From andrew.j.grimm at gmail.com Fri Jul 1 03:40:04 2011 From: andrew.j.grimm at gmail.com (Andrew Grimm) Date: Fri, 1 Jul 2011 17:40:04 +1000 Subject: [BioRuby] Use of NameError versus respond_to? Message-ID: This isn't a bug report, just a request for enlightenment. Why does some of the code use begin ... rescue NameError rather than respond_to ? For example, in Bio::Alignment::OriginalPrivate#extract_seq, there's for m in [ :seq, :naseq, :aaseq ] begin seq = s.send(m) rescue NameError, ArgumentError seq = nil end break if seq end Is this because some objects implement seq, naseq or aaseq without indicating it in respond_to? Or is this just how code was written back in older times? https://github.com/bioruby/bioruby/commit/7b26a41e0a515e77d4b7470936b7fbf68a7b09a8 indicates the module was first written back in 2003. Andrew From ngoto at gen-info.osaka-u.ac.jp Wed Jul 6 11:16:10 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Thu, 7 Jul 2011 00:16:10 +0900 Subject: [BioRuby] Use of NameError versus respond_to? In-Reply-To: References: Message-ID: <20110706151610.6F4481CBC41F@idnmail.gen-info.osaka-u.ac.jp> Hi Andrew, On Fri, 1 Jul 2011 17:40:04 +1000 Andrew Grimm wrote: > This isn't a bug report, just a request for enlightenment. > > Why does some of the code use begin ... rescue NameError rather than > respond_to ? The "begin ... rescue" can skip errors other than NomethodError, e.g. mismatch of the number of arguments. > For example, in Bio::Alignment::OriginalPrivate#extract_seq, there's > > for m in [ :seq, :naseq, :aaseq ] > begin > seq = s.send(m) > rescue NameError, ArgumentError > seq = nil > end > break if seq > end > > Is this because some objects implement seq, naseq or aaseq without > indicating it in respond_to? The code can be extend to skip various errors that may occur even if the method exists, by adding error classes to the "rescue" line. > Or is this just how code was written back in older times? > https://github.com/bioruby/bioruby/commit/7b26a41e0a515e77d4b7470936b7fbf68a7b09a8 > indicates the module was first written back in 2003. Indeed, the code is very old. I'd like to reconsider the design of the alignment and the sequence classes. Thanks, Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From ktym at hgc.jp Sun Jul 17 06:44:34 2011 From: ktym at hgc.jp (Toshiaki Katayama) Date: Sun, 17 Jul 2011 19:44:34 +0900 Subject: [BioRuby] Anyone else attending RubyKaigi 2011? In-Reply-To: References: Message-ID: <3D3FE55B-C474-4EB7-B268-EB882E243956@hgc.jp> Hi Andrew, It was great that we could eventually meet at the platform of Nerima station. Enjoy your party and see you tomorrow again. Tomorrow, Gogo-san will give a lightning talk before a keynote from Matz. The final Ruby Kaigi is fascinating. Guys, are there any news/reports from BOSC? Regards, Toshiaki On 2011/07/17, at 16:40, Toshiaki Katayama wrote: > Hi Andrew, > > Sorry but I missed your post until heard from Goto-san today. > I'm now in. Still not sure I can attend your session tommorrow (due to private schedule) but will be back by Goto-san's LT. > > Cheers, > Toshiaki > > > On 2011/06/26, at 19:16, Andrew Grimm wrote: > >> I noticed that Goto-san's talk got accepted as a lightning talk. >> >> Are any other BioRuby contributors or users attending? >> >> I'll be giving a talk, but I'll only briefly mention bioinformatics. >> I'll be talking about the Small Eigen Collider. In describing why I >> created the Small Eigen Collider, I'll mention that I'm a >> bioinformatician, and that I deal with enough information that I am >> tempted to run Ruby code under implementations other than YARV. >> http://rubykaigi.org/2011/en/schedule/details/18S03 >> >> Andrew >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby From p.j.a.cock at googlemail.com Tue Jul 19 08:46:12 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 19 Jul 2011 13:46:12 +0100 Subject: [BioRuby] Dinner tonight in Vienna after ISMB? Message-ID: Hi all, Apologies to those not still in Vienna, but if anyone wants to meet up tonight for dinner, please email me directly (off list since most people on the mailing list won't be interested). I know there are quite a few BioRuby guys still here at least ;) Thanks, Peter From andrew.j.grimm at gmail.com Sat Jul 23 06:08:08 2011 From: andrew.j.grimm at gmail.com (Andrew Grimm) Date: Sat, 23 Jul 2011 20:08:08 +1000 Subject: [BioRuby] Anyone else attending RubyKaigi 2011? In-Reply-To: <3D3FE55B-C474-4EB7-B268-EB882E243956@hgc.jp> References: <3D3FE55B-C474-4EB7-B268-EB882E243956@hgc.jp> Message-ID: There's currently videos of my talk at http://www.ustream.tv/recorded/16078396 , and at http://vimeo.com/26560146 I assume that videos of the lightning talks exist as well. Andrew On Sun, Jul 17, 2011 at 8:44 PM, Toshiaki Katayama wrote: > Hi Andrew, > > It was great that we could eventually meet at the platform of Nerima station. > Enjoy your party and see you tomorrow again. > > Tomorrow, Gogo-san will give a lightning talk before a keynote from Matz. > The final Ruby Kaigi is fascinating. > > Guys, are there any news/reports from BOSC? > > Regards, > Toshiaki > > On 2011/07/17, at 16:40, Toshiaki Katayama wrote: > >> Hi Andrew, >> >> Sorry but I missed your post until heard from Goto-san today. >> I'm now in. Still not sure I can attend your session tommorrow (due to private schedule) but will be back by Goto-san's LT. >> >> Cheers, >> Toshiaki >> >> >> On 2011/06/26, at 19:16, Andrew Grimm wrote: >> >>> I noticed that Goto-san's talk got accepted as a lightning talk. >>> >>> Are any other BioRuby contributors or users attending? >>> >>> I'll be giving a talk, but I'll only briefly mention bioinformatics. >>> I'll be talking about the Small Eigen Collider. In describing why I >>> created the Small Eigen Collider, I'll mention that I'm a >>> bioinformatician, and that I deal with enough information that I am >>> tempted to run Ruby code under implementations other than YARV. >>> http://rubykaigi.org/2011/en/schedule/details/18S03 >>> >>> Andrew >>> _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Sun Jul 24 07:09:49 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 24 Jul 2011 13:09:49 +0200 Subject: [BioRuby] rq: Zero configuration job scheduler for computer clusters and multi-core Message-ID: <20110724110949.GA22219@thebird.nl> Use those cores! I just created a functional gem for rq, a job scheduler created by Ara Howard. It allows running jobs in parallel, without any configuration (just a shared directory between processes/machines). QUICK START install rq using rubygems, after installing sqlite 2.x (dev version, on Debian apt-get install libsqlite0-dev) gem1.8 install rq-ruby1.8 the binary is in /var/lib/gems/1.8/bin/, so add that to the path, or create a symbolic link ln -sf `gem1.8 contents rq-ruby1.8|grep bin/rq$` /usr/local/bin/rq now rq should work rq --help run the integration test /var/lib/gems/1.8/bin/test_rq.rb set up a directory for your queue - this can be a local, or an NFS/sshfs mounted drive: rq dir create on every node create a queue runner, specifying the number of cores (here 8) rq dir feed --daemon --log=rq.log --max_feed=8 submit two jobs - shell style rq dir submit 'sleep 10' rq dir submit 'sleep 9' check status rq dir status shows --- jobs: pending: 0 holding: 0 running: 2 finished: 0 dead: 0 total: 2 temporal: running: min: {2: 00h00m03.49s} max: {1: 00h00m03.60s} performance: avg_time_per_job: 00h00m00.00s n_jobs_in_last_hrs: 1: 0 12: 0 24: 0 exit_status: successes: 0 failures: 0 ok: 0 Now, that was easy!! rq will be a standard feature of the BioLinux VMs. I also ported the code to Ruby1.9 - it is sitting in the ruby1.9 branch on github: https://github.com/pjotrp/rq/tree/ruby1.9 it would be good if others were to test that in some production setup, before I push that to rubygems. Pj. From pjotr.public14 at thebird.nl Sat Jul 30 09:54:48 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 30 Jul 2011 15:54:48 +0200 Subject: [BioRuby] New site: http://biogems.info Message-ID: <20110730135448.GA17613@thebird.nl> >From the Biogem project we have created Biogems.info http://biogems.info/ which lists all available biogems. We have an amazing 21 new biogems, since the introduction of the biogem tool and BioRuby plugins, reflecting a 10x increase in new Ruby code for Bioinformatics in the last 8 months, compared to the same period a year before. Keep them coming! PS The website can be improved. The code is at https://github.com/pjotrp/biogems.info. Feel free! PS If you want a different description / URLs for your gem, update your project Rakefile and run 'rake gemspec ; rake release'. PS If your gem is not listed - host it on rubygems and pass the info to me. The script automatically harvests gems that start with bio- (bio and dash). From francesco.strozzi at gmail.com Sat Jul 30 10:10:15 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Sat, 30 Jul 2011 16:10:15 +0200 Subject: [BioRuby] New site: http://biogems.info In-Reply-To: <20110730135448.GA17613@thebird.nl> References: <20110730135448.GA17613@thebird.nl> Message-ID: Nice and well done!! Cheers Francesco On Sat, Jul 30, 2011 at 15:54, Pjotr Prins wrote: > >From the Biogem project we have created Biogems.info > > http://biogems.info/ > > which lists all available biogems. We have an amazing 21 new biogems, > since the introduction of the biogem tool and BioRuby plugins, > reflecting a 10x increase in new Ruby code for Bioinformatics in the > last 8 months, compared to the same period a year before. > > Keep them coming! > > PS The website can be improved. The code is at > https://github.com/pjotrp/biogems.info. Feel free! > > PS If you want a different description / URLs for your gem, update > your project Rakefile and run 'rake gemspec ; rake release'. > > PS If your gem is not listed - host it on rubygems and pass the info > to me. The script automatically harvests gems that start with bio- > (bio and dash). > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Francesco From donttrustben at gmail.com Sat Jul 30 20:54:37 2011 From: donttrustben at gmail.com (Ben Woodcroft) Date: Sun, 31 Jul 2011 10:54:37 +1000 Subject: [BioRuby] New site: http://biogems.info In-Reply-To: References: <20110730135448.GA17613@thebird.nl> Message-ID: Nice idea Pjotr. Would it be easy and useful to make an RSS feed or similar available? ben On 31 July 2011 00:10, Francesco Strozzi wrote: > Nice and well done!! > > Cheers > Francesco > > On Sat, Jul 30, 2011 at 15:54, Pjotr Prins >wrote: > > > >From the Biogem project we have created Biogems.info > > > > http://biogems.info/ > > > > which lists all available biogems. We have an amazing 21 new biogems, > > since the introduction of the biogem tool and BioRuby plugins, > > reflecting a 10x increase in new Ruby code for Bioinformatics in the > > last 8 months, compared to the same period a year before. > > > > Keep them coming! > > > > PS The website can be improved. The code is at > > https://github.com/pjotrp/biogems.info. Feel free! > > > > PS If you want a different description / URLs for your gem, update > > your project Rakefile and run 'rake gemspec ; rake release'. > > > > PS If your gem is not listed - host it on rubygems and pass the info > > to me. The script automatically harvests gems that start with bio- > > (bio and dash). > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > -- > > Francesco > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Ben J Woodcroft, BE (Hons) PhD Candidate Ralph Laboratory The University of Melbourne Melbourne, Australia tel: (+613) 8344 2319 b.woodcroft at pgrad.unimelb.edu.au From pjotr.public14 at thebird.nl Sun Jul 31 02:33:24 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 31 Jul 2011 08:33:24 +0200 Subject: [BioRuby] New site: http://biogems.info In-Reply-To: References: <20110730135448.GA17613@thebird.nl> Message-ID: <20110731063324.GA23078@thebird.nl> On Sun, Jul 31, 2011 at 10:54:37AM +1000, Ben Woodcroft wrote: > Nice idea Pjotr. Would it be easy and useful to make an RSS feed or > similar available? > ben Yes, that is a good idea! An RSS for new biogems, and we are also thinking of some type of feedback system. Raoul came up with 'like' - 'dislike', but that may be somewhat harsh. We could have that as a time-limited feature. I am thinking of a biogem connected 'blog' page, or message board - which could have RSS. I want to show recent commit activity, somehow, another RSS. The RSS feeds could be channeled into twitter too, and showed on the main bioruby website. Anyone interested in helping out with the programming? It would be nice to make it a team effort. If you check the source code, you can see it is pretty straightforward. Pj. From pjotr.public14 at thebird.nl Sun Jul 31 06:00:16 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 31 Jul 2011 12:00:16 +0200 Subject: [BioRuby] New site: http://biogems.info In-Reply-To: References: <20110730135448.GA17613@thebird.nl> Message-ID: <20110731100016.GA23872@thebird.nl> The biogems are now ranked by 90 days downloads activity: http://biogems.info/ Also the description link should find functional rdoc documentation, either defined in the gem, or generated on rubyinfo. Pj. From bonnal at ingm.org Sun Jul 31 14:14:43 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Sun, 31 Jul 2011 20:14:43 +0200 Subject: [BioRuby] New site: http://biogems.info In-Reply-To: <20110730135448.GA17613@thebird.nl> Message-ID: <20110731181443.565a6fe0@mail.ingm.it> I like it :-) well done. _____ From: Pjotr Prins [mailto:pjotr.public14 at thebird.nl] To: bioruby [mailto:bioruby at lists.open-bio.org] Sent: Sat, 30 Jul 2011 15:54:48 +0200 Subject: [BioRuby] New site: http://biogems.info >From the Biogem project we have created Biogems.info http://biogems.info/ which lists all available biogems. We have an amazing 21 new biogems, since the introduction of the biogem tool and BioRuby plugins, reflecting a 10x increase in new Ruby code for Bioinformatics in the last 8 months, compared to the same period a year before. Keep them coming! PS The website can be improved. The code is at https://github.com/pjotrp/biogems.info. Feel free! PS If you want a different description / URLs for your gem, update your project Rakefile and run 'rake gemspec ; rake release'. PS If your gem is not listed - host it on rubygems and pass the info to me. The script automatically harvests gems that start with bio- (bio and dash). _______________________________________________ BioRuby Project - http://www.bioruby.org/ BioRuby mailing list BioRuby at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioruby From andrew.j.grimm at gmail.com Fri Jul 1 07:40:04 2011 From: andrew.j.grimm at gmail.com (Andrew Grimm) Date: Fri, 1 Jul 2011 17:40:04 +1000 Subject: [BioRuby] Use of NameError versus respond_to? Message-ID: This isn't a bug report, just a request for enlightenment. Why does some of the code use begin ... rescue NameError rather than respond_to ? For example, in Bio::Alignment::OriginalPrivate#extract_seq, there's for m in [ :seq, :naseq, :aaseq ] begin seq = s.send(m) rescue NameError, ArgumentError seq = nil end break if seq end Is this because some objects implement seq, naseq or aaseq without indicating it in respond_to? Or is this just how code was written back in older times? https://github.com/bioruby/bioruby/commit/7b26a41e0a515e77d4b7470936b7fbf68a7b09a8 indicates the module was first written back in 2003. Andrew From ngoto at gen-info.osaka-u.ac.jp Wed Jul 6 15:16:10 2011 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Thu, 7 Jul 2011 00:16:10 +0900 Subject: [BioRuby] Use of NameError versus respond_to? In-Reply-To: References: Message-ID: <20110706151610.6F4481CBC41F@idnmail.gen-info.osaka-u.ac.jp> Hi Andrew, On Fri, 1 Jul 2011 17:40:04 +1000 Andrew Grimm wrote: > This isn't a bug report, just a request for enlightenment. > > Why does some of the code use begin ... rescue NameError rather than > respond_to ? The "begin ... rescue" can skip errors other than NomethodError, e.g. mismatch of the number of arguments. > For example, in Bio::Alignment::OriginalPrivate#extract_seq, there's > > for m in [ :seq, :naseq, :aaseq ] > begin > seq = s.send(m) > rescue NameError, ArgumentError > seq = nil > end > break if seq > end > > Is this because some objects implement seq, naseq or aaseq without > indicating it in respond_to? The code can be extend to skip various errors that may occur even if the method exists, by adding error classes to the "rescue" line. > Or is this just how code was written back in older times? > https://github.com/bioruby/bioruby/commit/7b26a41e0a515e77d4b7470936b7fbf68a7b09a8 > indicates the module was first written back in 2003. Indeed, the code is very old. I'd like to reconsider the design of the alignment and the sequence classes. Thanks, Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From ktym at hgc.jp Sun Jul 17 10:44:34 2011 From: ktym at hgc.jp (Toshiaki Katayama) Date: Sun, 17 Jul 2011 19:44:34 +0900 Subject: [BioRuby] Anyone else attending RubyKaigi 2011? In-Reply-To: References: Message-ID: <3D3FE55B-C474-4EB7-B268-EB882E243956@hgc.jp> Hi Andrew, It was great that we could eventually meet at the platform of Nerima station. Enjoy your party and see you tomorrow again. Tomorrow, Gogo-san will give a lightning talk before a keynote from Matz. The final Ruby Kaigi is fascinating. Guys, are there any news/reports from BOSC? Regards, Toshiaki On 2011/07/17, at 16:40, Toshiaki Katayama wrote: > Hi Andrew, > > Sorry but I missed your post until heard from Goto-san today. > I'm now in. Still not sure I can attend your session tommorrow (due to private schedule) but will be back by Goto-san's LT. > > Cheers, > Toshiaki > > > On 2011/06/26, at 19:16, Andrew Grimm wrote: > >> I noticed that Goto-san's talk got accepted as a lightning talk. >> >> Are any other BioRuby contributors or users attending? >> >> I'll be giving a talk, but I'll only briefly mention bioinformatics. >> I'll be talking about the Small Eigen Collider. In describing why I >> created the Small Eigen Collider, I'll mention that I'm a >> bioinformatician, and that I deal with enough information that I am >> tempted to run Ruby code under implementations other than YARV. >> http://rubykaigi.org/2011/en/schedule/details/18S03 >> >> Andrew >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby From p.j.a.cock at googlemail.com Tue Jul 19 12:46:12 2011 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 19 Jul 2011 13:46:12 +0100 Subject: [BioRuby] Dinner tonight in Vienna after ISMB? Message-ID: Hi all, Apologies to those not still in Vienna, but if anyone wants to meet up tonight for dinner, please email me directly (off list since most people on the mailing list won't be interested). I know there are quite a few BioRuby guys still here at least ;) Thanks, Peter From andrew.j.grimm at gmail.com Sat Jul 23 10:08:08 2011 From: andrew.j.grimm at gmail.com (Andrew Grimm) Date: Sat, 23 Jul 2011 20:08:08 +1000 Subject: [BioRuby] Anyone else attending RubyKaigi 2011? In-Reply-To: <3D3FE55B-C474-4EB7-B268-EB882E243956@hgc.jp> References: <3D3FE55B-C474-4EB7-B268-EB882E243956@hgc.jp> Message-ID: There's currently videos of my talk at http://www.ustream.tv/recorded/16078396 , and at http://vimeo.com/26560146 I assume that videos of the lightning talks exist as well. Andrew On Sun, Jul 17, 2011 at 8:44 PM, Toshiaki Katayama wrote: > Hi Andrew, > > It was great that we could eventually meet at the platform of Nerima station. > Enjoy your party and see you tomorrow again. > > Tomorrow, Gogo-san will give a lightning talk before a keynote from Matz. > The final Ruby Kaigi is fascinating. > > Guys, are there any news/reports from BOSC? > > Regards, > Toshiaki > > On 2011/07/17, at 16:40, Toshiaki Katayama wrote: > >> Hi Andrew, >> >> Sorry but I missed your post until heard from Goto-san today. >> I'm now in. Still not sure I can attend your session tommorrow (due to private schedule) but will be back by Goto-san's LT. >> >> Cheers, >> Toshiaki >> >> >> On 2011/06/26, at 19:16, Andrew Grimm wrote: >> >>> I noticed that Goto-san's talk got accepted as a lightning talk. >>> >>> Are any other BioRuby contributors or users attending? >>> >>> I'll be giving a talk, but I'll only briefly mention bioinformatics. >>> I'll be talking about the Small Eigen Collider. In describing why I >>> created the Small Eigen Collider, I'll mention that I'm a >>> bioinformatician, and that I deal with enough information that I am >>> tempted to run Ruby code under implementations other than YARV. >>> http://rubykaigi.org/2011/en/schedule/details/18S03 >>> >>> Andrew >>> _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Sun Jul 24 11:09:49 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 24 Jul 2011 13:09:49 +0200 Subject: [BioRuby] rq: Zero configuration job scheduler for computer clusters and multi-core Message-ID: <20110724110949.GA22219@thebird.nl> Use those cores! I just created a functional gem for rq, a job scheduler created by Ara Howard. It allows running jobs in parallel, without any configuration (just a shared directory between processes/machines). QUICK START install rq using rubygems, after installing sqlite 2.x (dev version, on Debian apt-get install libsqlite0-dev) gem1.8 install rq-ruby1.8 the binary is in /var/lib/gems/1.8/bin/, so add that to the path, or create a symbolic link ln -sf `gem1.8 contents rq-ruby1.8|grep bin/rq$` /usr/local/bin/rq now rq should work rq --help run the integration test /var/lib/gems/1.8/bin/test_rq.rb set up a directory for your queue - this can be a local, or an NFS/sshfs mounted drive: rq dir create on every node create a queue runner, specifying the number of cores (here 8) rq dir feed --daemon --log=rq.log --max_feed=8 submit two jobs - shell style rq dir submit 'sleep 10' rq dir submit 'sleep 9' check status rq dir status shows --- jobs: pending: 0 holding: 0 running: 2 finished: 0 dead: 0 total: 2 temporal: running: min: {2: 00h00m03.49s} max: {1: 00h00m03.60s} performance: avg_time_per_job: 00h00m00.00s n_jobs_in_last_hrs: 1: 0 12: 0 24: 0 exit_status: successes: 0 failures: 0 ok: 0 Now, that was easy!! rq will be a standard feature of the BioLinux VMs. I also ported the code to Ruby1.9 - it is sitting in the ruby1.9 branch on github: https://github.com/pjotrp/rq/tree/ruby1.9 it would be good if others were to test that in some production setup, before I push that to rubygems. Pj. From pjotr.public14 at thebird.nl Sat Jul 30 13:54:48 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 30 Jul 2011 15:54:48 +0200 Subject: [BioRuby] New site: http://biogems.info Message-ID: <20110730135448.GA17613@thebird.nl> >From the Biogem project we have created Biogems.info http://biogems.info/ which lists all available biogems. We have an amazing 21 new biogems, since the introduction of the biogem tool and BioRuby plugins, reflecting a 10x increase in new Ruby code for Bioinformatics in the last 8 months, compared to the same period a year before. Keep them coming! PS The website can be improved. The code is at https://github.com/pjotrp/biogems.info. Feel free! PS If you want a different description / URLs for your gem, update your project Rakefile and run 'rake gemspec ; rake release'. PS If your gem is not listed - host it on rubygems and pass the info to me. The script automatically harvests gems that start with bio- (bio and dash). From francesco.strozzi at gmail.com Sat Jul 30 14:10:15 2011 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Sat, 30 Jul 2011 16:10:15 +0200 Subject: [BioRuby] New site: http://biogems.info In-Reply-To: <20110730135448.GA17613@thebird.nl> References: <20110730135448.GA17613@thebird.nl> Message-ID: Nice and well done!! Cheers Francesco On Sat, Jul 30, 2011 at 15:54, Pjotr Prins wrote: > >From the Biogem project we have created Biogems.info > > http://biogems.info/ > > which lists all available biogems. We have an amazing 21 new biogems, > since the introduction of the biogem tool and BioRuby plugins, > reflecting a 10x increase in new Ruby code for Bioinformatics in the > last 8 months, compared to the same period a year before. > > Keep them coming! > > PS The website can be improved. The code is at > https://github.com/pjotrp/biogems.info. Feel free! > > PS If you want a different description / URLs for your gem, update > your project Rakefile and run 'rake gemspec ; rake release'. > > PS If your gem is not listed - host it on rubygems and pass the info > to me. The script automatically harvests gems that start with bio- > (bio and dash). > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Francesco From donttrustben at gmail.com Sun Jul 31 00:54:37 2011 From: donttrustben at gmail.com (Ben Woodcroft) Date: Sun, 31 Jul 2011 10:54:37 +1000 Subject: [BioRuby] New site: http://biogems.info In-Reply-To: References: <20110730135448.GA17613@thebird.nl> Message-ID: Nice idea Pjotr. Would it be easy and useful to make an RSS feed or similar available? ben On 31 July 2011 00:10, Francesco Strozzi wrote: > Nice and well done!! > > Cheers > Francesco > > On Sat, Jul 30, 2011 at 15:54, Pjotr Prins >wrote: > > > >From the Biogem project we have created Biogems.info > > > > http://biogems.info/ > > > > which lists all available biogems. We have an amazing 21 new biogems, > > since the introduction of the biogem tool and BioRuby plugins, > > reflecting a 10x increase in new Ruby code for Bioinformatics in the > > last 8 months, compared to the same period a year before. > > > > Keep them coming! > > > > PS The website can be improved. The code is at > > https://github.com/pjotrp/biogems.info. Feel free! > > > > PS If you want a different description / URLs for your gem, update > > your project Rakefile and run 'rake gemspec ; rake release'. > > > > PS If your gem is not listed - host it on rubygems and pass the info > > to me. The script automatically harvests gems that start with bio- > > (bio and dash). > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > -- > > Francesco > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Ben J Woodcroft, BE (Hons) PhD Candidate Ralph Laboratory The University of Melbourne Melbourne, Australia tel: (+613) 8344 2319 b.woodcroft at pgrad.unimelb.edu.au From pjotr.public14 at thebird.nl Sun Jul 31 06:33:24 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 31 Jul 2011 08:33:24 +0200 Subject: [BioRuby] New site: http://biogems.info In-Reply-To: References: <20110730135448.GA17613@thebird.nl> Message-ID: <20110731063324.GA23078@thebird.nl> On Sun, Jul 31, 2011 at 10:54:37AM +1000, Ben Woodcroft wrote: > Nice idea Pjotr. Would it be easy and useful to make an RSS feed or > similar available? > ben Yes, that is a good idea! An RSS for new biogems, and we are also thinking of some type of feedback system. Raoul came up with 'like' - 'dislike', but that may be somewhat harsh. We could have that as a time-limited feature. I am thinking of a biogem connected 'blog' page, or message board - which could have RSS. I want to show recent commit activity, somehow, another RSS. The RSS feeds could be channeled into twitter too, and showed on the main bioruby website. Anyone interested in helping out with the programming? It would be nice to make it a team effort. If you check the source code, you can see it is pretty straightforward. Pj. From pjotr.public14 at thebird.nl Sun Jul 31 10:00:16 2011 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 31 Jul 2011 12:00:16 +0200 Subject: [BioRuby] New site: http://biogems.info In-Reply-To: References: <20110730135448.GA17613@thebird.nl> Message-ID: <20110731100016.GA23872@thebird.nl> The biogems are now ranked by 90 days downloads activity: http://biogems.info/ Also the description link should find functional rdoc documentation, either defined in the gem, or generated on rubyinfo. Pj. From bonnal at ingm.org Sun Jul 31 18:14:43 2011 From: bonnal at ingm.org (Raoul Bonnal) Date: Sun, 31 Jul 2011 20:14:43 +0200 Subject: [BioRuby] New site: http://biogems.info In-Reply-To: <20110730135448.GA17613@thebird.nl> Message-ID: <20110731181443.565a6fe0@mail.ingm.it> I like it :-) well done. _____ From: Pjotr Prins [mailto:pjotr.public14 at thebird.nl] To: bioruby [mailto:bioruby at lists.open-bio.org] Sent: Sat, 30 Jul 2011 15:54:48 +0200 Subject: [BioRuby] New site: http://biogems.info >From the Biogem project we have created Biogems.info http://biogems.info/ which lists all available biogems. We have an amazing 21 new biogems, since the introduction of the biogem tool and BioRuby plugins, reflecting a 10x increase in new Ruby code for Bioinformatics in the last 8 months, compared to the same period a year before. Keep them coming! PS The website can be improved. The code is at https://github.com/pjotrp/biogems.info. Feel free! PS If you want a different description / URLs for your gem, update your project Rakefile and run 'rake gemspec ; rake release'. PS If your gem is not listed - host it on rubygems and pass the info to me. The script automatically harvests gems that start with bio- (bio and dash). _______________________________________________ BioRuby Project - http://www.bioruby.org/ BioRuby mailing list BioRuby at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioruby