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From: Max K. <m.k...@tu...> - 2015-04-02 13:56:18
|
I've installed the Taverna 2.5 because the wiki suggested to get the *latest* version :) Egon's hint to use the 2.3 version worked well and now the Plugin is up and running. I will need it only for some testing purpose yet, so there is no urgent need to call someone back from his holidays ;) Anyway, I wish you all a Happy Easter and thank you all for your quick reply. Max Am 01.04.2015 um 19:46 schrieb Achim Zielesny: > Dear Max, dear Egon, > > I passed the problem to Andreas (Truszkowski) but unfortunately (ok, > depends on perspective) he is on vacation over Easter. > > Best regards, > Achim > > > 2015-04-01 19:31 GMT+02:00 Egon Willighagen > <ego...@gm... <mailto:ego...@gm...>>: > > On Wed, Apr 1, 2015 at 5:57 PM, Max Kretzschmar > <m.k...@tu... <mailto:m.k...@tu...>> wrote: > > I've encountered a problem with the installation of the > CDK-Taverna Plugin. > > I've downloaded the recent version of Taverna (2.5) and followed > all the > > steps given in the excellent wiki install guide. I got stuck > after the "add > > plugin site" window, where I have to fill in the URL of the > plugin source. > > Afterwards I always get the same error "This update site > contains no new > > plugins". > > A possible reason could perhaps be that the plugins on that website > are too old for your Taverna version? Not sure... > > This config file may actually suggest it is for Taverna 2.3? > > http://www.ts-concepts.de/cdk-taverna2/plugin/cdk-taverna-2-2.0.5.4.xml > > > I tried this on my Ubuntu 14.04 machine and I can reproduce this > error as > > well on my Windows 7 PC. This happens with the URL given in the Wiki > > http://www.ts-concepts.de/cdk-taverna2/plugin/ and > > http://cdk-taverna.de/plugin although I can open both of them in > my browser, > > so they don't seem to be offline. > > I am pretty sure it is likely a version issue, and nothing to do with > your system... > > But I am not sure how to recompile CDK-Taverna for Taverna 2.5... > > I'll ask around! > > Egon > > -- > E.L. Willighagen > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/) > Homepage: http://egonw.github.com/ > LinkedIn: http://se.linkedin.com/in/egonw > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > ORCID: 0000-0001-7542-0286 > ImpactStory: https://impactstory.org/EgonWillighagen > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming The Go Parallel > Website, sponsored > by Intel and developed in partnership with Slashdot Media, is your > hub for all > things parallel software development, from weekly thought > leadership blogs to > news, videos, case studies, tutorials and more. Take a look and > join the > conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > Cdk-taverna mailing list > Cdk...@li... > <mailto:Cdk...@li...> > https://lists.sourceforge.net/lists/listinfo/cdk-taverna > > > > > -- > Prof. Dr. Achim Zielesny > > Westfälische Hochschule > Institut für biologische und chemische Informatik > August-Schmidt-Ring 10 > 45665 Recklinghausen > > Westphalian University of Applied Sciences > Institute for Bioinformatics and Chemoinformatics > August-Schmidt-Ring 10 > D-45665 Recklinghausen, Germany > > E-Mail ach...@w-... <mailto:ach...@w-...> / > ach...@go... <mailto:ach...@go...> > Internet http://www.bio.w-hs.de/zielesny > |
From: Achim Z. <ach...@go...> - 2015-04-01 17:47:06
|
Dear Max, dear Egon, I passed the problem to Andreas (Truszkowski) but unfortunately (ok, depends on perspective) he is on vacation over Easter. Best regards, Achim 2015-04-01 19:31 GMT+02:00 Egon Willighagen <ego...@gm...>: > On Wed, Apr 1, 2015 at 5:57 PM, Max Kretzschmar <m.k...@tu...> > wrote: > > I've encountered a problem with the installation of the CDK-Taverna > Plugin. > > I've downloaded the recent version of Taverna (2.5) and followed all the > > steps given in the excellent wiki install guide. I got stuck after the > "add > > plugin site" window, where I have to fill in the URL of the plugin > source. > > Afterwards I always get the same error "This update site contains no new > > plugins". > > A possible reason could perhaps be that the plugins on that website > are too old for your Taverna version? Not sure... > > This config file may actually suggest it is for Taverna 2.3? > > http://www.ts-concepts.de/cdk-taverna2/plugin/cdk-taverna-2-2.0.5.4.xml > > > I tried this on my Ubuntu 14.04 machine and I can reproduce this error as > > well on my Windows 7 PC. This happens with the URL given in the Wiki > > http://www.ts-concepts.de/cdk-taverna2/plugin/ and > > http://cdk-taverna.de/plugin although I can open both of them in my > browser, > > so they don't seem to be offline. > > I am pretty sure it is likely a version issue, and nothing to do with > your system... > > But I am not sure how to recompile CDK-Taverna for Taverna 2.5... > > I'll ask around! > > Egon > > -- > E.L. Willighagen > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/) > Homepage: http://egonw.github.com/ > LinkedIn: http://se.linkedin.com/in/egonw > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > ORCID: 0000-0001-7542-0286 > ImpactStory: https://impactstory.org/EgonWillighagen > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming The Go Parallel Website, > sponsored > by Intel and developed in partnership with Slashdot Media, is your hub for > all > things parallel software development, from weekly thought leadership blogs > to > news, videos, case studies, tutorials and more. Take a look and join the > conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > Cdk-taverna mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-taverna > -- Prof. Dr. Achim Zielesny Westfälische Hochschule Institut für biologische und chemische Informatik August-Schmidt-Ring 10 45665 Recklinghausen Westphalian University of Applied Sciences Institute for Bioinformatics and Chemoinformatics August-Schmidt-Ring 10 D-45665 Recklinghausen, Germany E-Mail ach...@w-... / ach...@go... Internet http://www.bio.w-hs.de/zielesny |
From: Christoph S. <ste...@eb...> - 2015-04-01 17:41:09
|
Yes, we haven’t been updating this for a long time. Hope that one of the people who did the last releases are listening and can comment at some point. Kind regards, Chris -- Dr. Christoph Steinbeck, Head of Cheminformatics and Metabolism European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Phone +44 1223 49 2640, Email: ste...@eb..., Admin: kh...@eb... https://www.ebi.ac.uk/about/people/christoph-steinbeck What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. > On 1 Apr 02015, at 18:31, Egon Willighagen <ego...@gm...> wrote: > > On Wed, Apr 1, 2015 at 5:57 PM, Max Kretzschmar <m.k...@tu...> wrote: >> I've encountered a problem with the installation of the CDK-Taverna Plugin. >> I've downloaded the recent version of Taverna (2.5) and followed all the >> steps given in the excellent wiki install guide. I got stuck after the "add >> plugin site" window, where I have to fill in the URL of the plugin source. >> Afterwards I always get the same error "This update site contains no new >> plugins". > > A possible reason could perhaps be that the plugins on that website > are too old for your Taverna version? Not sure... > > This config file may actually suggest it is for Taverna 2.3? > > http://www.ts-concepts.de/cdk-taverna2/plugin/cdk-taverna-2-2.0.5.4.xml > >> I tried this on my Ubuntu 14.04 machine and I can reproduce this error as >> well on my Windows 7 PC. This happens with the URL given in the Wiki >> http://www.ts-concepts.de/cdk-taverna2/plugin/ and >> http://cdk-taverna.de/plugin although I can open both of them in my browser, >> so they don't seem to be offline. > > I am pretty sure it is likely a version issue, and nothing to do with > your system... > > But I am not sure how to recompile CDK-Taverna for Taverna 2.5... > > I'll ask around! > > Egon > > -- > E.L. Willighagen > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/) > Homepage: http://egonw.github.com/ > LinkedIn: http://se.linkedin.com/in/egonw > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > ORCID: 0000-0001-7542-0286 > ImpactStory: https://impactstory.org/EgonWillighagen > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming The Go Parallel Website, sponsored > by Intel and developed in partnership with Slashdot Media, is your hub for all > things parallel software development, from weekly thought leadership blogs to > news, videos, case studies, tutorials and more. Take a look and join the > conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > Cdk-taverna mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-taverna |
From: Egon W. <ego...@gm...> - 2015-04-01 17:32:22
|
On Wed, Apr 1, 2015 at 5:57 PM, Max Kretzschmar <m.k...@tu...> wrote: > I've encountered a problem with the installation of the CDK-Taverna Plugin. > I've downloaded the recent version of Taverna (2.5) and followed all the > steps given in the excellent wiki install guide. I got stuck after the "add > plugin site" window, where I have to fill in the URL of the plugin source. > Afterwards I always get the same error "This update site contains no new > plugins". A possible reason could perhaps be that the plugins on that website are too old for your Taverna version? Not sure... This config file may actually suggest it is for Taverna 2.3? http://www.ts-concepts.de/cdk-taverna2/plugin/cdk-taverna-2-2.0.5.4.xml > I tried this on my Ubuntu 14.04 machine and I can reproduce this error as > well on my Windows 7 PC. This happens with the URL given in the Wiki > http://www.ts-concepts.de/cdk-taverna2/plugin/ and > http://cdk-taverna.de/plugin although I can open both of them in my browser, > so they don't seem to be offline. I am pretty sure it is likely a version issue, and nothing to do with your system... But I am not sure how to recompile CDK-Taverna for Taverna 2.5... I'll ask around! Egon -- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ORCID: 0000-0001-7542-0286 ImpactStory: https://impactstory.org/EgonWillighagen |
From: Max K. <m.k...@tu...> - 2015-04-01 16:57:29
|
Dear all, I've encountered a problem with the installation of the CDK-Taverna Plugin. I've downloaded the recent version of Taverna (2.5) and followed all the steps given in the excellent wiki install guide. I got stuck after the "add plugin site" window, where I have to fill in the URL of the plugin source. Afterwards I always get the same error "This update site contains no new plugins". I tried this on my Ubuntu 14.04 machine and I can reproduce this error as well on my Windows 7 PC. This happens with the URL given in the Wiki /http://www.ts-concepts.de/cdk-taverna2/plugin// and /http://cdk-taverna.de/plugin/ although I can open both of them in my browser, so they don't seem to be offline. I appreciate any help on this topic. Thanks in advance Max Kretzschmar PhD Student Workgroup Prof. Baumann Technische Universität Braunschweig, Germany |
From: Raquel T. <raq...@ho...> - 2013-01-23 10:06:44
|
Hello! I start to use Taverna now, and I don't understand how can I open the interface to QSAR descriptor presented in this website http://cdk-taverna-2.ts-concepts.de/wiki/index.php?title=Full_Descriptions_Of_Available_Activities I am sorry if it is a silly question, but I already try to run workflows with the qsar descriptor in their structure, and they don't work... Thank you! |
From: Egon W. <ego...@gm...> - 2012-04-15 10:32:01
|
On Sun, Apr 15, 2012 at 12:15 PM, Alan R Williams <al...@cs...> wrote: > 2.4 is very nearly ready to go, so this has just squeaked in :-) > >> I have signed the contributor agreement, but do not think I currently >> have write access to the Google code SVN repository. > > Do you want me to add you? Yeah, why not? I did sign the contributor agreement, and will not push anything with discussing it on the mailing list. One thing I like to look into, if you do not say it is impossible, is to have a renderer for CDK objects, textual... right now, these Java object are 'rendered' by a cryptic Java String dump... In Bioclipse, it would print the molecular formula: > cdk.fromSMILES("COC") CDKMolecule:C2H6O Something like that might be more useful for people starting with CDK-Taverna. It would at least be helpful in seeing if and what goes wrong. But I do not have a lot of time for this, so no promises about ETAs. Egon PS. I will be in Manchester in the next two days, visiting the Open PHACTS team of Carole Goble. -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Egon W. <ego...@gm...> - 2012-04-14 11:48:11
|
Kleo, 2012/4/14 Kleo Achilleos <kle...@gm...>: > Thank you very much for your answer and the time you dedicated. > I am doing my thesis on workflow management systems. I don't have any > support only Google and Taverna users forum, and I thought I was doing > something wrong. I am not the current 'dr Who' of CDK-Taverna... we should await what Andreas finds out... please do subscribe to the cdk-taverna@ mailing list: https://lists.sourceforge.net/lists/listinfo/cdk-taverna Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Egon W. <ego...@gm...> - 2012-04-14 10:22:00
|
cc: cdk...@li... 2012/4/10 Kleo Achilleos <kle...@gm...>: > I have tried connecting the ouput to some other CDK processor like > SMILES_File_Writer but it fails. That is why I thought the data wasn't read > properly. I just tried a simple workflow: input .smi file, then counting atoms using the atom count molecular descriptor. But I cannot get it to work either... this needs debugging. One problem is that we do not have a proper 'visualizer' for CDK classes... that needs solving (in some far past, I have written one based on JChemPaint... but no idea what happened to that code...) Simpler, we can just render the molecular formula, which is the approach we take in Bioclipse too... that is more useful than a serialization of some Java object... Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |