- galaxy-dev - lists.galaxyproject.org

Search box in tools menu / uncomplete wrappers list
by Sarah Maman 12 Nov '18

12 Nov '18

Hello, When I'm searching a keyword in the « search » box in left « tools » menu, results are sometimes false because the wrappers' list generated by the query thanks to a keyword is not full, some tools are missing. In fact, some wrappers are not listed even if the keyword is in the tool name and/or the tool description. Could you please help us to understand why ? Thanks, Sarah Maman _____________________________ Sarah Maman Bioinformatique/Bioinformatics INRA | SIGENAE | GenPhySE Centre Inra Occitanie-Toulouse Tél. : +33(0)5.61.28.57.08 _____________________________ Chemin de Borde Rouge CS 52627 31326 Castanet Tolosan cedex www.toulouse.inra.fr<http://www.toulouse.inra.fr/> Suivez-nous sur Twitter !

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November 2018 Galactic News: Platforms Directory; new events, pubs, blog posts, servers, tools and releases!
by Mo Heydarian 01 Nov '18

01 Nov '18

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galaxy kickstart failed to install tools
by Rui Wang 31 Oct '18

31 Oct '18

Hi Folks, I tried to install some tools into the galaxy kickstart, and had the following issues: 1. Tons of warnings were generated: [WARNING]: sftp transfer mechanism failed on [localhost]. Use ANSIBLE_DEBUG=1 to see detailed information 2. I wasn't able to install the data manager or tools. Error are like: "stderr": "(1/3) Installing repository tophat2 from devteam to section \"ngs-rna-tools\" at revision 5c5517d2a9e9 (TRT: 0:00:01.238735)\r\n\t* Error installing a repository (after 0:00:00.007585 seconds)! Name: tophat2,owner: devteam, revision: 5c5517d2a9e9, error: {\"err_msg\": \"You are not authorized to request the latest installable revision for a repository in this Galaxy instance.\", \"err_code\": 403006} I tried to use different revision number, but it's the same error. I also tried to use the tool list file that comes with kickstart, it's the same. Not sure if anyone saw this before. Please give me a hand? Thanks, Rui

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Galaxy Administrator Training, Jan 28 - Feb 1, Penn State University
by Mo Heydarian 31 Oct '18

31 Oct '18

Hello all, We would like to remind everyone that* the 2019 Galaxy Admin Training <https://galaxyproject.org/events/2019-admin-training/> will be offered January 28 through February 1 at Penn State University* (where the Galaxy Project got started over ten years ago). The workshop offers a 2 day introductory session <https://github.com/galaxyproject/dagobah-training#basic-sessions> followed by a 3 day advanced topics session <https://github.com/galaxyproject/dagobah-training#advanced-sessions>. Participants can register for one or both sessions. This workshop will cover what you need to know to set up your own high-performance and multi-user production Galaxy instance. Sessions will be *intensive and hands-on*, and taught by experienced instructors from the Galaxy Community. Participants will learn how to install, configure, customize, and extend their own Galaxy servers. Topics include tool configuration, authentication and user management, using heterogeneous storage and compute services, and many other topics that will enable you to get your own Galaxy server up and running, performing well, and used by your community. Registration <https://galaxyproject.org/events/2019-admin-training/#registration> is now open and starts at $40 / day for participants from non-profits and academia. *Early registration ends TODAY October 31, register now before rates increase.* However, the 2016 and 2018 admin training were both full, so you are strongly encouraged to *register now*. *The workshop does have prerequisites <https://galaxyproject.org/events/2019-admin-training/#prerequisites>. Please read them before you register.* Cheers, Mo Heydarian *About Galaxy * Galaxy is an open web based platform for biomedical data integration and analysis. It is deployed at large and small organizations around the world and used in a broad range of biomedical research domains, and across the tree of life.

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Problem with cleanup.py
by George Weingart 30 Oct '18

30 Oct '18

Hello, We are incurring a problem with cleanup.py: We have already run two cycles of cleanup.py (1-6) with a cut off of 30 days, we see in the logs that many datasets are deleted, but when we do df -kh to check the file system, we see creeping up utilization of space - no relinquishing of any space. We are running in a docker environment and our cleanup job looks as follows: ================================================================ #!/bin/bash export GALAXY_VIRTUAL_ENV=/galaxy_venv source $GALAXY_VIRTUAL_ENV/bin/activate export script="/galaxy-central/scripts/cleanup_datasets/cleanup_datasets.py" export config="/etc/galaxy/galaxy.ini" export logdir="/export/galaxy-central/logs" export days=30 export num=$1 nohup $script $config -d $days -$num -r -f >> $logdir/cleanup$num.log & ================================================================ and we run it with ./run_cleanup.sh 1 or 2, 3 etc. Any ideas ? Thanks! George Weingart PhD Huttenhower Lab Harvard School of Public Health

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Reinstall Galaxy by keeping database, database files and tools
by Jochen Bick 29 Oct '18

29 Oct '18

Hi, is it possible to clone a fresh galaxy and reinstall all tools from an existing galaxy (old) by keeping the database and all files? Cheers Jochen

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Galaxy 18.09 Release
by Dannon Baker 29 Oct '18

29 Oct '18

We are pleased to announce the *release of Galaxy 18.09 <https://docs.galaxyproject.org/en/release_18.09/releases/18.09_announce.html>*. A few release highlights are: <http://localhost:8095/news/2018-9-galaxy-release/#extensive-workflow-enhanc…> Extensive Workflow Enhancements Workflows got a lot of love this time around, with new runtime parameters for subworkflows, exposed workflow versions, and zoom capability in the editor, to name a few. There were also a number of usability enhancements including better labeling, links, overhauled workflow import interfaces, and many more. <http://localhost:8095/news/2018-9-galaxy-release/#group-tags> Group Tags Galaxy now contains powerful new features for multiple factor analysis of collections of datasets. The concept of group tags has been added to Galaxy. These are a special class of tags that describe key-value pairs that can be attached to the contents of a collection during upload or using collection operation tools. These tags can describe multiple sets of variables for the contents of a collection. Once set, these tags can be consumed intelligently by tools that need to divide collections into multiple overlapping factors or sets of datasets. A special thanks to @mvdbeek for devising and implementing this approach. <http://localhost:8095/news/2018-9-galaxy-release/#python-3-beta-support> Python 3 Beta Support After almost 3 years of work and more than 100 pull requests, we are proud to announce the Beta-stage support for running Galaxy under Python 3. Lint, unit, API, framework, integration and Selenium tests all pass, time for you to give it a try and report any bug you find! Please see the full release notes <https://docs.galaxyproject.org/en/release_18.09/releases/18.09_announce.html> for more information, including how to upgrade today! *Thanks for using Galaxy!*

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regarding galaxy kickstart
by Rui Wang 23 Oct '18

23 Oct '18

Hi Folks, I spent sometime playing with the kickstart, and sort of got it working. Still a couple things not clear: 1. Is it true that there is no start/stop? My guess is that whenever you need to restart, just re-run the playbook? Anything you want to update(for example add new tools), you re-run the updated playbook too, correct? Before you re-run it, do you have to manually kill everything? 2. Seems tools could easily added by editing the tool list. How about genome data? What if I want to add a specific repo or genome data? Is there a role for this purpose? Please give me a hand if you could. Any input will be greatly appreciated. :-) Thanks so much, Rui

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Running Cloudlaunch against a new OpenStack cloud
by Peter van Heusden 18 Oct '18

18 Oct '18

Hi there I'd like to set up cloudlaunch to be able to set up on-demand Galaxy servers and associated clusters on the new Ilifu OpenStack cloud. From looking around the repositories it looks like Cloudlaunch is at least 2 components: 1. The cloudlaunch server 2. The UI - either cloudlaunch-ui or cloudlaunch-cli I'm trying to get cloudlaunch server installed on a Ubuntu 18.04 VM. The only requirement seems to be python3-pip. For postgresql support I installed the python3-psycopg2 module, the postgresql-10 server and create a user and db (both named cloud). Then I installed the server with `pip3 install cloudlaunch-server` and ran commands: cloudlaunch-server django migrate cloudlaunch-server django createsuperuser cloudlaunch-server django runserver The next step (https://github.com/galaxyproject/cloudlaunch) refers to redis-server. Installing this package seemed to satisfy that requirement, running it manually didn't work so I just ran the celery command as illustrated. And finally relaunched the django server. Then nodejs and npm were installed, the cloudlaunch-ui cloned from github, the various npm package specified installed and finally npm start brings up the cloudlaunch user interface. So far so good but: 1. Is there more extensive documentation anywhere? Specifically documentation about running this in production. 2. Is there a docker container that can be used instead of all this manual installation? 3. How are appliances configured and added to the Appliance Catalogue? Thanks! Peter

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Get Data and 'xlsx'
by D K 15 Oct '18

15 Oct '18

It looks like uploading 'xlsx' data through 'Get Data' is not working. When I try this on my local Galaxy (v18.05) and on usegalaxy.org it gets automatically converted to 'BLAST xml' when using Automatic Detection. If I select 'xlsx' during uploading I get the error message ( Warning: The file 'Type' was set to 'xlsx' but the file does not appear to be of that type ) Does anyone have any suggestions?

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