- galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Search box in tools menu / uncomplete wrappers list
by Matthias Bernt 12 Nov '18

12 Nov '18

Hi, I observed similar Problems on my Galaxy. But I think not all cases can be explained by Martins answer. For instance, if I search for "hisat" I don't get any result, but HISAT2 is definitely installed. Cheers, Matthias > Message: 1 > Date: Fri, 9 Nov 2018 15:54:16 +0000 > From: Sarah Maman <sarah.maman(a)inra.fr> > To: "galaxy-dev(a)lists.galaxyproject.org" > <galaxy-dev(a)lists.galaxyproject.org> > Subject: [galaxy-dev] Search box in tools menu / uncomplete wrappers > list > Message-ID: <1541778855881.43440(a)inra.fr> > Content-Type: text/plain; charset="iso-8859-1" > > > 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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Bug in data manager for the STAR aligner indices
by Previti 12 Nov '18

12 Nov '18

Dear all, I've been wanting to point this out for a while, but the latest update to the STAR data manager didn't fix it either (or maybe I messed up again). The .loc file indicating which genomes have been installed/indices have been made for STAR uses the last column to indicate if there is a gene model/annotation that it should use (0 - for no, 1 - for yes). This seems to be empty...there is a tab at the end of the row, but no number. It works if you manually but in 1 or 0, but not that's not very convenient. Please let me know if I'm missing something... Cheers, 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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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 02 Nov '18

02 Nov '18

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galaxy kickstart failed to install tools
by Rui Wang 01 Nov '18

01 Nov '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 01 Nov '18

01 Nov '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 30 Oct '18

30 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 30 Oct '18

30 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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