From Simon.Wagstaff at liverpool.ac.uk Wed Aug 15 09:59:22 2012 From: Simon.Wagstaff at liverpool.ac.uk (Wagstaff, Simon) Date: Wed, 15 Aug 2012 13:59:22 +0000 Subject: [Bio-linux-dev] BL-6 Galaxy history export error Message-ID: <834710117A5F2048B9EC075D397DDB1B23C7ED0E@CHEXMBX1.livad.liv.ac.uk> Hi Tim, I'm running a local installation of Galaxy on BL-6. On the 'analyze data' page, when I go to the history pane and drop down the options menu to 'export to file' I get the error pasted below: This doesn't happen with all histories - this particular one is a large RNASeq workflow (100+ steps). I can't see this error on the Galaxy so I've reported it here in the first instance in case it's a packaging issue. With Thanks, Simon Error Traceback: View as: Interactive | Text | XML (full) ? AttributeError: 'NoneType' object has no attribute 'hid' URL: http://localhost:8080/history/export_archive Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view >> environ, self.app) Module paste.wsgilib:539 in intercept_output view >> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view >> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view >> body = method( trans, **kwargs ) Module galaxy.web.controllers.history:679 in export_archive view >> history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) Module galaxy.tools:1661 in execute view >> return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) Module galaxy.tools.actions.history_imp_exp:108 in execute view >> include_deleted=incoming[ 'include_deleted' ] ) Module galaxy.tools.imp_exp:419 in setup_job view >> input_datasets = [ assoc.dataset.hid for assoc in job.input_datasets ] AttributeError: 'NoneType' object has no attribute 'hid' ***************************************** Dr. Simon Wagstaff Liverpool School of Tropical Medicine Pembroke Place Liverpool L3 5QA UK Tel: +44-151-705-3164 Fax: +44-151-705-3371 email: simonw at liv.ac.uk http://venoms.liv.ac.uk ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Wed Aug 15 11:06:52 2012 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 15 Aug 2012 16:06:52 +0100 Subject: [Bio-linux-dev] BL-6 Galaxy history export error In-Reply-To: <834710117A5F2048B9EC075D397DDB1B23C7ED0E@CHEXMBX1.livad.liv.ac.uk> References: <834710117A5F2048B9EC075D397DDB1B23C7ED0E@CHEXMBX1.livad.liv.ac.uk> Message-ID: <1345043212.2737.160.camel@balisaur> Hi Simon, It looks at first glance like a Galaxy bug, but as you say it could also be something in the packaging if, say, Galaxy is failing to read or write a file and not trapping that error correctly. I'm going to give you a cop-out answer - I have a half-done updated Galaxy package which I'll get back to working on after I'm done with Qiime. Maybe if Galaxy is updated the problem will go away! Cheers, TIM On Wed, 2012-08-15 at 14:59 +0100, Wagstaff, Simon wrote: > Hi Tim, > > I'm running a local installation of Galaxy on BL-6. On the 'analyze > data' page, when I go to the history pane and drop down the options > menu to 'export to file' I get the error pasted below: > > This doesn't happen with all histories - this particular one is a > large RNASeq workflow (100+ steps). > > > > I can't see this error on the Galaxy so I've reported it here in the > first instance in case it's a packaging issue. > > > > With Thanks, > > > > Simon > > > Error Traceback: > View as: Interactive | Text | XML (full) > > ?AttributeError: 'NoneType' object has no attribute 'hid' > > URL: http://localhost:8080/history/export_archive > > Module weberror.evalexception.middleware:364 in respond view > >> app_iter= self.application(environ,detect_start_response) > > Module paste.debug.prints:98 in __call__ view > >> environ,self.app) > > Module paste.wsgilib:539 in intercept_output view > >> app_iter= application(environ,replacement_start_response) > > Module paste.recursive:80 in __call__ view > >> returnself.application(environ,start_response) > > Module paste.httpexceptions:632 in __call__ view > >> returnself.application(environ,start_response) > > Module galaxy.web.framework.base:160 in __call__ view > >> body= method(trans,**kwargs) > > Module galaxy.web.controllers.history:679 in export_archive > view > >> history_exp_tool.execute(trans,incoming= params,set_output_hid= > True) > > Module galaxy.tools:1661 in execute view > >> returnself.tool_action.execute(self,trans,incoming=incoming,set_output_hid=set_output_hid,history=history,**kwargs) > > Module galaxy.tools.actions.history_imp_exp:108 in execute view > >> include_deleted=incoming['include_deleted'] ) > > Module galaxy.tools.imp_exp:419 in setup_job view > >> input_datasets= [ assoc.dataset.hidforassocinjob.input_datasets] > > AttributeError: 'NoneType' object has no attribute 'hid' > > > > > > ***************************************** > Dr. Simon Wagstaff > Liverpool School of Tropical Medicine > Pembroke Place > Liverpool > L3 5QA UK > Tel: +44-151-705-3164 > Fax: +44-151-705-3371 > email: simonw at liv.ac.uk > > http://venoms.liv.ac.uk > ***************************************** > > > > -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From william.spooner at eaglegenomics.com Wed Aug 15 12:00:42 2012 From: william.spooner at eaglegenomics.com (William Spooner) Date: Wed, 15 Aug 2012 17:00:42 +0100 Subject: [Bio-linux-dev] bio-linux v. debian-med in 10.04, 12.04 Message-ID: <49E6D956-0B22-4676-A88C-DEF4A375AB75@eaglegenomics.com> There are various packages in the set of cloud-bio-linux sources that are bio-linux v. debian-med duplicates on the Lucid (10.04) distro. A good example would be emboss. 1. Has anyone created a mapping? 2. Should I prefer the debian-med packages over the bio-linux packages? 3. Will the dups still be there for Precise (12.04)? Thanks in advance, Will --- William Spooner http://eaglegenomics.com M:07779-663045 E:william.spooner at eaglegenomics.com From tbooth at ceh.ac.uk Wed Aug 15 12:58:11 2012 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 15 Aug 2012 17:58:11 +0100 Subject: [Bio-linux-dev] bio-linux v. debian-med in 10.04, 12.04 In-Reply-To: <49E6D956-0B22-4676-A88C-DEF4A375AB75@eaglegenomics.com> References: <49E6D956-0B22-4676-A88C-DEF4A375AB75@eaglegenomics.com> Message-ID: <1345049891.2737.173.camel@balisaur> Hi Will, This is what I'm working on just now. By the time I'm done, all the bio-linux-* packages will either contain a piece of software for which there is no regular Debian package (eg. bio-linux-fastqc) or they will be a wrapper package that depends on the regular package (eg. bio-linux-arb). The wrapper packages may include things specific to Bio-Linux - like extra documentation or example files or scripts or icons. Debian policy is you only package what is in the upstream release. Bio-Linux policy is to bung in other stuff if it looks useful. Users may choose what they prefer. Also, the versions of packages on BL may be more recent than on Precise (for example I've just rebuilt BLAST+ 2.2.26) but I've done it by updating the regular ncbi-blast+ package rather than updating the redundant bio-linux-blast-plus package. Also some packages are not in Precise because they are still in Debian Experimental but I've brought them into Bio-Linux. Work in progress is here: https://launchpad.net/~nebc/+archive/bio-linux BL7 will pull packages directly from this repo. I've just done "qiime" so I'm getting there. Some packages aren't behaving themselves and it's taking a while. Cheers, TIM On Wed, 2012-08-15 at 17:00 +0100, William Spooner wrote: > There are various packages in the set of cloud-bio-linux sources that are bio-linux v. debian-med duplicates on the Lucid (10.04) distro. A good example would be emboss. > > 1. Has anyone created a mapping? > 2. Should I prefer the debian-med packages over the bio-linux packages? > 3. Will the dups still be there for Precise (12.04)? > > Thanks in advance, > > Will > > --- > William Spooner http://eaglegenomics.com > M:07779-663045 E:william.spooner at eaglegenomics.com > > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From william.spooner at eaglegenomics.com Wed Aug 15 14:05:30 2012 From: william.spooner at eaglegenomics.com (William Spooner) Date: Wed, 15 Aug 2012 19:05:30 +0100 Subject: [Bio-linux-dev] bio-linux v. debian-med in 10.04, 12.04 In-Reply-To: <1345049891.2737.173.camel@balisaur> References: <49E6D956-0B22-4676-A88C-DEF4A375AB75@eaglegenomics.com> <1345049891.2737.173.camel@balisaur> Message-ID: <25E7D20B-E49F-45D6-ACB3-DAFAFED34755@eaglegenomics.com> Thanks Tim, that's fantastic. In which case I will use the bio-linux-* packages wherever possible. Should I presume that everything in http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux will work on Lucid? How do you separate the packages in BL6 from those in BL7? Did bio-linux ever package any of the tools that are now in precise/universe? Namely bioconductor, vcftools and bedtools? Best, Will On 15 Aug 2012, at 17:58, Tim Booth wrote: > Hi Will, > > This is what I'm working on just now. By the time I'm done, all the > bio-linux-* packages will either contain a piece of software for which > there is no regular Debian package (eg. bio-linux-fastqc) or they will > be a wrapper package that depends on the regular package (eg. > bio-linux-arb). > > The wrapper packages may include things specific to Bio-Linux - like > extra documentation or example files or scripts or icons. Debian policy > is you only package what is in the upstream release. Bio-Linux policy > is to bung in other stuff if it looks useful. Users may choose what > they prefer. > > Also, the versions of packages on BL may be more recent than on Precise > (for example I've just rebuilt BLAST+ 2.2.26) but I've done it by > updating the regular ncbi-blast+ package rather than updating the > redundant bio-linux-blast-plus package. Also some packages are not in > Precise because they are still in Debian Experimental but I've brought > them into Bio-Linux. Work in progress is here: > > https://launchpad.net/~nebc/+archive/bio-linux > > BL7 will pull packages directly from this repo. > > I've just done "qiime" so I'm getting there. Some packages aren't > behaving themselves and it's taking a while. > > Cheers, > > TIM > > On Wed, 2012-08-15 at 17:00 +0100, William Spooner wrote: >> There are various packages in the set of cloud-bio-linux sources that are bio-linux v. debian-med duplicates on the Lucid (10.04) distro. A good example would be emboss. >> >> 1. Has anyone created a mapping? >> 2. Should I prefer the debian-med packages over the bio-linux packages? >> 3. Will the dups still be there for Precise (12.04)? >> >> Thanks in advance, >> >> Will >> >> --- >> William Spooner http://eaglegenomics.com >> M:07779-663045 E:william.spooner at eaglegenomics.com >> >> _______________________________________________ >> Bio-Linux-dev mailing list >> Bio-Linux-dev at nebclists.nerc.ac.uk >> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > -- > This message (and any attachments) is for the recipient only. NERC > is subject to the Freedom of Information Act 2000 and the contents > of this email and any reply you make may be disclosed by NERC unless > it is exempt from release under the Act. Any material supplied to > NERC may be stored in an electronic records management system. > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev --- William Spooner http://eaglegenomics.com M:07779-663045 E:william.spooner at eaglegenomics.com From tbooth at ceh.ac.uk Thu Aug 16 04:37:04 2012 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 16 Aug 2012 09:37:04 +0100 Subject: [Bio-linux-dev] bio-linux v. debian-med in 10.04, 12.04 In-Reply-To: <25E7D20B-E49F-45D6-ACB3-DAFAFED34755@eaglegenomics.com> References: <49E6D956-0B22-4676-A88C-DEF4A375AB75@eaglegenomics.com> <1345049891.2737.173.camel@balisaur> <25E7D20B-E49F-45D6-ACB3-DAFAFED34755@eaglegenomics.com> Message-ID: <1345106224.2737.179.camel@balisaur> Hi, > Should I presume that everything in > http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux will work on > Lucid? How do you separate the packages in BL6 from those in BL7? Yes, all that should work on Lucid. Once I've finished my clean-ups they should all work on Precise too, so there won't be a need to separate these. > Did bio-linux ever package any of the tools that are now in > precise/universe? Namely bioconductor, vcftools and bedtools? Nope - I've contributed to various Debian-Med packages but none of those are ours. TIM -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From tbooth at ceh.ac.uk Fri Aug 17 11:18:05 2012 From: tbooth at ceh.ac.uk (Tim Booth) Date: Fri, 17 Aug 2012 16:18:05 +0100 Subject: [Bio-linux-dev] PredictProtein was accepted into Debian - how about Bio-Linux 7? In-Reply-To: <502E23BD.7050000@rostlab.org> References: <502E23BD.7050000@rostlab.org> Message-ID: <1345216685.2737.298.camel@balisaur> Hi Laszlo, Nice one. Of course I'd love to put PredictProtein into BL7. I've just sent it, and the various dependencies, to build on the PPA: https://launchpad.net/~nebc/+archive/bio-linux/+packages Unfortunately the build queue right now is about 40 hours, so it's taking a while to go through. Should I also include the pp-popularity-contest package or are you now able to get the stats you need through the regular Popcon (which should be enabled on BL7 for most users)? Cheers, TIM On Fri, 2012-08-17 at 11:58 +0100, Laszlo Kajan wrote: > Hello Tim! > > Last night PredictProtein was accepted into Debian. > > It would be an honour for us if you could include it in Bio-Linux 7! > > I used to have my own version of a Bio-Linux 6 image where I had > PredictProtein installed from our repository, but there would be no > need for > this if you could officially include it. > > There is no (free) graphical front end for PredictProtein. It is a > command line tool. But it is well documented by man pages with > examples. > > Best regards, > > Laszlo -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From lkajan at rostlab.org Fri Aug 17 11:42:15 2012 From: lkajan at rostlab.org (Laszlo Kajan) Date: Fri, 17 Aug 2012 17:42:15 +0200 Subject: [Bio-linux-dev] PredictProtein was accepted into Debian - how about Bio-Linux 7? In-Reply-To: <1345216685.2737.298.camel@balisaur> References: <502E23BD.7050000@rostlab.org> <1345216685.2737.298.camel@balisaur> Message-ID: <502E6657.408@rostlab.org> Hello Tim! Wow thank you, this is great news! Let me know if there is anything with the build, but I may not be able to respond for a while, because I will be on vacation for two weeks from Monday. pp-popularity-contest is different, the Debian popularity contest does not really replace it. It counts the number of predictions made by each of the tools. It would be really nice if you could install it along PredictProtein. But if you decide not to, then make sure there is an executable called 'pp_popcon_cnt' on the path, or our various tools will print warning messages about the missing pp-popularity-contest. The executable does not need to do anything, it just has to be callable. That silences the warning. Best regards, Laszlo On 17/08/12 17:18, Tim Booth wrote: > Hi Laszlo, > > Nice one. Of course I'd love to put PredictProtein into BL7. I've just > sent it, and the various dependencies, to build on the PPA: > > https://launchpad.net/~nebc/+archive/bio-linux/+packages > > Unfortunately the build queue right now is about 40 hours, so it's > taking a while to go through. > > Should I also include the pp-popularity-contest package or are you now > able to get the stats you need through the regular Popcon (which should > be enabled on BL7 for most users)? > > Cheers, > > TIM > > On Fri, 2012-08-17 at 11:58 +0100, Laszlo Kajan wrote: >> Hello Tim! >> >> Last night PredictProtein was accepted into Debian. >> >> It would be an honour for us if you could include it in Bio-Linux 7! >> >> I used to have my own version of a Bio-Linux 6 image where I had >> PredictProtein installed from our repository, but there would be no >> need for >> this if you could officially include it. >> >> There is no (free) graphical front end for PredictProtein. It is a >> command line tool. But it is well documented by man pages with >> examples. >> >> Best regards, >> >> Laszlo >