- galaxy-dev - lists.galaxyproject.org

tool IO graph
by Matthias Bernt 01 Feb '18

01 Feb '18

Dear list, I started a little toy project (.. aka procrastination) that I would like to share here. It produces a graph connecting tool ids and input/output formats. As input it takes an arbitrary number of tool xml files https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tool-io-graph I could imagine some use cases: - could be nice for auto-generation of the documentation of a single tool (planemo?) - for tool suites one could easily check if the all tools are connected (I would expect this) - one could explore how tools could be plugged together, find out which tools generate a needed format currently it outputs dot formatted graphs. I can easily see some extensions - filter for subsets of tools / formats - get the surrounding of a tool (e.g. all nodes in distance 2, 4, ...) - filter paths from an available input to a desired output format 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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Help with downloading an ouput from RepeatExplorer
by Kareen Seignon 01 Feb '18

01 Feb '18

Hello, I am not quit sure if I am in the right mailing list to ask this question. To this email, i have attached my RepeatExplorer workflow. I downloaded the "Archive with clustering results from dataset 2" output from RepeatExplorer using the Ftp server. I followed the instruction provided by RepeatExplorer to transfer the data to the ftp server (I have attached to this email). The data was successfully transferred (see screenshot attached). The downloaded file seems to be in text format. I put that file on Zipeg to extract the files but it is not working. I changed the extension of that file to (.gz) then (.zip). I am still unable to extract those files. I am wondering if I could get some insight on how to unzip that file Best, Kareen

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Galaxy News: GCCBOSC Training Topic Voting closes Wednesday!
by Dave Clements 31 Jan '18

31 Jan '18

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abnormal termination at worker using supervisord
by Vipin TS 31 Jan '18

31 Jan '18

Dear developers, We are experiencing a job dispatching issue on our public galaxy instance ( https://galaxy.inf.ethz.ch/) On the compute machine, I am not able to start the workers. The following messages got from the worker log file: migrate.versioning.repository DEBUG 2018-01-30 12:23:41,816 Repository lib/galaxy/model/migrate loaded successfully migrate.versioning.repository DEBUG 2018-01-30 12:23:41,816 Config: OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'), ('repository_id', 'Galaxy'), ('version_table', 'migrate_version'), ('required_dbs', '[]')]))]) After this line, it is restarting the process again and stop at the same message. I have checked the status of the workers through supervisor few times and it exited. -bash-4.2$ supervisorctl status galaxy:worker0 STARTING galaxy:worker0 BACKOFF Exited too quickly (process log may have details) galaxy:worker0 FATAL Exited too quickly (process log may have details) my config/galaxy.ini [server:worker0] use = egg:Paste#http port = 9999 host = COMPUTE.MACHINE.IP use_threadpool = true threadpool_workers = 5 config/job_conf.xml <plugins workers="8"> <plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> </plugins> <handlers default="handlers"> <handler id="worker0" tags="handlers"/> </handlers> <destinations default="worker0"> <destination id="worker0" runner="condor"> <param id="request_cpus">1</param> </destination> </destinations> config/galaxy_supervisor.conf [program:galaxy_worker] command = /tools/galaxy_ratschlab/.venv/bin/python ./lib/galaxy/main.py -c /tools/galaxy_ratschlab/config/galaxy.ini --server-name=worker%(process_num)s --log-file=/tools/galaxy_ratschlab/worker%(process_num)s.log directory = /tools/galaxy_ratschlab process_name = worker%(process_num)s numprocs = 2 umask = 022 autostart = true autorestart = true startsecs = 20 user = galaxy environment = VIRTUAL_ENV="/tools/galaxy_ratschlab/.venv",PATH="/tools/galaxy_ratschlab/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",PYTHONHOME="/tools/galaxy_ratschlab/.venv" I tried to restart but didn't help, anything wrong with my configuration? Please let me know what you think and need. Thanks in advance! Vipin

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Cluster Install Path Errors
by John Letaw 30 Jan '18

30 Jan '18

Hi all, I have been trying to finish up a production cluster Galaxy installation, and am having trouble with the below error. In the past, when seeing something along these lines, I usually can adjust environmental variables either in startup scripts, or by including a script for Galaxy to source before it sends out a job. I have tried all of these different methods, but I can’t seem to get rid of this error message in any tool invocation. I currently have “embed_metadata_in_job” set to False in my job_conf.xml file. This removes a “No module named galaxy_ext.metadata.set_metadata” error, but this hashlib error remains. If I could understand a little more about the steps that are taken when sending out a job, perhaps I could better diagnose this? “”” Could not find platform dependent libraries Consider setting $PYTHONHOME to [:] Traceback (most recent call last): File "~/galaxydev/galaxy/tools/data_source/upload.py", line 14, in import tempfile File "/usr/lib64/python2.7/tempfile.py", line 35, in from random import Random as _Random File "/usr/lib64/python2.7/random.py", line 49, in import hashlib as _hashlib File "/usr/lib64/python2.7/hashlib.py", line 116, in import _hashlib ImportError: No module named _hashlib “”” Thanks, John

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Archive of Histories
by Matthias Enders 25 Jan '18

25 Jan '18

Dear Dev Mailing List, is there any possibility build into galaxy to "archive" histories? By "archive" I mean not deleting them, but hiding them from the normal views? Many thanks in advance! Mit freundlichen Grüßen Matthias Enders ----------------------------------------------------------------------- GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: + 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360 Email: m.enders(a)german-seed-alliance.de Firmensitz Köln Amtsgericht Köln, HRB 73844 -----Ursprüngliche Nachricht----- Von: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] Im Auftrag von galaxy-dev-request(a)lists.galaxyproject.org Gesendet: Dienstag, 23. Januar 2018 18:00 An: galaxy-dev(a)lists.galaxyproject.org Betreff: galaxy-dev Digest, Vol 139, Issue 12 Send galaxy-dev mailing list submissions to galaxy-dev(a)lists.galaxyproject.org To subscribe or unsubscribe via the World Wide Web, visit https://lists.galaxyproject.org/listinfo/galaxy-dev or, via email, send a message with subject or body 'help' to galaxy-dev-request(a)lists.galaxyproject.org You can reach the person managing the list at galaxy-dev-owner(a)lists.galaxyproject.org When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. GCCBOSC 2018 Training Topic Voting is now open (Dave Clements) ---------------------------------------------------------------------- Message: 1 Date: Mon, 22 Jan 2018 11:06:01 -0800 From: Dave Clements <clements(a)galaxyproject.org> To: Galaxy Dev List <galaxy-dev(a)lists.galaxyproject.org>, Galaxy Announcements List <galaxy-announce(a)lists.galaxyproject.org> Cc: GCCBOSC 2018 Organizers <gccbosc2018-org(a)lists.galaxyproject.org> Subject: [galaxy-dev] GCCBOSC 2018 Training Topic Voting is now open Message-ID: <CA+He-X_e7frd_nT8dK0-XieKdZ+q0fOSgqJdv32TsK1MFcD=vw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello all, Voting is now open <http://bit.ly/gccbosc2018-vote> on what training topics <https://galaxyproject.org/events/gccbosc2018/training/> will be offered at GCCBOSC 2018 <https://gccbosc2018.sched.com/>. Your vote <http://bit.ly/gccbosc2018-vote> will determine the topics that are offered, which topics should be offered more than once, and which ones should not be scheduled at the same time. Your vote matters. *Topic voting closes January 31.* The Training schedule, including instructors, will be published before early registration opens. GCCBOSC2018 <https://gccbosc2018.sched.com/> will be held 25-30 June in Portland, Oregon, United States. It will feature two days of training: the second of which is multi-track and will feature content for both the BOSC and Galaxy communities. Workshops will be hands-on and participants will be strongly encouraged to bring a laptop and follow along. If you work in data-intensive biomedical research, there is no better place than GCCBOSC 2018 to present your work and to learn from others. Thanks, and see you in Portland! The GCCBOSC 2018 Organizers <https://galaxyproject.org/events/gccbosc2018/organizers> -- https://galaxyproject.org/ https://usegalaxy.org/ -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/attachments/20180122/3…> ------------------------------ Subject: Digest Footer _______________________________________________ galaxy-dev mailing list galaxy-dev(a)lists.galaxyproject.org https://lists.galaxyproject.org/listinfo/galaxy-dev To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ------------------------------ End of galaxy-dev Digest, Vol 139, Issue 12 *******************************************

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GCCBOSC 2018 Training Topic Voting is now open
by Dave Clements 23 Jan '18

23 Jan '18

Hello all, Voting is now open <http://bit.ly/gccbosc2018-vote> on what training topics <https://galaxyproject.org/events/gccbosc2018/training/> will be offered at GCCBOSC 2018 <https://gccbosc2018.sched.com/>. Your vote <http://bit.ly/gccbosc2018-vote> will determine the topics that are offered, which topics should be offered more than once, and which ones should not be scheduled at the same time. Your vote matters. *Topic voting closes January 31.* The Training schedule, including instructors, will be published before early registration opens. GCCBOSC2018 <https://gccbosc2018.sched.com/> will be held 25-30 June in Portland, Oregon, United States. It will feature two days of training: the second of which is multi-track and will feature content for both the BOSC and Galaxy communities. Workshops will be hands-on and participants will be strongly encouraged to bring a laptop and follow along. If you work in data-intensive biomedical research, there is no better place than GCCBOSC 2018 to present your work and to learn from others. Thanks, and see you in Portland! The GCCBOSC 2018 Organizers <https://galaxyproject.org/events/gccbosc2018/organizers> -- https://galaxyproject.org/ https://usegalaxy.org/

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Re: [galaxy-dev] "Edit attributes" for interval dataset not consistent with documentation
by nsoranzo＠tiscali.it 23 Jan '18

23 Jan '18

Dear Peter,this bug has been recently reported in https://github.com/galaxyproject/galaxy/issues/4966 and fixed in https://github.com/galaxyproject/galaxy/pull/5027 for the upcoming 18.01 Galaxy release.Not sure if this is worth a backport, but if you need it for 17.09 and want to try, it should be feasible. Cheers,Nicola ------ Messaggio originale------Da: Peter BriggsData: gio 18 gen 2018 12:11A: galaxy-dev(a)lists.galaxyproject.org;CC: Oggetto:[galaxy-dev] "Edit attributes" for interval dataset not consistent with documentation Dear Devs One of my local users has noticed that the "edit attributes" function for "interval"-type datasets is not consistent with the documentation at: https://galaxyproject.org/learn/datatypes/#interval This states that only CHROM, START, and END are required, with the implication that other fields are optional. However when editing the attributes for a dataset, if either of "Strand" or "Name" are not set to an explicit column number then "Save attributes" fails with the message: "Error occurred while saving. Please fill all the required fields and try again." This is true on both our local Galaxy running release_17.09 and also on Galaxy main. Is this a bug in the documentation, or the implementation? Thanks, Peter -- Peter Briggs peter.briggs(a)manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/

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No legal value defined in a planemo test for param type="select" and options="from_file"
by Olivier Inizan 19 Jan '18

19 Jan '18

Dear list, I am trying to write a test with a param type "select" and options "from_file". I have the following param section in the wrapper:  <param name="ref_file" type="select" label="Using reference database" help="Select reference from the list"> <options from_file="frogs_db.loc"> <column name="name" index="0"/> <column name="value" index="1"/> </options> </param> And I wrote the following test section: <test> ... <param name="ref_file" value="db.fasta"/> </test> The planemo test command failed with the following message: RunToolException: Error creating a job for these tool inputs - Parameter ref_file requires a value, but has no legal values defined. Looking at the planemo documentation I saw the entry "test index (.loc) data": http://planemo.readthedocs.io/en/latest/writing_how_do_i.html#test-index-lo… but it seems to work with <options from_data_table>. Have you any test example working with <options from_file> ? Thanks for your help. Olivier Olivier INIZAN olivier.inizan(a)inra.fr<mailto:olivier.inizan@inra.fr> Unité Mathématiques & Informatique Appliquées du Génome à l'Environnement Plateforme bioinformatique Migale Bâtiment 233 Domaine de Vilvert 78352 Jouy-en-Josas

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upload from dropbox
by Matthias Bernt 18 Jan '18

18 Jan '18

Dear list and a happy new year, does anyone has experience with upload from dropbox to galaxy (by pasting the shared link)? I always get an empty dataset with the additional info "The uploaded file contains inappropriate HTML content". I guess the dropbox download link is not actually a real download link but a link to a website that contains some javascript button that starts the download... 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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