From mmhohman at northwestern.edu Sat Nov 13 13:13:33 2004 From: mmhohman at northwestern.edu (Moses Hohman) Date: Sat Nov 13 13:11:44 2004 Subject: [BioRuby] moving to Ruby 1.8? Message-ID: Hi, What version(s) of Ruby does bioruby officially support? >=1.8.1? Is 1.6 support being phased out? I just want to make sure that stuff I check into CVS (mostly unit tests and maybe some small refactorings) fits the standard and everyone's expectations. thanks, Moses From ktym at hgc.jp Sun Nov 14 10:13:18 2004 From: ktym at hgc.jp (Toshiaki Katayama) Date: Sun Nov 14 10:12:33 2004 Subject: [BioRuby] moving to Ruby 1.8? In-Reply-To: References: Message-ID: Hi Moses, Thank you for your contributions. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - To ALL: Unit tests are now merged in the CVS tree and can be run with 'ruby install.rb test'. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - I think BioRuby still compatible with Ruby 1.6.8. How about to keep BioRuby 0.6 series with support for Ruby 1.6, and preparing 0.7 series which may require >=1.8.1? I'm fine even if the unit tests fails with Ruby 1.6 during the above transition, as far as the BioRuby library can be installed and used with Ruby 1.6. Thanks, Toshiaki Katayama On 2004/11/14, at 3:13, Moses Hohman wrote: > Hi, > > What version(s) of Ruby does bioruby officially support? >=1.8.1? Is > 1.6 support being phased out? I just want to make sure that stuff I > check into CVS (mostly unit tests and maybe some small refactorings) > fits the standard and everyone's expectations. > > thanks, > > Moses > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby From mmhohman at northwestern.edu Sun Nov 14 20:52:46 2004 From: mmhohman at northwestern.edu (Moses Hohman) Date: Mon Nov 15 00:17:41 2004 Subject: [BioRuby] moving to Ruby 1.8? In-Reply-To: References: Message-ID: <0C160867-36A9-11D9-B942-000393DB7722@northwestern.edu> This sounds good. So, for now, don't check anything into lib that doesn't work with Ruby 1.6? And at some point in the future, once the final 0.6.* release has gone out, we'll check things in to lib that move toward 1.8.1, is that right? How many more 0.6.* releases are planned? Or do we want to use branches in CVS to accomplish this? Moses On Nov 14, 2004, at 9:13 AM, Toshiaki Katayama wrote: > Hi Moses, > > Thank you for your contributions. > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > To ALL: > Unit tests are now merged in the CVS tree and can be run > with 'ruby install.rb test'. > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > > I think BioRuby still compatible with Ruby 1.6.8. > > How about to keep BioRuby 0.6 series with support for Ruby 1.6, > and preparing 0.7 series which may require >=1.8.1? > > I'm fine even if the unit tests fails with Ruby 1.6 during the > above transition, as far as the BioRuby library can be installed > and used with Ruby 1.6. > > Thanks, > Toshiaki Katayama > > On 2004/11/14, at 3:13, Moses Hohman wrote: > >> Hi, >> >> What version(s) of Ruby does bioruby officially support? >=1.8.1? Is >> 1.6 support being phased out? I just want to make sure that stuff I >> check into CVS (mostly unit tests and maybe some small refactorings) >> fits the standard and everyone's expectations. >> >> thanks, >> >> Moses >> >> _______________________________________________ >> BioRuby mailing list >> BioRuby@open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From ktym at hgc.jp Mon Nov 15 00:56:53 2004 From: ktym at hgc.jp (Toshiaki Katayama) Date: Mon Nov 15 00:54:55 2004 Subject: [BioRuby] moving to Ruby 1.8? In-Reply-To: <0C160867-36A9-11D9-B942-000393DB7722@northwestern.edu> References: <0C160867-36A9-11D9-B942-000393DB7722@northwestern.edu> Message-ID: <269B45DE-36CB-11D9-B539-000D93347CEA@hgc.jp> On 2004/11/15, at 10:52, Moses Hohman wrote: > This sounds good. So, for now, don't check anything into lib that > doesn't work with Ruby 1.6? And at some point in the future, once the > final 0.6.* release has gone out, we'll check things in to lib that > move toward 1.8.1, is that right? How many more 0.6.* releases are > planned? Right. It depends on when we move to >=1.8.1, however, not so many 0.6 releases are planed (one or zero, maybe). e.g. Should we wait for OS X shipped with Ruby 1.8 series? > Or do we want to use branches in CVS to accomplish this? This will be the right way to go. The problem is, to be honest, I'm not so familiar with the CVS branching. Toshiaki > Moses > > On Nov 14, 2004, at 9:13 AM, Toshiaki Katayama wrote: > >> Hi Moses, >> >> Thank you for your contributions. >> >> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >> To ALL: >> Unit tests are now merged in the CVS tree and can be run >> with 'ruby install.rb test'. >> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >> >> I think BioRuby still compatible with Ruby 1.6.8. >> >> How about to keep BioRuby 0.6 series with support for Ruby 1.6, >> and preparing 0.7 series which may require >=1.8.1? >> >> I'm fine even if the unit tests fails with Ruby 1.6 during the >> above transition, as far as the BioRuby library can be installed >> and used with Ruby 1.6. >> >> Thanks, >> Toshiaki Katayama >> >> On 2004/11/14, at 3:13, Moses Hohman wrote: >> >>> Hi, >>> >>> What version(s) of Ruby does bioruby officially support? >=1.8.1? Is >>> 1.6 support being phased out? I just want to make sure that stuff I >>> check into CVS (mostly unit tests and maybe some small refactorings) >>> fits the standard and everyone's expectations. >>> >>> thanks, >>> >>> Moses >>> >>> _______________________________________________ >>> BioRuby mailing list >>> BioRuby@open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioruby >> >> _______________________________________________ >> BioRuby mailing list >> BioRuby@open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioruby >> > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby From mmhohman at northwestern.edu Mon Nov 15 17:03:59 2004 From: mmhohman at northwestern.edu (Moses Hohman) Date: Mon Nov 15 17:02:34 2004 Subject: [BioRuby] moving to Ruby 1.8? In-Reply-To: <269B45DE-36CB-11D9-B539-000D93347CEA@hgc.jp> References: <0C160867-36A9-11D9-B942-000393DB7722@northwestern.edu> <269B45DE-36CB-11D9-B539-000D93347CEA@hgc.jp> Message-ID: <40C8C432-3752-11D9-969A-000393DB7722@northwestern.edu> I am very familiar with CVS branching (we've been using them for several releases here at work, and I think we've worked out the kinks in their use), and could prepare an email guide for others. I could put the guide on the wiki, actually. Moses On Nov 14, 2004, at 11:56 PM, Toshiaki Katayama wrote: > On 2004/11/15, at 10:52, Moses Hohman wrote: >> This sounds good. So, for now, don't check anything into lib that >> doesn't work with Ruby 1.6? And at some point in the future, once the >> final 0.6.* release has gone out, we'll check things in to lib that >> move toward 1.8.1, is that right? How many more 0.6.* releases are >> planned? > > Right. > > It depends on when we move to >=1.8.1, however, not so many > 0.6 releases are planed (one or zero, maybe). > > e.g. Should we wait for OS X shipped with Ruby 1.8 series? > >> Or do we want to use branches in CVS to accomplish this? > > This will be the right way to go. > The problem is, to be honest, I'm not so familiar with > the CVS branching. > > Toshiaki > > > >> Moses >> >> On Nov 14, 2004, at 9:13 AM, Toshiaki Katayama wrote: >> >>> Hi Moses, >>> >>> Thank you for your contributions. >>> >>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >>> To ALL: >>> Unit tests are now merged in the CVS tree and can be run >>> with 'ruby install.rb test'. >>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >>> >>> I think BioRuby still compatible with Ruby 1.6.8. >>> >>> How about to keep BioRuby 0.6 series with support for Ruby 1.6, >>> and preparing 0.7 series which may require >=1.8.1? >>> >>> I'm fine even if the unit tests fails with Ruby 1.6 during the >>> above transition, as far as the BioRuby library can be installed >>> and used with Ruby 1.6. >>> >>> Thanks, >>> Toshiaki Katayama >>> >>> On 2004/11/14, at 3:13, Moses Hohman wrote: >>> >>>> Hi, >>>> >>>> What version(s) of Ruby does bioruby officially support? >=1.8.1? >>>> Is 1.6 support being phased out? I just want to make sure that >>>> stuff I check into CVS (mostly unit tests and maybe some small >>>> refactorings) fits the standard and everyone's expectations. >>>> >>>> thanks, >>>> >>>> Moses >>>> >>>> _______________________________________________ >>>> BioRuby mailing list >>>> BioRuby@open-bio.org >>>> http://portal.open-bio.org/mailman/listinfo/bioruby >>> >>> _______________________________________________ >>> BioRuby mailing list >>> BioRuby@open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioruby >>> >> >> _______________________________________________ >> BioRuby mailing list >> BioRuby@open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From mmhohman at northwestern.edu Mon Nov 15 17:03:59 2004 From: mmhohman at northwestern.edu (Moses Hohman) Date: Mon Nov 15 17:02:35 2004 Subject: [BioRuby] moving to Ruby 1.8? In-Reply-To: <269B45DE-36CB-11D9-B539-000D93347CEA@hgc.jp> References: <0C160867-36A9-11D9-B942-000393DB7722@northwestern.edu> <269B45DE-36CB-11D9-B539-000D93347CEA@hgc.jp> Message-ID: <40C8C432-3752-11D9-969A-000393DB7722@northwestern.edu> I am very familiar with CVS branching (we've been using them for several releases here at work, and I think we've worked out the kinks in their use), and could prepare an email guide for others. I could put the guide on the wiki, actually. Moses On Nov 14, 2004, at 11:56 PM, Toshiaki Katayama wrote: > On 2004/11/15, at 10:52, Moses Hohman wrote: >> This sounds good. So, for now, don't check anything into lib that >> doesn't work with Ruby 1.6? And at some point in the future, once the >> final 0.6.* release has gone out, we'll check things in to lib that >> move toward 1.8.1, is that right? How many more 0.6.* releases are >> planned? > > Right. > > It depends on when we move to >=1.8.1, however, not so many > 0.6 releases are planed (one or zero, maybe). > > e.g. Should we wait for OS X shipped with Ruby 1.8 series? > >> Or do we want to use branches in CVS to accomplish this? > > This will be the right way to go. > The problem is, to be honest, I'm not so familiar with > the CVS branching. > > Toshiaki > > > >> Moses >> >> On Nov 14, 2004, at 9:13 AM, Toshiaki Katayama wrote: >> >>> Hi Moses, >>> >>> Thank you for your contributions. >>> >>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >>> To ALL: >>> Unit tests are now merged in the CVS tree and can be run >>> with 'ruby install.rb test'. >>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >>> >>> I think BioRuby still compatible with Ruby 1.6.8. >>> >>> How about to keep BioRuby 0.6 series with support for Ruby 1.6, >>> and preparing 0.7 series which may require >=1.8.1? >>> >>> I'm fine even if the unit tests fails with Ruby 1.6 during the >>> above transition, as far as the BioRuby library can be installed >>> and used with Ruby 1.6. >>> >>> Thanks, >>> Toshiaki Katayama >>> >>> On 2004/11/14, at 3:13, Moses Hohman wrote: >>> >>>> Hi, >>>> >>>> What version(s) of Ruby does bioruby officially support? >=1.8.1? >>>> Is 1.6 support being phased out? I just want to make sure that >>>> stuff I check into CVS (mostly unit tests and maybe some small >>>> refactorings) fits the standard and everyone's expectations. >>>> >>>> thanks, >>>> >>>> Moses >>>> >>>> _______________________________________________ >>>> BioRuby mailing list >>>> BioRuby@open-bio.org >>>> http://portal.open-bio.org/mailman/listinfo/bioruby >>> >>> _______________________________________________ >>> BioRuby mailing list >>> BioRuby@open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioruby >>> >> >> _______________________________________________ >> BioRuby mailing list >> BioRuby@open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From mmhohman at northwestern.edu Mon Nov 15 17:07:36 2004 From: mmhohman at northwestern.edu (Moses Hohman) Date: Mon Nov 15 17:06:05 2004 Subject: [BioRuby] moving to Ruby 1.8? In-Reply-To: <269B45DE-36CB-11D9-B539-000D93347CEA@hgc.jp> References: <0C160867-36A9-11D9-B942-000393DB7722@northwestern.edu> <269B45DE-36CB-11D9-B539-000D93347CEA@hgc.jp> Message-ID: Also, on the OS X/Ruby 1.8 question, I think that if the older releases are still available, then we shouldn't wait, because in fact it is pretty easy to install Ruby 1.8 on OS X. But that is just my perspective. I admit I'm very comfortable with the whole ./configure, make, make install thing, and others may not be as comfortable. However, "configure/make/sudo make install" does run very smoothly, on 10.3 at least. Moses On Nov 14, 2004, at 11:56 PM, Toshiaki Katayama wrote: > On 2004/11/15, at 10:52, Moses Hohman wrote: >> This sounds good. So, for now, don't check anything into lib that >> doesn't work with Ruby 1.6? And at some point in the future, once the >> final 0.6.* release has gone out, we'll check things in to lib that >> move toward 1.8.1, is that right? How many more 0.6.* releases are >> planned? > > Right. > > It depends on when we move to >=1.8.1, however, not so many > 0.6 releases are planed (one or zero, maybe). > > e.g. Should we wait for OS X shipped with Ruby 1.8 series? > >> Or do we want to use branches in CVS to accomplish this? > > This will be the right way to go. > The problem is, to be honest, I'm not so familiar with > the CVS branching. > > Toshiaki > > > >> Moses >> >> On Nov 14, 2004, at 9:13 AM, Toshiaki Katayama wrote: >> >>> Hi Moses, >>> >>> Thank you for your contributions. >>> >>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >>> To ALL: >>> Unit tests are now merged in the CVS tree and can be run >>> with 'ruby install.rb test'. >>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >>> >>> I think BioRuby still compatible with Ruby 1.6.8. >>> >>> How about to keep BioRuby 0.6 series with support for Ruby 1.6, >>> and preparing 0.7 series which may require >=1.8.1? >>> >>> I'm fine even if the unit tests fails with Ruby 1.6 during the >>> above transition, as far as the BioRuby library can be installed >>> and used with Ruby 1.6. >>> >>> Thanks, >>> Toshiaki Katayama >>> >>> On 2004/11/14, at 3:13, Moses Hohman wrote: >>> >>>> Hi, >>>> >>>> What version(s) of Ruby does bioruby officially support? >=1.8.1? >>>> Is 1.6 support being phased out? I just want to make sure that >>>> stuff I check into CVS (mostly unit tests and maybe some small >>>> refactorings) fits the standard and everyone's expectations. >>>> >>>> thanks, >>>> >>>> Moses >>>> >>>> _______________________________________________ >>>> BioRuby mailing list >>>> BioRuby@open-bio.org >>>> http://portal.open-bio.org/mailman/listinfo/bioruby >>> >>> _______________________________________________ >>> BioRuby mailing list >>> BioRuby@open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioruby >>> >> >> _______________________________________________ >> BioRuby mailing list >> BioRuby@open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From mmhohman at northwestern.edu Mon Nov 15 17:07:36 2004 From: mmhohman at northwestern.edu (Moses Hohman) Date: Mon Nov 15 17:06:08 2004 Subject: [BioRuby] moving to Ruby 1.8? In-Reply-To: <269B45DE-36CB-11D9-B539-000D93347CEA@hgc.jp> References: <0C160867-36A9-11D9-B942-000393DB7722@northwestern.edu> <269B45DE-36CB-11D9-B539-000D93347CEA@hgc.jp> Message-ID: Also, on the OS X/Ruby 1.8 question, I think that if the older releases are still available, then we shouldn't wait, because in fact it is pretty easy to install Ruby 1.8 on OS X. But that is just my perspective. I admit I'm very comfortable with the whole ./configure, make, make install thing, and others may not be as comfortable. However, "configure/make/sudo make install" does run very smoothly, on 10.3 at least. Moses On Nov 14, 2004, at 11:56 PM, Toshiaki Katayama wrote: > On 2004/11/15, at 10:52, Moses Hohman wrote: >> This sounds good. So, for now, don't check anything into lib that >> doesn't work with Ruby 1.6? And at some point in the future, once the >> final 0.6.* release has gone out, we'll check things in to lib that >> move toward 1.8.1, is that right? How many more 0.6.* releases are >> planned? > > Right. > > It depends on when we move to >=1.8.1, however, not so many > 0.6 releases are planed (one or zero, maybe). > > e.g. Should we wait for OS X shipped with Ruby 1.8 series? > >> Or do we want to use branches in CVS to accomplish this? > > This will be the right way to go. > The problem is, to be honest, I'm not so familiar with > the CVS branching. > > Toshiaki > > > >> Moses >> >> On Nov 14, 2004, at 9:13 AM, Toshiaki Katayama wrote: >> >>> Hi Moses, >>> >>> Thank you for your contributions. >>> >>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >>> To ALL: >>> Unit tests are now merged in the CVS tree and can be run >>> with 'ruby install.rb test'. >>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >>> >>> I think BioRuby still compatible with Ruby 1.6.8. >>> >>> How about to keep BioRuby 0.6 series with support for Ruby 1.6, >>> and preparing 0.7 series which may require >=1.8.1? >>> >>> I'm fine even if the unit tests fails with Ruby 1.6 during the >>> above transition, as far as the BioRuby library can be installed >>> and used with Ruby 1.6. >>> >>> Thanks, >>> Toshiaki Katayama >>> >>> On 2004/11/14, at 3:13, Moses Hohman wrote: >>> >>>> Hi, >>>> >>>> What version(s) of Ruby does bioruby officially support? >=1.8.1? >>>> Is 1.6 support being phased out? I just want to make sure that >>>> stuff I check into CVS (mostly unit tests and maybe some small >>>> refactorings) fits the standard and everyone's expectations. >>>> >>>> thanks, >>>> >>>> Moses >>>> >>>> _______________________________________________ >>>> BioRuby mailing list >>>> BioRuby@open-bio.org >>>> http://portal.open-bio.org/mailman/listinfo/bioruby >>> >>> _______________________________________________ >>> BioRuby mailing list >>> BioRuby@open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioruby >>> >> >> _______________________________________________ >> BioRuby mailing list >> BioRuby@open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From ktym at hgc.jp Wed Nov 17 02:57:02 2004 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed Nov 17 02:55:07 2004 Subject: [BioRuby] moving to Ruby 1.8? In-Reply-To: <40C8C432-3752-11D9-969A-000393DB7722@northwestern.edu> References: <0C160867-36A9-11D9-B942-000393DB7722@northwestern.edu> <269B45DE-36CB-11D9-B539-000D93347CEA@hgc.jp> <40C8C432-3752-11D9-969A-000393DB7722@northwestern.edu> Message-ID: <44156293-386E-11D9-B539-000D93347CEA@hgc.jp> Hi, OK, let's branch for 1.8. Your guide will be helpful for all developers. Putting on wiki also sounds good. Sorry for the delay in responding. Thanks, Toshiaki Katayama On 2004/11/16, at 7:03, Moses Hohman wrote: > I am very familiar with CVS branching (we've been using them for > several releases here at work, and I think we've worked out the kinks > in their use), and could prepare an email guide for others. I could > put the guide on the wiki, actually. > > Moses > > On Nov 14, 2004, at 11:56 PM, Toshiaki Katayama wrote: > >> On 2004/11/15, at 10:52, Moses Hohman wrote: >>> This sounds good. So, for now, don't check anything into lib that >>> doesn't work with Ruby 1.6? And at some point in the future, once >>> the final 0.6.* release has gone out, we'll check things in to lib >>> that move toward 1.8.1, is that right? How many more 0.6.* releases >>> are planned? >> >> Right. >> >> It depends on when we move to >=1.8.1, however, not so many >> 0.6 releases are planed (one or zero, maybe). >> >> e.g. Should we wait for OS X shipped with Ruby 1.8 series? >> >>> Or do we want to use branches in CVS to accomplish this? >> >> This will be the right way to go. >> The problem is, to be honest, I'm not so familiar with >> the CVS branching. >> >> Toshiaki >> >> >> >>> Moses >>> >>> On Nov 14, 2004, at 9:13 AM, Toshiaki Katayama wrote: >>> >>>> Hi Moses, >>>> >>>> Thank you for your contributions. >>>> >>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >>>> To ALL: >>>> Unit tests are now merged in the CVS tree and can be run >>>> with 'ruby install.rb test'. >>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - >>>> >>>> I think BioRuby still compatible with Ruby 1.6.8. >>>> >>>> How about to keep BioRuby 0.6 series with support for Ruby 1.6, >>>> and preparing 0.7 series which may require >=1.8.1? >>>> >>>> I'm fine even if the unit tests fails with Ruby 1.6 during the >>>> above transition, as far as the BioRuby library can be installed >>>> and used with Ruby 1.6. >>>> >>>> Thanks, >>>> Toshiaki Katayama >>>> >>>> On 2004/11/14, at 3:13, Moses Hohman wrote: >>>> >>>>> Hi, >>>>> >>>>> What version(s) of Ruby does bioruby officially support? >=1.8.1? >>>>> Is 1.6 support being phased out? I just want to make sure that >>>>> stuff I check into CVS (mostly unit tests and maybe some small >>>>> refactorings) fits the standard and everyone's expectations. >>>>> >>>>> thanks, >>>>> >>>>> Moses >>>>> >>>>> _______________________________________________ >>>>> BioRuby mailing list >>>>> BioRuby@open-bio.org >>>>> http://portal.open-bio.org/mailman/listinfo/bioruby >>>> >>>> _______________________________________________ >>>> BioRuby mailing list >>>> BioRuby@open-bio.org >>>> http://portal.open-bio.org/mailman/listinfo/bioruby >>>> >>> >>> _______________________________________________ >>> BioRuby mailing list >>> BioRuby@open-bio.org >>> http://portal.open-bio.org/mailman/listinfo/bioruby >> >> _______________________________________________ >> BioRuby mailing list >> BioRuby@open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioruby >> > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby From danny at amelang.net Thu Nov 25 01:16:56 2004 From: danny at amelang.net (Daniel Amelang) Date: Thu Nov 25 01:14:53 2004 Subject: [BioRuby] New member Message-ID: <41A578D8.7060905@amelang.net> Hello fellow ruby bioinformaticians! Just wanted to introduce myself. My name is Dan Amelang, I've been programming in ruby for about two years now. I'm a computer science/bioinformatics double major at BYU in Utah. I founded the Ruby Users group there that's 15 members going and strong. I've been very disappointed w/ having to use BioPerl and am excited to see BioRuby (boy am I). Keep up the good work! I'll try to see where I can contribute here and there. Dan From danny at amelang.net Thu Nov 25 01:49:30 2004 From: danny at amelang.net (Daniel Amelang) Date: Thu Nov 25 01:47:18 2004 Subject: [BioRuby] Wiki Message-ID: <41A5807A.6030706@amelang.net> So, how does one get authorization to modify the wiki? Dan From danny at amelang.net Thu Nov 25 01:51:53 2004 From: danny at amelang.net (Daniel Amelang) Date: Thu Nov 25 01:49:38 2004 Subject: [BioRuby] Tree classes Message-ID: <41A58109.30507@amelang.net> So, any plans on implementing the different trees (newick etc) in bioruby? Like TreeIO in perl? Dan From danny at amelang.net Thu Nov 25 01:57:20 2004 From: danny at amelang.net (Daniel Amelang) Date: Thu Nov 25 01:55:06 2004 Subject: [BioRuby] Ruby gems or RPA Message-ID: <41A58250.7050901@amelang.net> Sorry to flood this mailing list all of a sudden :) Any plans on creating a ruby gem or rpa entry for bioruby? I see that there are various 'optional' dependencies for bioruby that I'd like to have, but the inconvenience of installing each one at a time is bothersome. Dan From ngoto at gen-info.osaka-u.ac.jp Thu Nov 25 02:00:26 2004 From: ngoto at gen-info.osaka-u.ac.jp (GOTO Naohisa) Date: Thu Nov 25 01:58:14 2004 Subject: [BioRuby] Wiki In-Reply-To: <41A5807A.6030706@amelang.net> References: <41A5807A.6030706@amelang.net> Message-ID: <200411250658.iAP6w8Ks014583@portal.open-bio.org> Hi, Dan, > So, how does one get authorization to modify the wiki? After Wiki pages had been hit by spammers, we set simple authentication. Please use user: bioruby and pass: wiki to edit the site. -- Naohisa GOTO ngoto@gen-info.osaka-u.ac.jp Genome Information Research Center, Osaka University, Japan From ktym at hgc.jp Thu Nov 25 02:50:11 2004 From: ktym at hgc.jp (Toshiaki Katayama) Date: Thu Nov 25 02:47:59 2004 Subject: [BioRuby] Tree classes In-Reply-To: <41A58109.30507@amelang.net> References: <41A58109.30507@amelang.net> Message-ID: Hi Dan, Not yet planned as far as I know. I want to have that in BioRuby too. Regards, Toshiaki Katayama On 2004/11/25, at 15:51, Daniel Amelang wrote: > So, any plans on implementing the different trees (newick etc) in > bioruby? Like TreeIO in perl? > > Dan > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby From ktym at hgc.jp Thu Nov 25 02:53:29 2004 From: ktym at hgc.jp (Toshiaki Katayama) Date: Thu Nov 25 02:51:13 2004 Subject: [BioRuby] Ruby gems or RPA In-Reply-To: <41A58250.7050901@amelang.net> References: <41A58250.7050901@amelang.net> Message-ID: <18BDDB88-3EB7-11D9-8BC1-000D93347CEA@hgc.jp> Hi, I have never used gem or rpa, but it seems to be an nice idea to prepare them (especially for the ruby 1.6 users?). Regards, Toshiaki Katayama On 2004/11/25, at 15:57, Daniel Amelang wrote: > Sorry to flood this mailing list all of a sudden :) > > Any plans on creating a ruby gem or rpa entry for bioruby? I see that > there are various 'optional' dependencies for bioruby that I'd like to > have, but the inconvenience of installing each one at a time is > bothersome. > > Dan > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby