From cbraun at uni-goettingen.de Wed Jun 13 04:57:11 2012 From: cbraun at uni-goettingen.de (Christoph Braun) Date: Wed, 13 Jun 2012 10:57:11 +0200 Subject: [EMBOSS] DNAPlotter Message-ID: <4FD855E7.3000405@uni-goettingen.de> An HTML attachment was scrubbed... URL: From hnorpois at googlemail.com Sun Jun 17 12:54:17 2012 From: hnorpois at googlemail.com (Hermann Norpois) Date: Sun, 17 Jun 2012 18:54:17 +0200 Subject: [EMBOSS] jaspscan: succession of transcription factor binding Message-ID: Hello, the output of jaspscan reports the binding for each TF in the order of parsed transcription factors. I would prefer an order that reflects the sequence of transcription factor binding. I did not find an format for this? Is there a possibility doing that (without writing a perl script for instance)? Thanks Hermann Norpois From ppetrov at mail.student.oulu.fi Mon Jun 18 15:55:13 2012 From: ppetrov at mail.student.oulu.fi (Petar Petrov) Date: Mon, 18 Jun 2012 22:55:13 +0300 Subject: [EMBOSS] EMBOSS and primer3 In-Reply-To: <39217.82.26.12.214.1317827130.squirrel@imap04.ebi.ac.uk> References: <39217.82.26.12.214.1317827130.squirrel@imap04.ebi.ac.uk> Message-ID: <20120618225513.dntzkrbp28owgggw@webmail.oulu.fi> Hello to all, Does EMBOSS (eprimer or eprimer32) work with primer3 version 2.3.x? regards, Petar From charles-listes-emboss at plessy.org Thu Jun 21 20:23:15 2012 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Fri, 22 Jun 2012 09:23:15 +0900 Subject: [EMBOSS] Plans for EMBOSS 6.5.0 and 6.6.0, and source-less JAR files. Message-ID: <20120622002315.GA28425@falafel.plessy.net> Dear EMBOSS developers, after the good news about EMBOSS being updated to 6.4.0 in Debian, I am back with more issues about source code, that I hope can be solved with your help. But first of all, if you have a pre-release of 6.5.0 available, I would be pleased to test it and report potential build issues on Debian. While having a fresh look on our package when uploading 6.4.0, we realised that it contains a lot of Java JAR files for Jemboss, which are third-party Java libraries in a binary format, with no source code. The good news is that a lot of them are already packaged in Debian, so in theory, all we would have to do is to replace these JAR files from the emboss package in Debian by symbolic link to their own package. This means, however, that these libraries may be updated independantly of Jemboss. This is exactly what we want to do in a distribution, as it considerably eases bug fixing, but in the Java world (in contrary to C or Perl), it is quite uncommon. So my question is: do you think it has chances to work for Jemboss, and if yes, what is the best list or person to contact for assistance in our effort ? PS: on our "Popularity contest" page, you can monitor how the user base of EMBOSS is still increasing. http://qa.debian.org/popcon-graph.php?packages=emboss&show_vote=on&beenhere=1 -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From charles-listes-emboss at plessy.org Thu Jun 21 20:49:39 2012 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Fri, 22 Jun 2012 09:49:39 +0900 Subject: [EMBOSS] [SOLVED] Re: Files included in EMBOSS but licensed ... Message-ID: <20120622004939.GC28425@falafel.plessy.net> Le Sat, Jul 30, 2011 at 09:58:07AM +0100, Peter Rice a ?crit : > > The no-derivatives version is specifically there to > prevent derivatives - for example Debian distributing a modified > UniProt without permission. Dear Peter and everybody, it is my pleasure to announce that EMBOSS 6.4.0 has just been uploaded to Debian, thanks to a fruitful discussion with the UniProt consortium where we confirmed that the license indicated on each record is there to protect the database as a whole, and after disucssion within Debian where there was no opposition to the idea of ignoring this non-free license for the isolated records distributed in the test suite of EMBOSS, as we consider them to be a collection of facts with no creative work (the creative work being the database itself). Of course, only databases that also give the freedom to distribute modified copies are fitting with Debian's ideals, so the take home message is not that such non-free license is a good thing from Debian's point of view. But I am very pleased that we could work out this difference in a constructive way. I would like give many thanks to UniProt and everybody who helped or proposed their help to solve this issue. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From charles-listes-emboss at plessy.org Fri Jun 22 04:09:31 2012 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Fri, 22 Jun 2012 17:09:31 +0900 Subject: [EMBOSS] Plans for EMBOSS 6.5.0 and 6.6.0, and source-less JAR files. In-Reply-To: <20120622002315.GA28425@falafel.plessy.net> <20120622073430.GI32064@an3as.eu> Message-ID: <20120622080931.GA30090@falafel.plessy.net> Le Fri, Jun 22, 2012 at 09:23:15AM +0900, Charles Plessy a ?crit : > > But first of all, if you have a pre-release of 6.5.0 available, I would > be pleased to test it and report potential build issues on Debian. Sorry for the repeated posting; I forgot to mention that we would be greatly helped in our packaging of EMBASSY, if the version numbers could be incremented at each modification of the source tarball. Currently some packages such as domainatrix and related words receive updates of the build system at each EMBOSS release, but stay at version 0.1.0, which causes us to use version numbers such as 0.1.0+20110714, and makes us incapable of automatically detect updates. Have a nice week-end, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From cbraun at uni-goettingen.de Wed Jun 13 08:57:11 2012 From: cbraun at uni-goettingen.de (Christoph Braun) Date: Wed, 13 Jun 2012 10:57:11 +0200 Subject: [EMBOSS] DNAPlotter Message-ID: <4FD855E7.3000405@uni-goettingen.de> An HTML attachment was scrubbed... URL: From hnorpois at googlemail.com Sun Jun 17 16:54:17 2012 From: hnorpois at googlemail.com (Hermann Norpois) Date: Sun, 17 Jun 2012 18:54:17 +0200 Subject: [EMBOSS] jaspscan: succession of transcription factor binding Message-ID: Hello, the output of jaspscan reports the binding for each TF in the order of parsed transcription factors. I would prefer an order that reflects the sequence of transcription factor binding. I did not find an format for this? Is there a possibility doing that (without writing a perl script for instance)? Thanks Hermann Norpois From ppetrov at mail.student.oulu.fi Mon Jun 18 19:55:13 2012 From: ppetrov at mail.student.oulu.fi (Petar Petrov) Date: Mon, 18 Jun 2012 22:55:13 +0300 Subject: [EMBOSS] EMBOSS and primer3 In-Reply-To: <39217.82.26.12.214.1317827130.squirrel@imap04.ebi.ac.uk> References: <39217.82.26.12.214.1317827130.squirrel@imap04.ebi.ac.uk> Message-ID: <20120618225513.dntzkrbp28owgggw@webmail.oulu.fi> Hello to all, Does EMBOSS (eprimer or eprimer32) work with primer3 version 2.3.x? regards, Petar From charles-listes-emboss at plessy.org Fri Jun 22 00:23:15 2012 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Fri, 22 Jun 2012 09:23:15 +0900 Subject: [EMBOSS] Plans for EMBOSS 6.5.0 and 6.6.0, and source-less JAR files. Message-ID: <20120622002315.GA28425@falafel.plessy.net> Dear EMBOSS developers, after the good news about EMBOSS being updated to 6.4.0 in Debian, I am back with more issues about source code, that I hope can be solved with your help. But first of all, if you have a pre-release of 6.5.0 available, I would be pleased to test it and report potential build issues on Debian. While having a fresh look on our package when uploading 6.4.0, we realised that it contains a lot of Java JAR files for Jemboss, which are third-party Java libraries in a binary format, with no source code. The good news is that a lot of them are already packaged in Debian, so in theory, all we would have to do is to replace these JAR files from the emboss package in Debian by symbolic link to their own package. This means, however, that these libraries may be updated independantly of Jemboss. This is exactly what we want to do in a distribution, as it considerably eases bug fixing, but in the Java world (in contrary to C or Perl), it is quite uncommon. So my question is: do you think it has chances to work for Jemboss, and if yes, what is the best list or person to contact for assistance in our effort ? PS: on our "Popularity contest" page, you can monitor how the user base of EMBOSS is still increasing. http://qa.debian.org/popcon-graph.php?packages=emboss&show_vote=on&beenhere=1 -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From charles-listes-emboss at plessy.org Fri Jun 22 00:49:39 2012 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Fri, 22 Jun 2012 09:49:39 +0900 Subject: [EMBOSS] [SOLVED] Re: Files included in EMBOSS but licensed ... Message-ID: <20120622004939.GC28425@falafel.plessy.net> Le Sat, Jul 30, 2011 at 09:58:07AM +0100, Peter Rice a ?crit : > > The no-derivatives version is specifically there to > prevent derivatives - for example Debian distributing a modified > UniProt without permission. Dear Peter and everybody, it is my pleasure to announce that EMBOSS 6.4.0 has just been uploaded to Debian, thanks to a fruitful discussion with the UniProt consortium where we confirmed that the license indicated on each record is there to protect the database as a whole, and after disucssion within Debian where there was no opposition to the idea of ignoring this non-free license for the isolated records distributed in the test suite of EMBOSS, as we consider them to be a collection of facts with no creative work (the creative work being the database itself). Of course, only databases that also give the freedom to distribute modified copies are fitting with Debian's ideals, so the take home message is not that such non-free license is a good thing from Debian's point of view. But I am very pleased that we could work out this difference in a constructive way. I would like give many thanks to UniProt and everybody who helped or proposed their help to solve this issue. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan From charles-listes-emboss at plessy.org Fri Jun 22 08:09:31 2012 From: charles-listes-emboss at plessy.org (Charles Plessy) Date: Fri, 22 Jun 2012 17:09:31 +0900 Subject: [EMBOSS] Plans for EMBOSS 6.5.0 and 6.6.0, and source-less JAR files. In-Reply-To: <20120622002315.GA28425@falafel.plessy.net> <20120622073430.GI32064@an3as.eu> Message-ID: <20120622080931.GA30090@falafel.plessy.net> Le Fri, Jun 22, 2012 at 09:23:15AM +0900, Charles Plessy a ?crit : > > But first of all, if you have a pre-release of 6.5.0 available, I would > be pleased to test it and report potential build issues on Debian. Sorry for the repeated posting; I forgot to mention that we would be greatly helped in our packaging of EMBASSY, if the version numbers could be incremented at each modification of the source tarball. Currently some packages such as domainatrix and related words receive updates of the build system at each EMBOSS release, but stay at version 0.1.0, which causes us to use version numbers such as 0.1.0+20110714, and makes us incapable of automatically detect updates. Have a nice week-end, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan