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Unable to install dwgsim from toolshed
by Peter Briggs 21 Jan '20

21 Jan '20

Hello all I'm experiencing an issue trying to install the 'dwgsim' from the toolshed: https://toolshed.g2.bx.psu.edu/view/nilshomer/dwgsim/512671604bab I've tried installing into a couple of production instances (both running 19.05) as well as local instances running 19.05 and 19.09, but all attempts have failed. Installing other tools e.g. FastQC seems to work ok. From the log for the 19.09 local instance I'm seeing the following error: tool_shed.galaxy_install.install_manager ERROR 2020-01-20 14:36:19,721 [p:2159,w:1,m:0] [uWSGIWorker1Core3] Error attempting to retrieve installation information from tool shed https://toolshed.g2.bx.psu.edu/ for revision 512671604bab of repository dwgsim owned by nilshomer Traceback (most recent call last): File "lib/tool_shed/galaxy_install/install_manager.py", line 461, in __get_install_info_from_tool_shed raw_text = util.url_get(tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params) File "lib/galaxy/util/__init__.py", line 1677, in url_get response = urlopener.open(full_url) File "XXX/python/2.7.10/lib/python2.7/urllib2.py", line 437, in open response = meth(req, response) File "XXX/python/2.7.10/lib/python2.7/urllib2.py", line 550, in http_response 'http', request, response, code, msg, hdrs) File "XXX/apps/python/2.7.10/lib/python2.7/urllib2.py", line 475, in error return self._call_chain(*args) File "XXX/apps/python/2.7.10/lib/python2.7/urllib2.py", line 409, in _call_chain result = func(*args) File "XXX/apps/python/2.7.10/lib/python2.7/urllib2.py", line 558, in http_error_default raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error Is there something special about this tool which means it can't be installed from the tool shed? Any help is appreciated Best wishes Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482

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January Galaxy News: BCC2020, PAG & ABRF; New pubs, platforms, tutorials...
by Dave Clements 09 Jan '20

09 Jan '20

Hello all, The January 2020 Galactic News is out! https://galaxyproject.org/news/2020-01-galaxy-update/ - 13 Upcoming Events - BCC2020 training topic nominations, Register for Galaxy Admin Training, Galaxy @ PAG & ABRF, and training @ Earlham and Rennes. - 172 new publications - Six highlighted pubs from RT-qPCR to functional genomics - Two new blog posts - PGP-UK and Crowdsourcing Science - Galaxy Platform News - Three new platforms, UseGalaxy.* news, and platforms in pubs - Training material and doc updates - R, RStudio, ATAC-Seq, Scanpy, and Single Cell RNA-Seq - And other news too If you have anything to include to next month's newsletter, then please send it to outreach(a)galaxyproject.org. And a happy new year too, :-) Dave C on behalf of the Galaxy community -- https://galaxyproject.org/

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BCC2020 and Galaxy Admin Training
by Dave Clements 20 Dec '19

20 Dec '19

Hello all, There are three things going on that are of general interest to the Galaxy and GMOD communities, and that have some urgency to them (and thus this mid-month email). BCC2020 Schedule Structure ----------------------- The Bioinformatics Community Conference (BCC2020, https://bcc2020.github.io/) will be held in July, in Toronto, right after ISMB in Montréal. This event brings together the BOSC and Galaxy communities into one gathering. If you are considering attending BCC2020, then the organizers would like your input on several scheduling choices, BY JANUARY 7: https://bcc2020.github.io/blog/poll BCC2020 Training Topic Nominations ------------------------ The training offered at BCC2020 is determined by the community. We are now accepting nominations for training sessions. Nominated topics will be voted on by the community. Please submit your ideas by JANUARY 17. https://bcc2020.github.io/blog/training-nom 2020 Galaxy Admin Training ----------------------- A week long workshop on setting up your own production-grade Galaxy instance will be held in Barcelona the first week of March. Registration is now open, and is, well, pretty darn cheap too. https://galaxyproject.org/events/2020-03-admin/ And, of course, there is a lot of other stuff going on too: https://galaxyproject.org/events/ Happy Holidays, and hope to see you in the new year! Dave C, on behalf of the BCC2020 and Galaxy Admin Training organizers -- https://galaxyproject.org/

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December Galaxy News
by Dave Clements 09 Dec '19

09 Dec '19

Hello all, The December 2019 Galactic News is out! https://galaxyproject.org/news/2019-12-galaxy-update/ - 12 Upcoming Events - India, PAG, HTS, single cell/microbiome, Barcelona, and more - 191 new publications - Two new blog posts - g:Profiler, GalaxyP - Galaxy Platform News - Systems biology, Laniakea, OpenRefine, ... - Training material and doc updates - defining data types, citing GTN, Windows, account help, metatranscriptomics, Galaxy for everyone - Openings - with 5 organizations in Denmark, France, US, US, Germany - Releases - Galaxy 19.09 is out - And other news too Thanks for a superb year, and we are looking forward to an even better 2020. Dave C, on behalf of everyone -- https://galaxyproject.org/

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Problem with uploading data
by Rodrigo Machado 27 Nov '19

27 Nov '19

Hello and to whom it may concern. As I point out in the matter, I am having trouble uploading information, particularly a BIOPROJECT that has already uploaded. I am taking exactly the same steps that I previously used to load this database. I don't understand if Galaxy is not working properly today or what it can be. I am loading it from: Download from web or upload from disk / Upload data as: Collection (s) / Load tabular data from: (pasted table). Thank you in advance and sorry for the inconvenience Lic. Rodrigo Machado JTP Introducción a la Biología, TGG - UNER Becario Doctoral EEA INTA Concordia Estación Yuquerí - Ruta 22 y vías FFCC - CC 34 Concordia - Entre Ríos - Argentina Tel. +54-345-4290000 (int. 162)

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Question on RNA STAR Revision: 13:850f3679b9b4
by Sarah Maman 26 Nov '19

26 Nov '19

?Hello, Please could you help me to run this wrapper : RNA STAR Gapped-read mapper for RNA-seq data (Galaxy Version 2.7.2b) without this error: terminate called after throwing an instance of 'std::out_of_range' what(): basic_string::at /galaxydata/galaxy-prod/my_job_working_directory/000/282/282124/tool_script.sh: line 9: 48744 Aborted (core dumped) STAR --runThreadN ${GALAXY_SLOTS:-4}... Even if I increase the number of genome bins for coordinate-sorting, output files are all empty and I read this stderr above. Thanks in advance, Sarah Maman INRA | SIGENAE | GenPhySE | INRA Occitanie-Toulouse Tél. : +33(0)5.61.28.57.08 Télétravail lundi / vendredi

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The issue of privilege splitting for multiple Galaxy administrators.
by lizhi.hust.16＠gmail.com 26 Nov '19

26 Nov '19

Our team has multiple administrators to maintain the Galaxy platform in our cluster. And each administrator has their own account. But we met a problem, terms of reference for each administrator is ambiguous. For example, if users report a bug in the platform, two or three administrators will handle it. But sometimes, these administrators can't discuss timely to determine who handles these problems (because they are in different time zones). So usually, they will try to fix the issue immediately when they get reports. But sometimes, their solution may conflict. We try to arrange each administrator to handle one kind of issue to eliminate the conflict. But the reports cover lots of ranges. Our splitting can't work well. So we want to know if the galaxy can help us split the privilege of each admin accounts? Just let each admin account is in charge of developing one component of the galaxy. Such as A is in charge of tools uploading, B is in charge of fixing tools bug... May I ask is the galaxy has the function to provide this kind of privilege splitting for their admin accounts? Thanks!

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Release of Galaxy 19.09
by John Chilton 23 Nov '19

23 Nov '19

Dear Community, The Galaxy Committers team is pleased to announce the release of Galaxy 19.09. The release announcement for developers and admins can be found at https://docs.galaxyproject.org/en/master/releases/19.09_announce.html and user facing release notes are at https://docs.galaxyproject.org/en/master/releases/19.09_announce_user.html. A few release highlights are: Interactive Tools ---------------------- A new type of Galaxy tool has been implemented that allows interactive experiences like Galaxy Interactive Environments (via a proxy and Docker containers) but using plugins defined with Galaxy’s XML tool syntax. Workflow Invocation Reports --------------------------- Workflows may now define Markdown templates with Galaxy-specific embedded syntax extensions that can tie together workflow inputs, outputs, jobs, and metadata into rich reports. New Toolshed Client Interface ----------------------------- This project drove numerous enhancements to the Tool Shed API, including vastly improved search functionality. This interface has been completely re-imagined and feels much more interactive. Check out the release notes for a lot more details - there are many more enhancements such as new interface elements, visualizations, datatypes, and more. There are also important notes for Galaxy deployers - such as information about configuration changes in this release and the formal deprecation of Python 2.7 support (this will be the last release with formal support of Python 2). Thanks for using Galaxy!

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21 Nov '19

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21 Nov '19

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