April 2018 - galaxy-dev - lists.galaxyproject.org

ng-chm path error
by Aswathymary Paul 23 Apr '18

23 Apr '18

Hello, I tried to install ng-chm. I have done all the steps described in that manual. But when I generate the heat map, I am not getting a menu for visualization in galaxy and still the path is shown as /shed_tool/.... in my home directory not /galaxy/config. I have moved the zipped heat map into the visualization folder inside plugin. And unzipped there itself. But the path is not taking. Thank you Regards ------------------------------------------------------- Aswathy Mary Paul Ph.D. Student Computational biology and Bioinformatics Cancer Research Program [CRP-9] Rajiv Gandhi Center for Biotechnology Thycaud(P.O), Poojappura Thiruvananthapuram-695014, Kerala, lab extn : 247

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Save data from visualization plugin
by Keith Suderman 23 Apr '18

23 Apr '18

My Google-Fu is failing me... We have a visualization plugin that can also serve as an editor to modify the data it is visualizing. What is the best way to save the data from the visualizer back to Galaxy? I seem to recall reading (somewhere, sometime) that the REST API could not do this and the "best" solution is to invoke the upload tool to upload data into the current history. I have used the upload tool from the Python and Blend4J APIs, but I can not find a JavaScript example for invoking the upload tool. So two questions: 1. Is the upload tool (still) the recommended way to put data into the current history via API calls? 2. How do I invoke the upload tool from JavaScript? Thanks, Keith ---------------------- Keith Suderman Research Associate Department of Computer Science Vassar College, Poughkeepsie NY suderman(a)cs.vassar.edu

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Remove entry from Tool Data Table using via Data Manager
by Dan Fornika 23 Apr '18

23 Apr '18

Hello, I'm working on galaxy integration for an MLST tool called MentaLiST: https://github.com/WGS-TB/MentaLiST/tree/master/galaxy I've created data managers that create kmer databases and store their locations in a Tool Data Table. I'd like to allow users to remove entries from the Tool Data Table. Has anyone seen a Data Manager that provides that functionality? Should I create separate data managers for add and remove functionality, or can it be integrated into one? Thanks, Dan

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FTP service for galaxy with external authentication via SAML using shibboleth
by Martin Demko 17 Apr '18

17 Apr '18

Hi, I'm currently solving a problem with authentication to FTP service for users of our galaxy server. We've successfully established an authentication via shibboleth behind Nginx (not very easy, but doable :) but that also means that ProFTPD is not working anymore, as it doesn't support SAML authentication. So my question is obvious, I'm looking for an easy and free FTP server with SAML support, can anybody help me with an advice? I've already found CompleteFTP and CrushFTP but both are paid and one is Windows-only allegedly. So how do you - people using external authentication via SAML - do this? Thanks in advance for any kind of useful advice. Best wishes, Martin Demko

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planemo/toolshed error, assistance request
by Dennis, H. E. Cicada Brokaw 13 Apr '18

13 Apr '18

Hello, I am having a problem using planemo to upload a suite of tools into the testtoolshed. The tools at this point are all in the toolshed from using the shed_create and shed_update commands in the suite directory. However, along the way there were some errors in uploading some of the tools that I had to fix. Those are all fixed and all the tools show as up to date, except for the suite, which is returning the following error message, about which I have no idea what to do (and I have tried a lot of different things): The repository_dependencies.xml file contains an invalid <repository> tag. Invalid latest installable changeset_revision 000000000000 retrieved for repository ctat_metagenomics owned by trinity_ctat. Does anyone have an idea of what to do to fix this? Thanks, Cicada Dennis

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Doubts about FTP upload.
by Álvaro Rios 11 Apr '18

11 Apr '18

Dear I am trying to upload files via FTP. However, the following message appears. "Authentication required ftp://usegalaxy.org Your connection to this site is not private." I do not have the experience to use galaxy, What I need to do? Thank you. Álvaro Rios.

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April Galactic News: UseGalaxy.org gets some siblings, GCCBOSC and other event news; new pubs, servers, jobs, ...
by Dave Clements 11 Apr '18

11 Apr '18

Hello all, The April 2018 Galactic News <https://galaxyproject.org/galaxy-updates/2018-04/> highlights what's going on in the Galaxy (and it's actually quite cool). Take a look: - *UseGalaxy.eu and UseGalaxy.org.au Launched <https://galaxyproject.org/galaxy-updates/2018-04/#usegalaxyeu-and-usegalaxy…>* - Lots of GCCBOSC 2018 news <https://galaxyproject.org/galaxy-updates/2018-04/#gccbosc-2018>: - We are pleased to announce that Lucia Peixoto <https://galaxyproject.org/galaxy-updates/2018-04/#keynote-speakers> of Washington State University will be our third keynote speaker. - Please welcome *Google Cloud <https://galaxyproject.org/galaxy-updates/2018-04/#google-cloud>* as a GCCBOSC Platinum sponsor. - *GCC Lightning talk, poster and demo submissions are due by April 16 <https://galaxyproject.org/galaxy-updates/2018-04/#submit-gcc-lightning-talk…>* - Childcare for GCCBOSC <https://galaxyproject.org/galaxy-updates/2018-04/#childcare-at-gccbosc>! Space is limited, so register *now*. - Upcoming Events: - 2018 Big Genomics Data Skills Training course <https://galaxyproject.org/galaxy-updates/2018-04/#2018-big-genomics-data-sk…> - how to integrate genomic data analysis into undergraduate coursework - Gateways 2018 Call for Participation <https://galaxyproject.org/galaxy-updates/2018-04/#gateways-2018-call-for-pa…> - Upcoming events <https://galaxyproject.org/galaxy-updates/2018-04/#upcoming-events> (on four continents) - New: - 119 publications <https://galaxyproject.org/galaxy-updates/2018-04/#publications> (including 9 highlighted ones) - Openings in 9 groups on 2 continents <https://galaxyproject.org/galaxy-updates/2018-04/#whos-hiring> - Public Galaxy Server News <https://galaxyproject.org/galaxy-updates/2018-04/#public-galaxy-server-news> (a new server and an updated one too) - ToolShed contributions <https://galaxyproject.org/galaxy-updates/2018-04/#toolshed-contributions> - Releases <https://galaxyproject.org/galaxy-updates/2018-04/#releases> of Galaxy, Galaxy Docker, blend4j, and galaxy-lib - And other news <https://galaxyproject.org/galaxy-updates/2018-04/#other-news> too See the newsletter <https://galaxyproject.org/galaxy-updates/2018-04/> for the full story, and we hope to see you in Portland! Dave C, on behalf of the Galaxy -- https://gccbosc2018.sched.com/ https://galaxyproject.org/ https://usegalaxy.org/

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question regarding GALXY software
by דויד קורנספן [David Kornspan] 10 Apr '18

10 Apr '18

Hi, I would appreciate your advice regarding the recommended portable computer specifications which will enable running the GALXY software for analysis of DNA and RNA seq of bacterial genomes. Thanks, David Kornspan

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Ballgown does not work
by Jochen Bick 10 Apr '18

10 Apr '18

Hi, I'm trying to install Ballgown but it throws some error message after running it: cannot find 'dataset' while searching for 'param_name.dataset.dataset' the script does not have test-data file and it also does not install the requirements. Cheers Jochen

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