpgl file is monochrome. > > In the docs, the plotter pens are supposed to be preconfigured. How do I > configure them correctly? > > Ellis Golub > -- > ============================================================= > Ellis Golub Phone: (215) 898-4629 > Biochemistry Department FAX: (215) 898-3695 > School of Dental Medicine ellis at biochem.dental.upenn.edu > University of Pennsylvania > 240 South 40th Street > Philadelphia, PA 19104-6030 > Home: http://biochem.dental.upenn.edu/~ellis/ > PGP: http://biochem.dental.upenn.edu/~ellis/public_key.html > ============================================================== > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From mail at tobias-schwarz.net Sat Jun 6 16:41:16 2009 From: mail at tobias-schwarz.net (Tobias Schwarz) Date: Sat, 06 Jun 2009 18:41:16 +0200 Subject: [EMBOSS] kemboss GUI for EMBOSS 6.0.1 Message-ID: <4A2A9C2C.3020403@tobias-schwarz.net> Dear all, I am happy to announce kemboss, a graphical user interface for EMBOSS 6.0.1, based on the Kaptain scripts by Thomas Siegmund. In contrast to the scripts, kemboss is a compiled binary, and is therefore not dependent on kaptain. It thus offers some advantages, for example the possibility to save and load individual settings, print the program output, an integrated editor, etc. Kemboss 0.9 is based on Qt4 and thus is available for Linux, Windows, MacOS and many other Unix systems. Some screenshots, the source code, as well as binaries for the above-mentioned operating systems are available at: http://www.tobias-schwarz.net/kemboss.html Please report all problems, bugs and suggestions to kemboss at tobias-schwarz.net Have fun, Tobias -- Tobias Schwarz University of Wuerzburg Children's Hospital Josef-Schneider-Str. 2 97090 Wuerzburg, Germany www.tobias-schwarz.net From pmr at ebi.ac.uk Mon Jun 8 13:41:19 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 08 Jun 2009 14:41:19 +0100 Subject: [EMBOSS] EMBOSS Funding and New developments Message-ID: <4A2D14FF.9000109@ebi.ac.uk> Dear EMBOSS Users and Developers We bring you great news - EMBOSS is funded in full by the BBSRC "Bioinformatics and Biological Resources" Fund. We now have money for Alan Bleasby and 2 other positions (Jon Ison and Mahmut Uludag) from 1st May until the end of 2011. The core aims of the funding proposal were to continue support, maintenance and development of EMBOSS, and to provide extensive online training materials for users, developers and system administrators using text from a series of books to be published by Cambridge University Press. We are also explicitly targeting areas where we see EMBOSS can be expanded: * Richer data content in EMBOSS outputs leading to major improvements in the integration and visualisation of results in browsers. * Processing many more data fields in EMBOSS inputs (taxonomy, genes, GO terms, cross-references, keywords. * Extending and improving database access: better indexing, query language support and combining searches across multiple databases, support for non-sequence data resources and new data access methods * Scaling up the libraries and adding new applications to support the data volumes generated by next-generation sequencing runs. We anticipate many more users will be working with short read data mapped to reference sequences over the next few years. * We aim to add at least 100 new applications in these 3 years. Suggestions for new applications are very welcome. * Release 6.1.0 will appear, as usual, on 15th July. * Major work on new developments and new library code will start from August. We hope to meet many of you at BOSC/ISMB/ECCB in Stockholm at the end of this month, We will arrange a lunchtime "Birds of a Feather" session at ISMB to discuss the needs of users over the next 3 years. regards, Peter Rice From georgios at biotek.uio.no Tue Jun 9 08:40:17 2009 From: georgios at biotek.uio.no (George Magklaras) Date: Tue, 09 Jun 2009 10:40:17 +0200 Subject: [EMBOSS] [emboss-dev] EMBOSS Funding and New developments In-Reply-To: <4A2D14FF.9000109@ebi.ac.uk> References: <4A2D14FF.9000109@ebi.ac.uk> Message-ID: <4A2E1FF1.4030902@biotek.uio.no> That's very good news Peter. I would add to the list the production of documentation for the EMBOSS admins. In terms of improving the indexing, may node managers (including myself) have created scripts to automate the formatting of large databases. Maybe it might be an idea to include them in some sort of add-on section, so that people can have error-free formatted dbs with the click of a button or a script call. GM -- George Magklaras BSc Hons MPhil RHCE:805008309135525 Senior Computer Systems Engineer/EMBnet node manager EMBnet Technical Management Board The Biotechnology Centre of Oslo, University of Oslo http://www.no.embnet.org Tel: +47-22840535 -- Peter Rice wrote: > Dear EMBOSS Users and Developers > > We bring you great news - EMBOSS is funded in full by the BBSRC > "Bioinformatics and Biological Resources" Fund. We now have money for > Alan Bleasby and 2 other positions (Jon Ison and Mahmut Uludag) from 1st > May until the end of 2011. > > The core aims of the funding proposal were to continue support, > maintenance and development of EMBOSS, and to provide extensive online > training materials for users, developers and system administrators using > text from a series of books to be published by Cambridge University Press. > > We are also explicitly targeting areas where we see EMBOSS can be > expanded: > > * Richer data content in EMBOSS outputs leading to major improvements > in the integration and visualisation of results in browsers. > > * Processing many more data fields in EMBOSS inputs (taxonomy, > genes, GO terms, cross-references, keywords. > > * Extending and improving database access: better indexing, query > language support and combining searches across multiple databases, > support for non-sequence data resources and new data access methods > > * Scaling up the libraries and adding new applications to support the > data volumes generated by next-generation sequencing runs. We > anticipate many more users will be working with short read data > mapped to reference sequences over the next few years. > > * We aim to add at least 100 new applications in these 3 years. > Suggestions for new applications are very welcome. > > * Release 6.1.0 will appear, as usual, on 15th July. > > * Major work on new developments and new library code will start from > August. > > We hope to meet many of you at BOSC/ISMB/ECCB in Stockholm at the end of > this month, We will arrange a lunchtime "Birds of a Feather" session > at ISMB to discuss the needs of users over the next 3 years. > > regards, > > Peter Rice > _______________________________________________ > emboss-dev mailing list > emboss-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss-dev > From pmr at ebi.ac.uk Tue Jun 9 15:11:58 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 09 Jun 2009 16:11:58 +0100 Subject: [EMBOSS] [emboss-dev] EMBOSS Funding and New developments In-Reply-To: <4A2E1FF1.4030902@biotek.uio.no> References: <4A2D14FF.9000109@ebi.ac.uk> <4A2E1FF1.4030902@biotek.uio.no> Message-ID: <4A2E7BBE.8030500@ebi.ac.uk> George Magklaras wrote: > That's very good news Peter. > > I would add to the list the production of documentation for the EMBOSS > admins. In terms of improving the indexing, may node managers (including > myself) have created scripts to automate the formatting of large > databases. Maybe it might be an idea to include them in some sort of > add-on section, so that people can have error-free formatted dbs with > the click of a button or a script call. Documentation is on the way in the form of an Administrators Guide ... long promised but we are now adding the final touches to the text. The book will be open source and the text will also appear on the EMBOSS website. As to the scripts ... yes, and excellent suggestion. We could make a directory adminscripts in the distribution for these. Please contribute useful scripts for use to include. We would like to include some documentation on what the script is intended to do and how to modify it. As the target users are administrators, we can expect them to be able to make their own modifications. regards, Peter Rice From dalloliogm at gmail.com Tue Jun 9 15:44:54 2009 From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio) Date: Tue, 9 Jun 2009 17:44:54 +0200 Subject: [EMBOSS] EMBOSS Funding and New developments In-Reply-To: <4A2D14FF.9000109@ebi.ac.uk> References: <4A2D14FF.9000109@ebi.ac.uk> Message-ID: <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> On Mon, Jun 8, 2009 at 3:41 PM, Peter Rice wrote: > Dear EMBOSS Users and Developers > > Suggestions for new applications are very welcome. > I think EMBOSS is highly effective when combined with Makefiles or tools to describe pipelines. Maybe in the future you could add some recipe or example in the documentation, it would be useful. In any case, it would be good to add to the tutorials some references on methods to describe pipelines. Another need that people have asked me several times (I am administrator of a web forum on bioinformatics) is to have a standard and official web interface to the emboss tools, since the list at http://emboss.sourceforge.net/interfaces/#web is outdated and google doesn't return clear results. > > > We hope to meet many of you at BOSC/ISMB/ECCB in Stockholm at the end of > this month, We will arrange a lunchtime "Birds of a Feather" session > at ISMB to discuss the needs of users over the next 3 years. > > regards, > > Peter Rice > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > -- Giovanni Dall'Olio, phd student Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain) My blog on bioinformatics: http://bioinfoblog.it From pmr at ebi.ac.uk Tue Jun 9 15:59:45 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Tue, 09 Jun 2009 16:59:45 +0100 Subject: [EMBOSS] EMBOSS Funding and New developments In-Reply-To: <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> References: <4A2D14FF.9000109@ebi.ac.uk> <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> Message-ID: <4A2E86F1.2050507@ebi.ac.uk> Giovanni Marco Dall'Olio wrote: > I think EMBOSS is highly effective when combined with Makefiles or tools to > describe pipelines. > Maybe in the future you could add some recipe or example in the > documentation, it would be useful. In any case, it would be good to add to > the tutorials some references on methods to describe pipelines. What pipelines so users prefer? We have experience with Taverna and with SoapLab web services. We have also worked with Accelrys/Scitegic's Pipeline Pilot. These all include EMBOSS examples in their documentation. > Another need that people have asked me several times (I am administrator of > a web forum on bioinformatics) is to have a standard and official web > interface to the emboss tools, since the list at > http://emboss.sourceforge.net/interfaces/#web is outdated and google doesn't > return clear results. We have long hoped that one interface would become the standard. Our usual recommendation for web-based users is the wEMBOSS interface but when ever we ask which interfaces users prefer we get many different replies. So, please let us know which interfaces you like best and we will try to work with the developers to make sure it keeps up with changes to EMBOSS ... and we can try to help them by adding new features or by automatically building their interface to a new EMBOSS release. regards, Peter Rice From dalloliogm at gmail.com Tue Jun 9 17:11:11 2009 From: dalloliogm at gmail.com (Giovanni Marco Dall'Olio) Date: Tue, 9 Jun 2009 19:11:11 +0200 Subject: [EMBOSS] EMBOSS Funding and New developments In-Reply-To: <4A2E86F1.2050507@ebi.ac.uk> References: <4A2D14FF.9000109@ebi.ac.uk> <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> <4A2E86F1.2050507@ebi.ac.uk> Message-ID: <5aa3b3570906091011v16ea5f89h55c14928e4b4361d@mail.gmail.com> On Tue, Jun 9, 2009 at 5:59 PM, Peter Rice wrote: > Giovanni Marco Dall'Olio wrote: > > I think EMBOSS is highly effective when combined with Makefiles or tools > to > > describe pipelines. > > Maybe in the future you could add some recipe or example in the > > documentation, it would be useful. In any case, it would be good to add > to > > the tutorials some references on methods to describe pipelines. > > What pipelines so users prefer? > > We have experience with Taverna and with SoapLab web services. We have > also worked with Accelrys/Scitegic's Pipeline Pilot. These all include > EMBOSS examples in their documentation. Yes, taverna and soaplab services are very good but they are more oriented to write applications that connect to Internet and execute tools which are also web services. Sometimes you need much simpler tools, e.g. organize a workflow of command line tools to be run in local on an unix shell, and this is something for which emboss is very good, since it resembles many unix tools like grep and similar. My favorite introduction to Makefiles is the one on the Software Carpentry manual: - http://swc.scipy.org/lec/build.html I could write some example for you if you want, but actually I haven't been using emboss for a while, so.. let me re-read the documentation first :-) > Another need that people have asked me several times (I am administrator > of > > a web forum on bioinformatics) is to have a standard and official web > > interface to the emboss tools, since the list at > > http://emboss.sourceforge.net/interfaces/#web is outdated and google > doesn't > > return clear results. > > We have long hoped that one interface would become the standard. Our > usual recommendation for web-based users is the wEMBOSS interface but > when ever we ask which interfaces users prefer we get many different > replies. > > So, please let us know which interfaces you like best and we will try to > work with the developers to make sure it keeps up with changes to EMBOSS > ... and we can try to help them by adding new features or by > automatically building their interface to a new EMBOSS release. > the web forum is this one (in Italian): - http://www.molecularlab.it/forum/default.asp usually, people ask questions like 'how to I translate a sequence to protein?', 'how to create a dotplot', etc.. - there is not always a good answer to these questions, but in the past I have suggested the emboss tools because they seemed a kind of standard. (by the way, it would be good to know which tests have being applied to verify emboss code. I don't like telling people to use a command line tool, if there is no way to tell that it has been proved to work fine). I used to like very much this interface: - http://embossgui.sourceforge.net/demo/ which is very clear and has a list of all the tools, but is still running the 3.0 version. I also like the ebi interface, because it is hosted on an well-known server (people don't like using servers they don't know) but it supports very few tools; galaxy has also a nice web interface to emboss, but sometimes you just need to link a paste&submit interface to execute simple tasks like translating a sequence, and I haven't found anything like that yet. > regards, > > Peter Rice > -- Giovanni Dall'Olio, phd student Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain) My blog on bioinformatics: http://bioinfoblog.it From gbottu at vub.ac.be Thu Jun 11 14:41:10 2009 From: gbottu at vub.ac.be (Guy Bottu) Date: Thu, 11 Jun 2009 16:41:10 +0200 Subject: [EMBOSS] EMBOSS Funding and New developments In-Reply-To: <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> References: <4A2D14FF.9000109@ebi.ac.uk> <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde@mail.gmail.com> Message-ID: <4A311786.6000504@vub.ac.be> Giovanni Marco Dall'Olio wrote: > Another need that people have asked me several times (I am administrator of > a web forum on bioinformatics) is to have a standard and official web > interface to the emboss tools, since the list at > http://emboss.sourceforge.net/interfaces/#web is outdated and google doesn't > return clear results. Now that we are at it, could the hyperlink not be changed ? It is http://wemboss.sourceforge.net and not anymore http://www.wemboss.org Guy Bottu From belegdol at gmail.com Fri Jun 12 20:40:08 2009 From: belegdol at gmail.com (Julian Sikorski) Date: Fri, 12 Jun 2009 22:40:08 +0200 Subject: [EMBOSS] Packaging EMBOSS for Fedora Message-ID: Hi, a while ago I made an attempt to create an EMBOSS package for Fedora [1]. The progress was stalled for a while due to my MSc having higher priority, but I have recently picked up the work again. I have one crucial question: is it worth to package jemboss? It seems it didn't see development since 2005, and I have experienced some important issues when trying to use it (mainly not working with files with spaces in filenames). What do you think? Kind regards, Julian [1] https://bugzilla.redhat.com/show_bug.cgi?id=496133 From uludag at ebi.ac.uk Fri Jun 12 23:49:16 2009 From: uludag at ebi.ac.uk (Mahmut Uludag) Date: Sat, 13 Jun 2009 00:49:16 +0100 Subject: [EMBOSS] Packaging EMBOSS for Fedora In-Reply-To: References: Message-ID: <1244850556.8999.7.camel@login-svr1.ebi.ac.uk> Hi Julian, > I have one crucial question: is it worth to package jemboss? It seems it > didn't see development since 2005, and I have experienced some important > issues when trying to use it (mainly not working with files with spaces > in filenames). What do you think? I had a quick look into the files with spaces in filenames problem, we can include a fix in the coming release (6.1) for this problem. Previous release of EMBOSS (6.0) included some fixes of similar nature, as well as some small gui improvements. We recently have updated EMBOSS/Jemboss make/install machinery to make standalone Jemboss come out of box when users install EMBOSS, i think we were successful and this will be a new feature in EMBOSS 6.1. Regards, Mahmut From koenvanderdrift at gmail.com Mon Jun 15 17:30:47 2009 From: koenvanderdrift at gmail.com (Koen van der Drift) Date: Mon, 15 Jun 2009 13:30:47 -0400 Subject: [EMBOSS] Mac OS X instructions Message-ID: <5cba6b9f0906151030k1725891fmfd3f3e4faad746c@mail.gmail.com> Hi, Unless I missed it, I noticed that the EMBOSS website has some very outdated instructions on how to install EMBOSS on Mac OS X, eg here http://emboss.sourceforge.net/download/macosx.html and here (outside link from EMBOSS website): http://gnu-darwin.sourceforge.net/gdc/emboss.txt As most of you probably know there has been also the possibility for a while to use the fink package manager for this. I am the maintainer of that package, and try to keep it updated, version 6.0.1 is available including most of the patches. Fink is a very convenient means to install packages, and will take care of installing all the necessary third party packages and proper configuration. Is it possible to update the website to include this possibility, and maybe remove the older and outdated links? Thanks, - Koen. From hmenager at pasteur.fr Tue Jun 16 09:06:23 2009 From: hmenager at pasteur.fr (hmenager at pasteur.fr) Date: Tue, 16 Jun 2009 11:06:23 +0200 (CEST) Subject: [EMBOSS] EMBOSS Funding and New developments In-Reply-To: References: Message-ID: <56720.157.99.64.103.1245143183.squirrel@php.pasteur.fr> Hi, > I used to like very much this interface: > - http://embossgui.sourceforge.net/demo/ > which is very clear and has a list of all the tools, but is still running > the 3.0 version. > > I also like the ebi interface, because it is hosted on an well-known > server > (people don't like using servers they don't know) but it supports very few > tools; > > galaxy has also a nice web interface to emboss, but sometimes you just > need > to link a paste&submit interface to execute simple tasks like translating > a > sequence, and I haven't found anything like that yet. You could also give a try to Mobyle, which is the successor to Pise, mentionned on the EMBOSS web interfaces page, but not maintained anymore. Although it is not specific to EMBOSS, most of the package is supported by Mobyle, as well as some others (Phylip, Vienna RNA, BLASTs ...). You can try it for instance at: http://mobyle.pasteur.fr If you want information about the system, or to download it, refer to: http://bioweb2.pasteur.fr/projects/mobyle/ Regards, Herv? M?nager From hmenager at pasteur.fr Tue Jun 16 09:20:32 2009 From: hmenager at pasteur.fr (hmenager at pasteur.fr) Date: Tue, 16 Jun 2009 11:20:32 +0200 (CEST) Subject: [EMBOSS] EMBOSS Digest, Vol 48, Issue 2 In-Reply-To: References: Message-ID: <59215.157.99.64.103.1245144032.squirrel@php.pasteur.fr> > Send EMBOSS mailing list submissions to > emboss at lists.open-bio.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.open-bio.org/mailman/listinfo/emboss > or, via email, send a message with subject or body 'help' to > emboss-request at lists.open-bio.org > > You can reach the person managing the list at > emboss-owner at lists.open-bio.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of EMBOSS digest..." > > > Today's Topics: > > 1. Re: [emboss-dev] EMBOSS Funding and New developments (Peter Rice) > 2. Re: EMBOSS Funding and New developments (Giovanni Marco Dall'Olio) > 3. Re: EMBOSS Funding and New developments (Peter Rice) > 4. Re: EMBOSS Funding and New developments (Giovanni Marco Dall'Olio) > 5. Re: EMBOSS Funding and New developments (Guy Bottu) > 6. Packaging EMBOSS for Fedora (Julian Sikorski) > 7. Re: Packaging EMBOSS for Fedora (Mahmut Uludag) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 09 Jun 2009 16:11:58 +0100 > From: Peter Rice > Subject: Re: [EMBOSS] [emboss-dev] EMBOSS Funding and New developments > To: George Magklaras > Cc: emboss > Message-ID: <4A2E7BBE.8030500 at ebi.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1 > > George Magklaras wrote: >> That's very good news Peter. >> >> I would add to the list the production of documentation for the EMBOSS >> admins. In terms of improving the indexing, may node managers (including >> myself) have created scripts to automate the formatting of large >> databases. Maybe it might be an idea to include them in some sort of >> add-on section, so that people can have error-free formatted dbs with >> the click of a button or a script call. > > Documentation is on the way in the form of an Administrators Guide ... > long promised but we are now adding the final touches to the text. > > The book will be open source and the text will also appear on the EMBOSS > website. > > As to the scripts ... yes, and excellent suggestion. We could make a > directory adminscripts in the distribution for these. > > Please contribute useful scripts for use to include. We would like to > include some documentation on what the script is intended to do and how > to modify it. As the target users are administrators, we can expect them > to be able to make their own modifications. > > regards, > > Peter Rice > > > ------------------------------ > > Message: 2 > Date: Tue, 9 Jun 2009 17:44:54 +0200 > From: "Giovanni Marco Dall'Olio" > Subject: Re: [EMBOSS] EMBOSS Funding and New developments > To: Peter Rice > Cc: emboss-announce at emboss.open-bio.org, > emboss-dev at emboss.open-bio.org, emboss > Message-ID: > <5aa3b3570906090844r7e4e50c5w5edb7ccbfd687fde at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > On Mon, Jun 8, 2009 at 3:41 PM, Peter Rice wrote: > >> Dear EMBOSS Users and Developers >> > > >> Suggestions for new applications are very welcome. >> > > I think EMBOSS is highly effective when combined with Makefiles or tools > to > describe pipelines. > Maybe in the future you could add some recipe or example in the > documentation, it would be useful. In any case, it would be good to add to > the tutorials some references on methods to describe pipelines. > > Another need that people have asked me several times (I am administrator > of > a web forum on bioinformatics) is to have a standard and official web > interface to the emboss tools, since the list at > http://emboss.sourceforge.net/interfaces/#web is outdated and google > doesn't > return clear results. > > > > >> >> >> We hope to meet many of you at BOSC/ISMB/ECCB in Stockholm at the end of >> this month, We will arrange a lunchtime "Birds of a Feather" session >> at ISMB to discuss the needs of users over the next 3 years. >> >> regards, >> >> Peter Rice >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss >> > > > > -- > Giovanni Dall'Olio, phd student > Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain) > > My blog on bioinformatics: http://bioinfoblog.it > > > ------------------------------ > > Message: 3 > Date: Tue, 09 Jun 2009 16:59:45 +0100 > From: Peter Rice > Subject: Re: [EMBOSS] EMBOSS Funding and New developments > To: dalloliogm at gmail.com > Cc: emboss-dev at emboss.open-bio.org, emboss > > Message-ID: <4A2E86F1.2050507 at ebi.ac.uk> > Content-Type: text/plain; charset=UTF-8 > > Giovanni Marco Dall'Olio wrote: >> I think EMBOSS is highly effective when combined with Makefiles or tools >> to >> describe pipelines. >> Maybe in the future you could add some recipe or example in the >> documentation, it would be useful. In any case, it would be good to add >> to >> the tutorials some references on methods to describe pipelines. > > What pipelines so users prefer? > > We have experience with Taverna and with SoapLab web services. We have > also worked with Accelrys/Scitegic's Pipeline Pilot. These all include > EMBOSS examples in their documentation. > >> Another need that people have asked me several times (I am administrator >> of >> a web forum on bioinformatics) is to have a standard and official web >> interface to the emboss tools, since the list at >> http://emboss.sourceforge.net/interfaces/#web is outdated and google >> doesn't >> return clear results. > > We have long hoped that one interface would become the standard. Our > usual recommendation for web-based users is the wEMBOSS interface but > when ever we ask which interfaces users prefer we get many different > replies. > > So, please let us know which interfaces you like best and we will try to > work with the developers to make sure it keeps up with changes to EMBOSS > ... and we can try to help them by adding new features or by > automatically building their interface to a new EMBOSS release. > > regards, > > Peter Rice > > > ------------------------------ > > Message: 4 > Date: Tue, 9 Jun 2009 19:11:11 +0200 > From: "Giovanni Marco Dall'Olio" > Subject: Re: [EMBOSS] EMBOSS Funding and New developments > To: Peter Rice > Cc: emboss-dev at emboss.open-bio.org, emboss > > Message-ID: > <5aa3b3570906091011v16ea5f89h55c14928e4b4361d at mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > On Tue, Jun 9, 2009 at 5:59 PM, Peter Rice wrote: > >> Giovanni Marco Dall'Olio wrote: >> > I think EMBOSS is highly effective when combined with Makefiles or >> tools >> to >> > describe pipelines. >> > Maybe in the future you could add some recipe or example in the >> > documentation, it would be useful. In any case, it would be good to >> add >> to >> > the tutorials some references on methods to describe pipelines. >> >> What pipelines so users prefer? >> >> We have experience with Taverna and with SoapLab web services. We have >> also worked with Accelrys/Scitegic's Pipeline Pilot. These all include >> EMBOSS examples in their documentation. > > > Yes, taverna and soaplab services are very good but they are more oriented > to write applications that connect to Internet and execute tools which are > also web services. > > Sometimes you need much simpler tools, e.g. organize a workflow of command > line tools to be run in local on an unix shell, and this is something for > which emboss is very good, since it resembles many unix tools like grep > and > similar. > > My favorite introduction to Makefiles is the one on the Software Carpentry > manual: > - http://swc.scipy.org/lec/build.html > > I could write some example for you if you want, but actually I haven't > been > using emboss for a while, so.. let me re-read the documentation first :-) > > > > > Another need that people have asked me several times (I am > administrator >> of >> > a web forum on bioinformatics) is to have a standard and official web >> > interface to the emboss tools, since the list at >> > http://emboss.sourceforge.net/interfaces/#web is outdated and google >> doesn't >> > return clear results. >> >> We have long hoped that one interface would become the standard. Our >> usual recommendation for web-based users is the wEMBOSS interface but >> when ever we ask which interfaces users prefer we get many different >> replies. >> >> So, please let us know which interfaces you like best and we will try to >> work with the developers to make sure it keeps up with changes to EMBOSS >> ... and we can try to help them by adding new features or by >> automatically building their interface to a new EMBOSS release. >> > > the web forum is this one (in Italian): > - http://www.molecularlab.it/forum/default.asp > usually, people ask questions like 'how to I translate a sequence to > protein?', 'how to create a dotplot', etc.. - there is not always a good > answer to these questions, but in the past I have suggested the emboss > tools > because they seemed a kind of standard. > (by the way, it would be good to know which tests have being applied to > verify emboss code. I don't like telling people to use a command line > tool, > if there is no way to tell that it has been proved to work fine). > > I used to like very much this interface: > - http://embossgui.sourceforge.net/demo/ > which is very clear and has a list of all the tools, but is still running > the 3.0 version. > > I also like the ebi interface, because it is hosted on an well-known > server > (people don't like using servers they don't know) but it supports very few > tools; > > galaxy has also a nice web interface to emboss, but sometimes you just > need > to link a paste&submit interface to execute simple tasks like translating > a > sequence, and I haven't found anything like that yet. > > > >> regards, >> >> Peter Rice >> > > > > -- > Giovanni Dall'Olio, phd student > Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain) > > My blog on bioinformatics: http://bioinfoblog.it > > > ------------------------------ > > Message: 5 > Date: Thu, 11 Jun 2009 16:41:10 +0200 > From: Guy Bottu > Subject: Re: [EMBOSS] EMBOSS Funding and New developments > To: Peter Rice > Cc: emboss-dev at emboss.open-bio.org, emboss > > Message-ID: <4A311786.6000504 at vub.ac.be> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Giovanni Marco Dall'Olio wrote: >> Another need that people have asked me several times (I am administrator >> of >> a web forum on bioinformatics) is to have a standard and official web >> interface to the emboss tools, since the list at >> http://emboss.sourceforge.net/interfaces/#web is outdated and google >> doesn't >> return clear results. > > Now that we are at it, could the hyperlink not be changed ? It is > http://wemboss.sourceforge.net and not anymore http://www.wemboss.org > > Guy Bottu > > > > > ------------------------------ > > Message: 6 > Date: Fri, 12 Jun 2009 22:40:08 +0200 > From: Julian Sikorski > Subject: [EMBOSS] Packaging EMBOSS for Fedora > To: emboss at emboss.open-bio.org > Message-ID: > Content-Type: text/plain; charset=UTF-8 > > Hi, > > a while ago I made an attempt to create an EMBOSS package for Fedora > [1]. The progress was stalled for a while due to my MSc having higher > priority, but I have recently picked up the work again. > I have one crucial question: is it worth to package jemboss? It seems it > didn't see development since 2005, and I have experienced some important > issues when trying to use it (mainly not working with files with spaces > in filenames). What do you think? > > Kind regards, > Julian > > [1] https://bugzilla.redhat.com/show_bug.cgi?id=496133 > > > > ------------------------------ > > Message: 7 > Date: Sat, 13 Jun 2009 00:49:16 +0100 > From: Mahmut Uludag > Subject: Re: [EMBOSS] Packaging EMBOSS for Fedora > To: Julian Sikorski > Cc: emboss at emboss.open-bio.org > Message-ID: <1244850556.8999.7.camel at login-svr1.ebi.ac.uk> > Content-Type: text/plain > > Hi Julian, > >> I have one crucial question: is it worth to package jemboss? It seems it >> didn't see development since 2005, and I have experienced some important >> issues when trying to use it (mainly not working with files with spaces >> in filenames). What do you think? > > I had a quick look into the files with spaces in filenames problem, we > can include a fix in the coming release (6.1) for this problem. Previous > release of EMBOSS (6.0) included some fixes of similar nature, as well > as some small gui improvements. We recently have updated EMBOSS/Jemboss > make/install machinery to make standalone Jemboss come out of box when > users install EMBOSS, i think we were successful and this will be a new > feature in EMBOSS 6.1. > > Regards, > Mahmut > > > > > ------------------------------ > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > > > End of EMBOSS Digest, Vol 48, Issue 2 > ************************************* > From hmenager at pasteur.fr Tue Jun 16 09:57:36 2009 From: hmenager at pasteur.fr (=?ISO-8859-1?Q?Herv=E9_M=E9nager?=) Date: Tue, 16 Jun 2009 11:57:36 +0200 Subject: [EMBOSS] EMBOSS Funding and New developments In-Reply-To: References: Message-ID: <4A376C90.4020801@pasteur.fr> Hi, > Another need that people have asked me several times (I am administrator of > a web forum on bioinformatics) is to have a standard and official web > interface to the emboss tools, since the list at > http://emboss.sourceforge.net/interfaces/#web is outdated and google doesn't > return clear results. You can also give a try to Mobyle. Mobyle is the successor to the Pise system which is listed on the above page but not maintained anymore. Although it is not specific to EMBOSS, most of the package is interfaced, and it also supports other popular packages (ViennaRNA, Phylip...). You can try it at http://mobyle.pasteur.fr/cgi-bin/portal.py, and get further information at http://bioweb2.pasteur.fr/projects/mobyle/. Regards, Herv? M?nager From hmenager at pasteur.fr Tue Jun 16 19:55:44 2009 From: hmenager at pasteur.fr (hmenager at pasteur.fr) Date: Tue, 16 Jun 2009 21:55:44 +0200 (CEST) Subject: [EMBOSS] EMBOSS Funding and New developments In-Reply-To: References: Message-ID: <56269.157.99.64.103.1245182144.squirrel@php.pasteur.fr> To all: sorry about my previous repeated replies. It seems my webmail is completely messed up. Herv? M?nager From andrespinzon at gmail.com Mon Jun 22 14:32:52 2009 From: andrespinzon at gmail.com (Andres Pinzon) Date: Mon, 22 Jun 2009 10:32:52 -0400 Subject: [EMBOSS] extractfeat and "-join" option Message-ID: <8968fc7e0906220732r7b53117cq2e2cc3551f15b91b@mail.gmail.com> Hi everyone, The following line, should return a single fasta file with all the CDS in a single sequence: extractfeat environmental:DP000238 -type CDS -join stdout Instead it is returning each of them as a separate entry. Am I doing something wrong? Best, -- Andr?s Pinz?n http://bioinf.ibun.unal.edu.co/~apinzon/ Bioinformatics Center, Colombia EMBnet node http://bioinf.ibun.unal.edu.co Tel +57 3165000 ext 16961 Fax +571 3165415 Micology and Phytopathology Laboratory - Los Andes University. http://bioinf.uniandes.edu.co Tel +571 3394949 ext. 2768 From pmr at ebi.ac.uk Mon Jun 22 15:44:16 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Mon, 22 Jun 2009 16:44:16 +0100 Subject: [EMBOSS] extractfeat and "-join" option In-Reply-To: <8968fc7e0906220732r7b53117cq2e2cc3551f15b91b@mail.gmail.com> References: <8968fc7e0906220732r7b53117cq2e2cc3551f15b91b@mail.gmail.com> Message-ID: <4A3FA6D0.2030202@ebi.ac.uk> Andres Pinzon wrote: > Hi everyone, > The following line, should return a single fasta file with all the CDS > in a single sequence: > > extractfeat environmental:DP000238 -type CDS -join stdout > > Instead it is returning each of them as a separate entry. Am I doing > something wrong? The -join option combines all exons for one CDS (so that it can be translated as a complete reading frame). It is not intended to join all CDSs into one. for environmental:DP000238 I get 10 CDSs with -join set and 52 (one per exon) without -join. Hope this helps, Peter From andrespinzon at gmail.com Mon Jun 22 15:56:05 2009 From: andrespinzon at gmail.com (Andres Pinzon) Date: Mon, 22 Jun 2009 11:56:05 -0400 Subject: [EMBOSS] extractfeat and "-join" option In-Reply-To: <4A3FA6D0.2030202@ebi.ac.uk> References: <8968fc7e0906220732r7b53117cq2e2cc3551f15b91b@mail.gmail.com> <4A3FA6D0.2030202@ebi.ac.uk> Message-ID: <8968fc7e0906220856o5bf7f75fr545dfef536ec838b@mail.gmail.com> That's perfect, thank you. On Mon, Jun 22, 2009 at 11:44 AM, Peter Rice wrote: > Andres Pinzon wrote:' >> Hi everyone, >> The following line, should return a single fasta file with all the CDS >> in a single sequence: >> >> ?extractfeat environmental:DP000238 -type CDS -join stdout >> >> Instead it is returning each of them as a separate entry. Am I doing >> something wrong? > > The -join option combines all exons for one CDS (so that it can be > translated as a complete reading frame). > > It is not intended to join all CDSs into one. > > for environmental:DP000238 I get 10 CDSs with -join set and 52 (one per > exon) without -join. > > Hope this helps, > > Peter > > -- Andr?s Pinz?n http://bioinf.ibun.unal.edu.co/~apinzon/ Bioinformatics Center, Colombia EMBnet node http://bioinf.ibun.unal.edu.co Tel +57 3165000 ext 16961 Fax +571 3165415 Micology and Phytopathology Laboratory - Los Andes University. http://bioinf.uniandes.edu.co Tel +571 3394949 ext. 2768 From stephen.taylor at imm.ox.ac.uk Wed Jun 24 10:04:17 2009 From: stephen.taylor at imm.ox.ac.uk (Steve Taylor) Date: Wed, 24 Jun 2009 11:04:17 +0100 Subject: [EMBOSS] Seqret fetch by URL Message-ID: <4A41FA21.4030101@imm.ox.ac.uk> Hi, I am trying to fetch a sequence using seqret. In my EMBOSS defaults I have the following entry set up. I am using EMBOSS 6.0.1 both on Linux and Solaris. DB NCBI_prot [ method: url format: fasta type: P url: "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=%s&uids=&dopt=fasta&dispmax=5&sendto=t&fr om=begin&to=end" comment: "NCBI protein - FASTA seqs only" ] If I try: seqret NCBI_prot:ACA69081 I get: Reads and writes (returns) sequences Error: Unable to read sequence 'NCBI_prot:ACA69081' Died: seqret terminated: Bad value for '-sequence' and no prompt However, if I try http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=ACA69081&uids=&dopt=fasta&dispmax=5&sendto=t&from=begin&to=end I get >gi|169751563|gb|ACA69081.1| glycoside hydrolase family 1 [Yersinia pseudotuberculosis YPIII] MSYQQLPKDFLWGGAVAAHQVEGGWDKGGKGVSIADVLSGGSHGVDRVMTDGVLEGYRYPNHEAVDFYSH YKEDIALFAEMGFKCFRTSIAWTRIFPHGDEQQPNEAGLQFYDDMFDELLKYGIEPVITLSHFEMPWHLV KEYGGWKNRKVVDFFVKFSEVVMARYKSKVKYWMTFNEINNQRNWKYPLFGYCCSGVVFTEQENPEETLY QVLHHQFVASAKVVKLGHAINPEFKIGCMVAMVPLYPFSCHPDDMMYSVEAMRERYLFGDVHMRGYYPSY ILQEWARRGFNIHMEEGDLETLRDGCADYMGLSYYMSNAVSAINPGSGNSLSGFEGSVPNPHVKASDWGW QIDPVGLRYSLSVLYERYQKPLFIVENGFGAIDKVAADGMVHDDYRIAYLKAHIEQMKKAVFEDGVDLMG YTPWGCIDCVSFTTGEYSKRYGFIYVDKNDDGTGTMARSRKLSFDWYKKVIASNGEVL Any ideas why or is there a way I can get more verbose information about what is going on? Thanks, Steve From pmr at ebi.ac.uk Wed Jun 24 11:14:19 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Wed, 24 Jun 2009 12:14:19 +0100 Subject: [EMBOSS] Seqret fetch by URL In-Reply-To: <4A41FA21.4030101@imm.ox.ac.uk> References: <4A41FA21.4030101@imm.ox.ac.uk> Message-ID: <4A420A8B.3020900@ebi.ac.uk> Steve Taylor wrote: > > Hi, > > I am trying to fetch a sequence using seqret. In my EMBOSS defaults I > have the following entry set up. I am using EMBOSS 6.0.1 both on Linux > and Solaris. > > DB NCBI_prot [ method: url format: fasta type: P > url: > "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=%s&uids=&dopt=fasta&dispmax=5&sendto=t&fr > > om=begin&to=end" > comment: "NCBI protein - FASTA seqs only" > ] > > If I try: > > seqret NCBI_prot:ACA69081 > > I get: > Reads and writes (returns) sequences > Error: Unable to read sequence 'NCBI_prot:ACA69081' > Died: seqret terminated: Bad value for '-sequence' and no prompt They have gone away .... but not very far. seqret -debug gives the actual HTML returned in the seqret.dbg file > === File Buffer: Before ajFileBuffStripHtml === > * 952daa0 HTTP/1.1 301 Moved permanently > 951b540 Date: Wed, 24 Jun 2009 11:07:02 GMT > 951b570 Server: Apache > 951b358 Location: /sviewer/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=AC > A69081&uids=&dopt=fasta&dispmax=5&sendto=t&fr > 951b388 Content-Type: text/plain > 952fd10 Vary: Accept-Encoding > 952fd40 Content-Length: 0 > 952fd70 Connection: close > 951c2e8 If you change /entrez to /sviewer in your URL it should work. Your web browser is able to follow these HTML redirects, EMBOSS is a little more basic. We gave up on trying to interpret HTML error messages in the very early days when one site responded to failed requests with a nice picture of a flower (for those new to the net ... it was EBI :-) Thanks for letting us know, Peter From ajb at ebi.ac.uk Wed Jun 24 11:15:45 2009 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Wed, 24 Jun 2009 12:15:45 +0100 (BST) Subject: [EMBOSS] Seqret fetch by URL In-Reply-To: <4A41FA21.4030101@imm.ox.ac.uk> References: <4A41FA21.4030101@imm.ox.ac.uk> Message-ID: <38786.86.26.12.63.1245842145.squirrel@webmail.ebi.ac.uk> Hi Steve, NCBI added an extra line in their entrez output. We put a patch file on the ftp server a while ago that should fix this. ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/ If it doesn't then if you add '-debug' to any EMBOSS application you'll get an 'applicationname'.dbg file which gives verbose information on the workings (or not) of the application. HTH Alan > > Hi, > > I am trying to fetch a sequence using seqret. In my EMBOSS defaults I have > the following entry set up. I am using EMBOSS 6.0.1 both on Linux and > Solaris. > > DB NCBI_prot [ method: url format: fasta type: P > url: > "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=%s&uids=&dopt=fasta&dispmax=5&sendto=t&fr > om=begin&to=end" > comment: "NCBI protein - FASTA seqs only" > ] > > If I try: > > seqret NCBI_prot:ACA69081 > > I get: > Reads and writes (returns) sequences > Error: Unable to read sequence 'NCBI_prot:ACA69081' > Died: seqret terminated: Bad value for '-sequence' and no prompt > > However, if I try > > http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=ACA69081&uids=&dopt=fasta&dispmax=5&sendto=t&from=begin&to=end > > I get > >>gi|169751563|gb|ACA69081.1| glycoside hydrolase family 1 [Yersinia >> pseudotuberculosis YPIII] > MSYQQLPKDFLWGGAVAAHQVEGGWDKGGKGVSIADVLSGGSHGVDRVMTDGVLEGYRYPNHEAVDFYSH > YKEDIALFAEMGFKCFRTSIAWTRIFPHGDEQQPNEAGLQFYDDMFDELLKYGIEPVITLSHFEMPWHLV > KEYGGWKNRKVVDFFVKFSEVVMARYKSKVKYWMTFNEINNQRNWKYPLFGYCCSGVVFTEQENPEETLY > QVLHHQFVASAKVVKLGHAINPEFKIGCMVAMVPLYPFSCHPDDMMYSVEAMRERYLFGDVHMRGYYPSY > ILQEWARRGFNIHMEEGDLETLRDGCADYMGLSYYMSNAVSAINPGSGNSLSGFEGSVPNPHVKASDWGW > QIDPVGLRYSLSVLYERYQKPLFIVENGFGAIDKVAADGMVHDDYRIAYLKAHIEQMKKAVFEDGVDLMG > YTPWGCIDCVSFTTGEYSKRYGFIYVDKNDDGTGTMARSRKLSFDWYKKVIASNGEVL > > > Any ideas why or is there a way I can get more verbose information about > what is going on? > > Thanks, > > Steve > > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > From stephen.taylor at imm.ox.ac.uk Wed Jun 24 12:18:18 2009 From: stephen.taylor at imm.ox.ac.uk (Steve Taylor) Date: Wed, 24 Jun 2009 13:18:18 +0100 Subject: [EMBOSS] Seqret fetch by URL In-Reply-To: <38786.86.26.12.63.1245842145.squirrel@webmail.ebi.ac.uk> References: <4A41FA21.4030101@imm.ox.ac.uk> <38786.86.26.12.63.1245842145.squirrel@webmail.ebi.ac.uk> Message-ID: <4A42198A.2050902@imm.ox.ac.uk> Hi Peter/Alan, Thanks - I changed to entrez to sviewer and it all works fine now. Steve > > NCBI added an extra line in their entrez output. We put a patch file on > the ftp server a while ago that should fix this. > > ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/ > > If it doesn't then if you add '-debug' to any EMBOSS application > you'll get an 'applicationname'.dbg file which gives verbose information > on the workings (or not) of the application. > > HTH > > Alan > > >> Hi, >> >> I am trying to fetch a sequence using seqret. In my EMBOSS defaults I have >> the following entry set up. I am using EMBOSS 6.0.1 both on Linux and >> Solaris. >> >> DB NCBI_prot [ method: url format: fasta type: P >> url: >> "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=%s&uids=&dopt=fasta&dispmax=5&sendto=t&fr >> om=begin&to=end" >> comment: "NCBI protein - FASTA seqs only" >> ] >> >> If I try: >> >> seqret NCBI_prot:ACA69081 >> >> I get: >> Reads and writes (returns) sequences >> Error: Unable to read sequence 'NCBI_prot:ACA69081' >> Died: seqret terminated: Bad value for '-sequence' and no prompt >> >> However, if I try >> >> http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?db=protein&qty=1&c_start=1&list_uids=ACA69081&uids=&dopt=fasta&dispmax=5&sendto=t&from=begin&to=end >> >> I get >> >>> gi|169751563|gb|ACA69081.1| glycoside hydrolase family 1 [Yersinia >>> pseudotuberculosis YPIII] >> MSYQQLPKDFLWGGAVAAHQVEGGWDKGGKGVSIADVLSGGSHGVDRVMTDGVLEGYRYPNHEAVDFYSH >> YKEDIALFAEMGFKCFRTSIAWTRIFPHGDEQQPNEAGLQFYDDMFDELLKYGIEPVITLSHFEMPWHLV >> KEYGGWKNRKVVDFFVKFSEVVMARYKSKVKYWMTFNEINNQRNWKYPLFGYCCSGVVFTEQENPEETLY >> QVLHHQFVASAKVVKLGHAINPEFKIGCMVAMVPLYPFSCHPDDMMYSVEAMRERYLFGDVHMRGYYPSY >> ILQEWARRGFNIHMEEGDLETLRDGCADYMGLSYYMSNAVSAINPGSGNSLSGFEGSVPNPHVKASDWGW >> QIDPVGLRYSLSVLYERYQKPLFIVENGFGAIDKVAADGMVHDDYRIAYLKAHIEQMKKAVFEDGVDLMG >> YTPWGCIDCVSFTTGEYSKRYGFIYVDKNDDGTGTMARSRKLSFDWYKKVIASNGEVL >> >> >> Any ideas why or is there a way I can get more verbose information about >> what is going on? >> >> Thanks, >> >> Steve >> >> _______________________________________________ >> EMBOSS mailing list >> EMBOSS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/emboss >> > > From jasonzhang2002 at gmail.com Fri Jun 26 17:53:31 2009 From: jasonzhang2002 at gmail.com (jason zhang) Date: Fri, 26 Jun 2009 10:53:31 -0700 Subject: [EMBOSS] ehmmbuild does not support -o and -hmmfile together In-Reply-To: <4A41FA21.4030101@imm.ox.ac.uk> References: <4A41FA21.4030101@imm.ox.ac.uk> Message-ID: <4A450B1B.7010800@gmail.com> An HTML attachment was scrubbed... URL: From jasonzhang2002 at gmail.com Fri Jun 26 17:54:26 2009 From: jasonzhang2002 at gmail.com (jason zhang) Date: Fri, 26 Jun 2009 10:54:26 -0700 Subject: [EMBOSS] please support HMMERDB environment variable like HMMER Message-ID: <4A450B52.9020805@gmail.com> An HTML attachment was scrubbed... URL: From jasonzhang2002 at gmail.com Fri Jun 26 17:55:19 2009 From: jasonzhang2002 at gmail.com (jason zhang) Date: Fri, 26 Jun 2009 10:55:19 -0700 Subject: [EMBOSS] please modify two acd files for hmmer package Message-ID: <4A450B87.30802@gmail.com> please modify : default: 100 to default: "100" in ehmmsearch and ehmmpfam. I have a java parser for acd files. my parser choke for these acd files. From pmr at ebi.ac.uk Fri Jun 26 19:40:07 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 26 Jun 2009 20:40:07 +0100 Subject: [EMBOSS] ehmmbuild does not support -o and -hmmfile together In-Reply-To: <4A450B1B.7010800@gmail.com> References: <4A41FA21.4030101@imm.ox.ac.uk> <4A450B1B.7010800@gmail.com> Message-ID: <4A452417.9060501@ebi.ac.uk> jason zhang wrote: > >ehmmbuild -auto -stdout -alignfile globins50.msf -nhmm globins50 > -hmmfile globin.hmm -o out > Error: Unable to open file 'out/globin.hmm' for output > Died: ehmmbuild terminated: Bad value for '-hmmfile' with -auto defined > > It seems that -o is treated as a directory. But the document/acd lists it > as outfile. It will work with a different commandline order. With -o after -hmmfile it is incorrectly assumed to be -odirectory (it should be an ambiguous qualifier). This is fixed in the July 15th release of EMBOSS. regards, Peter Rice From pmr at ebi.ac.uk Fri Jun 26 19:41:13 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 26 Jun 2009 20:41:13 +0100 Subject: [EMBOSS] please support HMMERDB environment variable like HMMER In-Reply-To: <4A450B52.9020805@gmail.com> References: <4A450B52.9020805@gmail.com> Message-ID: <4A452459.50002@ebi.ac.uk> jason zhang wrote: > ehmmpfam does not recognize HMMERDB environment variable as hmmpfam does. > Could this be supported? Yes .. we have added the ability to specify an input file directory, and the ability to specify an environment variable as an ACD value. This will be in the 15th July release of EMBOSS. regards, Peter Rice From pmr at ebi.ac.uk Fri Jun 26 19:42:22 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 26 Jun 2009 20:42:22 +0100 Subject: [EMBOSS] please modify two acd files for hmmer package In-Reply-To: <4A450B87.30802@gmail.com> References: <4A450B87.30802@gmail.com> Message-ID: <4A45249E.50100@ebi.ac.uk> jason zhang wrote: > please modify : default: 100 to default: "100" in ehmmsearch and > ehmmpfam. I have a java parser for acd files. my parser choke for these acd > files. Fixed in the new release. I am curious ... what does your parser do? We have a few changes in the new release (extra attributes). regards, Peter From jasonzhang2002 at gmail.com Fri Jun 26 20:36:54 2009 From: jasonzhang2002 at gmail.com (jason zhang) Date: Fri, 26 Jun 2009 13:36:54 -0700 Subject: [EMBOSS] please modify two acd files for hmmer package In-Reply-To: <4A45249E.50100@ebi.ac.uk> References: <4A450B87.30802@gmail.com> <4A45249E.50100@ebi.ac.uk> Message-ID: <4A453166.50603@gmail.com> Hi, peter Peter Rice wrote: > jason zhang wrote: >> please modify : default: 100 to default: "100" in ehmmsearch and >> ehmmpfam. I have a java parser for acd files. my parser choke for >> these acd >> files. > > Fixed in the new release. > > I am curious ... what does your parser do? We have a few changes in > the new release (extra attributes). > I am coding an application which provides web interface and web service interface to a set of applications including EMBOSS. If you are interested, the web interface is here: http://174.129.249.18:8080/appweb. You can login in with testtest/123456 as the username/password. The application is currently at beta stage. The application parses ACD file and generates Web interface and Web Service (WSDL). Are the extra attributes in the new release documented somewhere? I will support them in my parser if web interface or Web Service are impacted. > regards, > > Peter > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > Regards -jason From pmr at ebi.ac.uk Fri Jun 26 20:55:12 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 26 Jun 2009 21:55:12 +0100 Subject: [EMBOSS] please modify two acd files for hmmer package In-Reply-To: <4A453166.50603@gmail.com> References: <4A450B87.30802@gmail.com> <4A45249E.50100@ebi.ac.uk> <4A453166.50603@gmail.com> Message-ID: <4A4535B0.7040500@ebi.ac.uk> jason zhang wrote: > Hi, peter > Peter Rice wrote: >> I am curious ... what does your parser do? We have a few changes in >> the new release (extra attributes). >> > I am coding an application which provides web interface and web service > interface to a set of applications including EMBOSS. If you are > interested, the web interface is here: > http://174.129.249.18:8080/appweb. Thanks. I gave it a try. looks like a good start. > The application is currently at beta stage. The application parses ACD > file and generates Web interface and Web Service (WSDL). Are the extra > attributes in the new release documented somewhere? I will support them > in my parser if web interface or Web Service are impacted. There is updated documentation at http://emboss.sourceforge.net/developers/acd/syntax.html which we automatically update with new datatypes and attributes (though I now notice it says version 3.0.0 - I will fix that!) I see your web interface includes every option ... rather like we do with the SoapLab web services. A few are not valid in all cases ... for example, when I run "antigenic" which only accepts protein sequences the -snucleotide option will break the run and -sprotein is unnecessary. On balance I find users are happiest when the options are always the same ... but you could consider hiding the less useful ones (sequence input options, anything in the "advanced" section of ACD ... with some way for the user to find them and use them. This is in line with the command line philosophy - even with -option on the command line these are never prompted for, but they can be used if the user reads the documentation or studies the -help options. Let us know if there is anything we can do to help ... for example, could we run your parser on each new release and send you the results (that implies running it aftre significant ACD changes and informing you if we see any problems at that stage). We can do the same for other ACD parsers if there is interest. regards, Peter Rice From jasonzhang2002 at gmail.com Fri Jun 26 21:31:45 2009 From: jasonzhang2002 at gmail.com (jason zhang) Date: Fri, 26 Jun 2009 14:31:45 -0700 Subject: [EMBOSS] please modify two acd files for hmmer package In-Reply-To: <4A4535B0.7040500@ebi.ac.uk> References: <4A450B87.30802@gmail.com> <4A45249E.50100@ebi.ac.uk> <4A453166.50603@gmail.com> <4A4535B0.7040500@ebi.ac.uk> Message-ID: <4A453E41.407@gmail.com> Hi, Peter Thank you for the suggestion. > I see your web interface includes every option ... rather like we do > with the SoapLab web services. A few are not valid in all cases ... > for example, when I run "antigenic" which only accepts protein > sequences the -snucleotide option will break the run and -sprotein is > unnecessary. On balance I find users are happiest when the options are > always the same ... but you could consider hiding the less useful ones > (sequence input options, anything in the "advanced" section of ACD ... > with some way for the user to find them and use them. This is in line > with the command line philosophy - even with -option on the command > line these are never prompted for, but they can be used if the user > reads the documentation or studies the -help options. I planned to hide those advanced options and they are visible only if the end users choose to. But due to the limitation in the web toolkit I used, I can not do that easily. With regards to -sprotein/-snucleotide for antigenic, the web interface can not tell that since there is no such information in ACD. I expect the end user has some basic knowledge about the program and will not make such mistake. Not all information in ACD is used. Some information such as variable, pattern can not be easily translated to javascript in web page. Again, I expect the end user can work it out. Otherwise error will occur at execution time. > > Let us know if there is anything we can do to help ... for example, > could we run your parser on each new release and send you the results > (that implies running it aftre significant ACD changes and informing > you if we see any problems at that stage). This is definitely helpful. I will discuss this with my boss and package a parser if he is ok. > > We can do the same for other ACD parsers if there is interest. > > regards, -jason From pmr at ebi.ac.uk Fri Jun 26 21:41:48 2009 From: pmr at ebi.ac.uk (Peter Rice) Date: Fri, 26 Jun 2009 22:41:48 +0100 Subject: [EMBOSS] please modify two acd files for hmmer package In-Reply-To: <4A453E41.407@gmail.com> References: <4A450B87.30802@gmail.com> <4A45249E.50100@ebi.ac.uk> <4A453166.50603@gmail.com> <4A4535B0.7040500@ebi.ac.uk> <4A453E41.407@gmail.com> Message-ID: <4A45409C.7090804@ebi.ac.uk> jason zhang wrote: > With regards to -sprotein/-snucleotide for antigenic, the web interface > can not tell that since there is no such information in ACD. I expect > the end user has some basic knowledge about the program and will not > make such mistake. Indeed, it is often best to trust the users. The information is in ACD, but it is in the sequence "type" which you would have to interpret as nucleotide, protein, or both. Some ACD files that allow both types also use a variable "ACDPROTEIN" that is set to the type of the first sequence - this allows you to make protein or nucleotide specific versions with appropriate default values - the alignment progams are common examples of this. > Not all information in ACD is used. Some information such as variable, > pattern can not be easily translated to javascript in web page. Again, I > expect the end user can work it out. Otherwise error will occur at > execution time. We try to avoid these. If you run "acdvalid " you may see warnings for things that can be difficult for parsers. Let us know if any of these give you major problems - or if there are problems we fail to detect. We try to reduce the number of acdvalid warnings for all emboss applications before each release. regards, Peter From gbottu at vub.ac.be Mon Jun 29 09:41:50 2009 From: gbottu at vub.ac.be (Guy Bottu) Date: Mon, 29 Jun 2009 11:41:50 +0200 Subject: [EMBOSS] announcing wEMBOSS version 2 Message-ID: <4A488C5E.9010301@vub.ac.be> Dear users of wEMBOSS, wEMBOSS has reached version 2. It has not much changed from the user's point of view but has changed substantially from the developer's and manager's point of view. In order to make further development easier, the code has been refreshed and is now maintained as a project under Eclipse with Epic plug-in. The development version is called wEMBOSSDEV and from this releases for distribution with name wEMBOSSDIST-x.x.x are regularly drawn. The new version does not anymore install its Perl libraries in the Perl system libraries. There was indeed no reason to do this, since the wEMBOSS libraries are not used by any other program. Storing them in a separate location makes it much easier to get rid of old versions, making sure they cannot interfere with newer versions. We have stopped the habit of distributing wrappers4EMBOSS inside wEMBOSS, since there was little to be gained by doing so. The 2 packages are now simply presented as separate tar archives for download. For the end user the main difference by now is that the included applets (Jalview for viewing multiple sequence alignments and ATV for viewing phylogenetic trees) have been upgraded to the latest version. Also, with the new version of wEMBOSS the Web Browser windows open in predetermined positions, making them better spread over the computer screen. Guy Bottu, wEMBOSS development team P.S. For those who already downloaded version 2.1 : it turned out to contain a number of bugs. These have been fixed with version 2.1.1 of 23 June, which you should definitively download. From ellis at biochem.dental.upenn.edu Mon Jun 29 18:23:59 2009 From: ellis at biochem.dental.upenn.edu (Ellis Golub) Date: Mon, 29 Jun 2009 14:23:59 -0400 Subject: [EMBOSS] HPGL driver Message-ID: <1090629142359.ZM606423@biochem.dental.upenn.edu> Hello -- I've just upgraded to version 6.0.1 from 3.0.0, and I've run into a problem with the hpgl plot driver. When I try to use it, I get a large number of Invalid pen selection errors, and the resulting hpgl file is monochrome. In the docs, the plotter pens are supposed to be preconfigured. How do I configure them correctly? Ellis Golub -- ============================================================= Ellis Golub Phone: (215) 898-4629 Biochemistry Department FAX: (215) 898-3695 School of Dental Medicine ellis at biochem.dental.upenn.edu University of Pennsylvania 240 South 40th Street Philadelphia, PA 19104-6030 Home: http://biochem.dental.upenn.edu/~ellis/ PGP: http://biochem.dental.upenn.edu/~ellis/public_key.html ============================================================== From ajb at ebi.ac.uk Tue Jun 30 12:02:08 2009 From: ajb at ebi.ac.uk (ajb at ebi.ac.uk) Date: Tue, 30 Jun 2009 13:02:08 +0100 (BST) Subject: [EMBOSS] HPGL driver In-Reply-To: <1090629142359.ZM606423@biochem.dental.upenn.edu> References: <1090629142359.ZM606423@biochem.dental.upenn.edu> Message-ID: <50168.86.26.12.63.1246363328.squirrel@webmail.ebi.ac.uk> Dear Ellis, Thanks for pointing this out. We're currently discussing the problem and hope to have a fix in place before the next release (Jul 15th). ATB Alan > Hello -- > > I've just upgraded to version 6.0.1 from 3.0.0, and I've run into a > problem > with the hpgl plot driver. When I try to use it, I get a large number of > Invalid pen selection errors, and the resulting hpgl file is monochrome. > > In the docs, the plotter pens are supposed to be preconfigured. How do I > configure them correctly? > > Ellis Golub > -- > ============================================================= > Ellis Golub Phone: (215) 898-4629 > Biochemistry Department FAX: (215) 898-3695 > School of Dental Medicine ellis at biochem.dental.upenn.edu > University of Pennsylvania > 240 South 40th Street > Philadelphia, PA 19104-6030 > Home: http://biochem.dental.upenn.edu/~ellis/ > PGP: http://biochem.dental.upenn.edu/~ellis/public_key.html > ============================================================== > _______________________________________________ > EMBOSS mailing list > EMBOSS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss >