- galaxy-dev - lists.galaxyproject.org

extract extra info (logs) from history
by Jochen Bick 02 May '18

02 May '18

Hi, I would like to use the info (log) HISAT is showing, for another tool. e.g.: 26781724 reads; of these: 26781724 (100.00%) were unpaired; of these: 2445411 (9.13%) aligned 0 times 20399099 (76.17%) aligned exactly 1 time 3937214 (14.70%) aligned >1 times 90.87% overall alignment rate [bam_sort_core] merging from 21 f Is it possible to access these logs? Cheers Jochen

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Gateways 2018 Call for Participation: Extended to May 16
by Katherine Lawrence 30 Apr '18

30 Apr '18

The deadline for the Gateways 2018 Call for Participation has been extended to Wednesday, May 16, 2018. Gateways 2018 (September 25-27, at the University of Texas at Austin) is accepting submissions of papers, demos, tutorials, and panels (2-4 pages) on the topic of science or engineering gateways. Topics may include their design, use, impact, development processes, sustainability, best practices, or any other aspect that you think fellow gateway creators or users will find interesting to learn. We also welcome educational topics directed toward the next generation of gateway creators. Submissions of papers, demos, tutorials, and panels are due May 16, 2018. There will be no further extension of this deadline. The poster session deadline (open to all) is August 1, 2018. Full submission details can be found here: https://sciencegateways.org/gateways2018/call

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tool_conf.xml
by Nancy Ide 30 Apr '18

30 Apr '18

Hello I’m trying to include some of the tools available from usegalaxy.org in the tool menu of our instance of Galaxy. When I look at the list of tools in the Galaxy tool_conf.xml.main file, it does not seem to line up with what you see in the menu at usegalaxy.org. I’ve searched through various versions etc. on GitHub, but no luck—they all seem to be identical and do not seem to correspond with the menu at usegalaxy.org (I am looking specifically at the Text Manipulation part of the menu). Any clues on where I should look? Thanks, Nancy Ide ----------------------------------------------------- Nancy Ide Professor of Computer Science Department of Computer Science Vassar College Poughkeepsie, New York 12604-0520 USA tel: (+1 845) 437 5988 fax: (+1 845) 437 7498 email: ide(a)cs.vassar.edu http://www.cs.vassar.edu/~ide -----------------------------------------------------

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Galaxy Cleanup
by Previti 27 Apr '18

27 Apr '18

Hi everybody, I have a hopefully basic questions regarding temporary output files. A user was generating >4TB output files via the program bedtools intersectbed. The jobs were cancelled, but I still see the (temporary) output files that were generated. Does Galaxy clean these up? Does it do this regularly? Would a quota prevent something like this from happening again or would the jobs have to finish before being "counted"? Thanks and best regards, Christopher -- *Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4661 christopher.previti(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist. Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung. Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.

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fonts on headless compute nodes
by Matthias Bernt 25 Apr '18

25 Apr '18

Dear list, I found that some tools (eg FastQC and MetaProSIP) have problems with missing fonts (the former is java and the latter caused by R) on our compute nodes which do not have xorg and no fonts installed. On the cluster head nodes several font related packages are installed: dejavu-fonts-common-2.33-1.el6.noarch xorg-x11-fonts-Type1-7.2-11.el6.noarch liberation-fonts-common-1.05.1.20090721-5.el6.noarch liberation-sans-fonts-1.05.1.20090721-5.el6.noarch dejavu-sans-fonts-2.33-1.el6.noarch urw-fonts-2.4-11.el6.noarch ghostscript-fonts-5.50-23.2.el6.noarch xorg-x11-fonts-misc-7.2-11.el6.noarch It seems that conda no fonts are available. Is there somebody with similar problems. Any hint which of the packages is/are actually needed. Maybe our admins could install them... I also found for MetaProSIP that several xorg-... packages are needed. Should such dependencies be handled by the conda packages or by the Galaxy tool. Best, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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Samtools running on submit-node and as a slurm job
by Previti 24 Apr '18

24 Apr '18

Dear all, We found something strange with our Galaxy instance... Our Galaxy server is configured as a submit node using slurm to submit to our cluster. This works fine for the most part, but today we saw a samtools index job running "locally" on the submit node instead of a cluster node. Is there any way of stopping this behavior? The submit nodes are not configured for data-intensive computation and everything runs significantly slower. I was running bamtools (splitting a bam-file into mapped into unmapped) at the time and the output bam-files were being indexed. Thanks and best regards, Christopher -- *Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4661 christopher.previti(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist. Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung. Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.

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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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