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

can't create user on a new instance
by Rui Wang 12 Oct '18

12 Oct '18

Hey Folks, I just installed a new 18.05 instance with a new postgresql db created. However, the UI doesn't allow me to create any user. After I provided all input information, it says galaxy.web.framework.webapp WARNING 2018-10-09 17:28:35,735 [p:32925,w:1,m:0] [uWSGIWorker1Core2] Wrong session token found, denying request in the server log. Btw, I enabled 'allow to create user' and admin user list is empty. I looked into it, and it's a function in lib/galaxy/web/framework/webapp.py: def check_csrf_token(self): session_csrf_token = self.request.params.get("session_csrf_token", None) problem = False if not session_csrf_token: log.warning("No session_csrf_token set, denying request.") problem = True elif session_csrf_token != self.session_csrf_token: log.warning("Wrong session token found, denying request.") problem = True if problem: return self.show_warn_message("Failed to authorize action.") Could someone give me a hand? :-) Cheers, Rui

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Error when trying to update tool vcf_to_alignment in testtoolshed
by Peter van Heusden 12 Oct '18

12 Oct '18

Hi there I had a failed updated (network problem) of the sanbi-uwc tool vcf_to_alignment and now when I try and do an update I get: $ planemo shed_update --shed_target testtoolshed cd '/home/pvh/Documents/code/SANBI/tools-sanbi-uwc/tools/vcf_to_alignment' && git rev-parse HEAD cd '/home/pvh/Documents/code/SANBI/tools-sanbi-uwc/tools/vcf_to_alignment' && git diff --quiet Could not update vcf_to_alignment ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response',)) Repository metadata updated successfully for repository 'vcf_to_alignment' on the test Tool Shed. Failed to update repository contents for repository 'vcf_to_alignment' on the test Tool Shed. Nothing that I try on my side seems to resolve this. Any ideas? Is the problem on the toolshed side? Thanks, Peter

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tool data confusion
by Matthias Bernt 05 Oct '18

05 Oct '18

Dear list, I still have problems to get my head around tool data. Lets consider diamond for example (lets ignore data managers for the moment). After installation it seems that there are two relevant xml files: - `config/shed_tool_data_table_conf.xml` - `tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/tool_data_table_conf.xml` and two loc files: - `tool-data/diamond_database.loc` - `tool-data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/64be1ac21109/diamond_database.loc` In both xml files the latter loc file is referenced. And therefor the tool-data/diamond_database.loc file is seemingly ignored. What is the rational to have a loc and xml file for each tool version? It seems that they are merged upon startup anyway. What would be the best way to administrate a single tool loc file? Cheers, 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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[CLI] Job sent to cluster never gets back
by Estelle Ancelet 04 Oct '18

04 Oct '18

Hello Galaxy community, We are trying to connect a Galaxy web server to a remote cluster by using the "CLI" approach. We do partially succeed : jobs are submitted to the cluster but seem not to be monitored. That is, jobs are executed on the cluster but Galaxy doesn't update the status in the history (stays grey) and never gets back the outputs. The Galaxy folder on the cluster is mounted to the Galaxy Server using sshfs : sshfs galaxyuser@cluster.fr:galaxy galaxy Galaxy (v18.05) is launched by a "sh run.sh" in the galaxy folder, from the Galaxy server side. Here is an extract of our job_conf.xml: <job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> <plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" workers="4"/> </plugins> <destinations default="ssh_slurm"> <destination id="local" runner="local"/> <destination id="ssh_slurm" runner="cli"> <param id="shell_plugin">SecureShell</param> <param id="job_plugin">Slurm</param> <param id="shell_username">galaxyuser</param> <param id="shell_hostname">cluster.fr</param> <param id="job_time">2:00:00</param> <param id="job_ncpus">4</param> <param id="job_partition">defq</param> </destination> </destinations> <tools> <tool id="runtask" destination="ssh_slurm" /> </tools> </job_conf> Did we miss something in the configuration? Or do we have to write additional code? Sincere thanks, Estelle

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learning pulsar for galaxy
by Wong, Kai Leung 03 Oct '18

03 Oct '18

Hello, We are working on a project in providing a Cloud based research platform for Health Informatics and Bioinformatics. Long story short, one of the components to be provided by the project is a Galaxy Server for our genomics researchers; and on the other hand, GWU also has a HPC system for high performance and high throughput computing. Our Galaxy Server for this project is hosing in the Cloud (Azure) and the HPC cluster is onsite at GW. To allow a galaxy server to utilize external compute power of a HPC, galaxy has provided job runner plugins of DRMAA for job schedulers as well as Pulsar. For our situation, the HPC is a remote system w.r.t. the Galaxy server in the cloud and thus there isn't a shared file system between them. It seems to me that Pulsar would be the appropriate solution for us. Am I on the right track? Any suggestions are much appreciated! Best, Adam --- Adam K. L. Wong, PhD. High Performance Computing Specialist for Genomics Division of Information Technology The George Washington University Email: aklwong(a)gwu.edu

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October 2018 Galactic News: SACNAS Workshops, European Galaxy Days, Admin Training; new Pubs, Public Servers, Job postings, and Blog posts!
by Mo Heydarian 01 Oct '18

01 Oct '18

Hello All, The October 2018 Galactic News <https://galaxyproject.org/news/2018-10-galaxy-update/> highlights what’s going on in the Galaxy this month, including: - Galactic Events: - 2018 SACNAS Workshops <https://galaxyproject.org/news/2018-10-galaxy-update/#2018-sacnas-pre-confe…>,10 October, USA - European Galaxy Days <https://galaxyproject.org/news/2018-10-galaxy-update/#european-galaxy-days-…>, 19 - 20 November, Germany - 2019 Galaxy Admin Training <https://galaxyproject.org/news/2018-10-galaxy-update/#2019-galaxy-admin-tra…>, 28 January - 1 February, USA - Other events <https://galaxyproject.org/news/2018-10-galaxy-update/#upcoming-events> across the world. - Galactic Blog <https://galaxyproject.org/news/2018-10-galaxy-update/#new-galactic-blog-pos…> : - Contributor of the Month: Yvan Le Bras <https://galaxyproject.org/news/2018-10-galaxy-update/#new-galactic-blog-pos…> - Tutorial of the month: “From Peaks to Genes” <https://galaxyproject.org/news/2018-10-galaxy-update/#new-galactic-blog-pos…> - Highlight: Hybrid Training delivering to far-reaching venues <https://galaxyproject.org/news/2018-10-galaxy-update/#new-galactic-blog-pos…> - New: - 200 publications <https://galaxyproject.org/news/2018-10-galaxy-update/#publications> - Public Galaxy Servers <https://galaxyproject.org/news/2018-10-galaxy-update/#public-galaxy-server-…>: MPDS-DM - Galactic Job Postings <https://galaxyproject.org/news/2018-10-galaxy-update/#whos-hiring> - Toolshed contributions <https://galaxyproject.org/news/2018-10-galaxy-update/#tools> - Releases <https://galaxyproject.org/news/2018-10-galaxy-update/#releases> of GVL 4.4.0, Planemo 0.55.0, and galaxy-lib. - And other news <https://galaxyproject.org/news/2018-10-galaxy-update/#other-news>. See the newslette <https://galaxyproject.org/news/2018-10-galaxy-update/>r for all of the details! Thanks for using Galaxy! Cheers, Mo, on behalf of Galaxy

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