Bug#493977: ITP: embassy-phylip -- EMBOSS conversions of the programs in the phylip package
Hi, Charles Plessy wrote: Hi Vincent, How about: [...] It is really better. My wife told me she understands this description ;-) Regards, Vincent -- Vincent Danjean GPG key ID 0x9D025E87 [EMAIL PROTECTED] GPG key fingerprint: FC95 08A6 854D DB48 4B9A 8A94 0BF7 7867 9D02 5E87 Unofficial pacakges: http://www-id.imag.fr/~danjean/deb.html#package APT repo: deb http://perso.debian.org/~vdanjean/debian unstable main -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#493977: ITP: embassy-phylip -- EMBOSS conversions of the programs in the phylip package
Package: wnpp Severity: wishlist Owner: Charles Plessy [EMAIL PROTECTED] Package name: embassy-phylip Version : 3.67 Upstream Author : The EMBOSS developpers and Joe Felsenstein URL : ftp://emboss.open-bio.org/pub/EMBOSS/PHYLIPNEW-3.67.tar.gz License : No profit (same as http://packages.debian.org/changelogs/pool/non-free/p/phylip/phylip_3.67-3/phylip.copyright) Programming Lang: C Description : EMBOSS conversions of the programs in the phylip package The embassy-phylip programs are EMBOSS conversions of the programs in Joe Felsenstein's PHYLIP package, a package of programs for inferring phylogenies. These programs all have the prefix f to distinguish them from the original programs. A user on the EMBOSS mailing lists expressed his interest for this package. My approach with non-free works is to only package them on user request, so I will package embassy-phylip. Have a nice day, -- Charles Plessy Debian Med packaging team Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#493977: ITP: embassy-phylip -- EMBOSS conversions of the programs in the phylip package
On Wed, Aug 06, 2008 at 07:31:19PM +0900, Charles Plessy wrote: Package name: embassy-phylip Description : EMBOSS conversions of the programs in the phylip package The embassy-phylip programs are EMBOSS conversions of the programs in Joe Felsenstein's PHYLIP package, a package of programs for inferring phylogenies. These programs all have the prefix f to distinguish them from the original programs. First of all, the description of the package should be self-contained. If it does the same as the phylip package, then copy the description of the phylip package, and only add at the end of the description that this is an EMBOSS conversion. Then there is the question what an EMBOSS conversion entails. Why would one want to use embassy-phylip instead of phylip? The only difference you describe is that there is an extra f in the filename. If the differences between embassy-phylip and phylip are small, then you should suggest both upstreams to work together. -- Met vriendelijke groet / with kind regards, Guus Sliepen [EMAIL PROTECTED] signature.asc Description: Digital signature
Bug#493977: ITP: embassy-phylip -- EMBOSS conversions of the programs in the phylip package
Le Wed, Aug 06, 2008 at 01:30:06PM +0200, Guus Sliepen a écrit : First of all, the description of the package should be self-contained. If it does the same as the phylip package, then copy the description of the phylip package, and only add at the end of the description that this is an EMBOSS conversion. Then there is the question what an EMBOSS conversion entails. Why would one want to use embassy-phylip instead of phylip? The only difference you describe is that there is an extra f in the filename. If the differences between embassy-phylip and phylip are small, then you should suggest both upstreams to work together. Hi Guus, I hope that the following revised description answers all your questions at the same time. PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters. . EMBASSY packages include applications with the same look and feel as EMBOSS applications, but which the author wishes to be kept separate from EMBOSS. This is usually because the packages are for specialised sequence analysis or for non-sequence based anaylsis, or are licensed differently to EMBOSS (i.e. non GPL). . EMBOSS - the European Molecular Biology Open Software Suite - is an analysis package specially developed for the needs of the molecular biology user community. . The EMBASSY PHYLIP programs all have the prefix f to distinguish them from the original programs. -- Charles Plessy Debian Med packaging team, Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#493977: ITP: embassy-phylip -- EMBOSS conversions of the programs in the phylip package
Hi, Here are some comments about the description (done with my wife who works as biologist with such kind of software). Charles Plessy wrote: PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters. . EMBASSY packages include applications with the same look and feel as EMBOSS applications, but which the author wishes to be kept separate from EMBOSS. This is usually because the packages are for specialised sequence analysis or for non-sequence based anaylsis, or are licensed differently to EMBOSS (i.e. non GPL). . EMBOSS - the European Molecular Biology Open Software Suite - is an analysis package specially developed for the needs of the molecular biology user community. . The EMBASSY PHYLIP programs all have the prefix f to distinguish them from the original programs. EMBOSS should be presented before EMBASSY as EMBASSY use EMBOSS in its definition. And we fail to see the relation between EMBOSS and PHYLIP. Does PHYLIP is a part of EMBOSS ? Moreover, reading your part on EMBASSY, I understand that EMBOSS is GPL but not necessarily EMBASSY. Am I right ? (I cannot because PHYLIP is not free, so either PHYLIP is not a part of EMBOSS or EMBOSS is not all GPL) Perhaps, you can keep the first paragraph about PHYLIP and then add something such as: Original PHYLIP software is not free. EMBASSY PHYLIP is a free rewrite in the context of the EMBOSS (European Molecular Biology Open Software Suite) project. The EMBASSY PHYLIP programs all have the prefix f to distinguish them from the original programs. [of course, I can be totaly wrong if I did not understand the relations between EMBOSS, EMBASSY and PHYLIP] Best regards, Vincent -- Vincent Danjean Adresse: Laboratoire d'Informatique de Grenoble Téléphone: +33 4 76 61 20 11ENSIMAG - antenne de Montbonnot Fax:+33 4 76 61 20 99ZIRST 51, avenue Jean Kuntzmann Email: [EMAIL PROTECTED] 38330 Montbonnot Saint Martin -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#493977: ITP: embassy-phylip -- EMBOSS conversions of the programs in the phylip package
On Wed, 6 Aug 2008, Charles Plessy wrote: The embassy-phylip programs are EMBOSS conversions of the programs in Joe Felsenstein's PHYLIP package, a package of programs for inferring phylogenies. These programs all have the prefix f to distinguish them from the original programs. Did you considered the chance to just use the xisting phylip package. It uses a wrapper anyway so perhaps we could just tweak the wrapper. Or we could do it the other way around: Find a way to use embassy-phylip for plain phylip usage and adapt the wrapper. I do not really know the difference between both so my idea might be naive - but at least checking whether we could go with a single code base makes sense to me. Greetings from Mar Del Plata Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
Bug#493977: ITP: embassy-phylip -- EMBOSS conversions of the programs in the phylip package
Hi Vincent, How about: This package is the adaptation of the PHYLIP package in which its programs can operate with the biological sequence formats and databases of the European Molecular Biology Open Software Suite (EMBOSS). The software packages adapted for EMBOSS are called EMBASSY. . PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters. . The EMBASSY PHYLIP programs all have the prefix f to distinguish them from the original programs and avoid namespace conflict. Moreover, reading your part on EMBASSY, I understand that EMBOSS is GPL but not necessarily EMBASSY. Am I right ? (I cannot because PHYLIP is not free, so either PHYLIP is not a part of EMBOSS or EMBOSS is not all GPL) Sorry for the confusion. EMBOSS applications are GPL and EMBOSS libraries are LGPL. As Andreas pointed out, there is a lot of source duplication between the PHYLIP and its EMBASSY fork. But building one from the other seems to be a lot of complication for no benefit, as the EMBASSY PHYLIP programs are not wrappers.. Have a nice day, -- Charles Plessy Debian Med packaging team, Tsurumi, Kanagawa, Japan -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of unsubscribe. Trouble? Contact [EMAIL PROTECTED]
