- galaxy-dev - lists.galaxyproject.org

Toolshed partial installation ? deeptools error
by julie dubois 03 Oct '17

03 Oct '17

Hi dev team, I have a very big problem since I updated to galaxy 17.05 with deeptools from toolshed. Due to a bug in galaxy 17.05 with toolshed installed tools (reported in this issue https://github.com/galaxyproject/galaxy/issues/4591) I re-installed deeptools to try to resolve it. Not resolved really but it's another problem. I temporarly bypassed it. Here is my problem : I've installed deeptools from toolshed and when we try to use "compute matrix" for example, we have this error message : Fatal error: Exit code 1 () Traceback (most recent call last): File "/usr/local/bin/computeMatrix", line 4, in <module> from deeptools.computeMatrix import main ImportError: No module named deeptools.computeMatrix It seems that wrapper are installed but not the tool "deeptools". For more information, here it's the way for the installation : search and install via toolshed Install "suite_deeptools" (version 2.5.1.1.0 : 3d68b716965a) Info in Manage tool dependencies : version=2.5.1, resolver=Conda, green check symbol in the line with a list of all deeptools. Galaxy 17.05, commit cfabe37 (21 sept 2017) I've tried to uninstall/reinstall dependencies with conda but without success. Have you any idea to install the deeptools please ? Thanks. Julie

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data_manager_gatk_picard_index_builder "no space left"
by laurent.fournier＠ulg.ac.be 03 Oct '17

03 Oct '17

Hi, I'm stuck on trying to index genome references for gatk. From what i see it happens (no space left) when the script try to create dictionnary (even it being small..). Anyway, using java, i tried the usual arguments, without success and now i don't know what to do/where to look anymore. For other picard tools, i just overwrote some arguments through job_conf.xml so for a start i added this one to the destination. After that, i've looked in the python script and tried to add to it the same arguments (previous attempt had been unsuccesful). Any ideas about "how to define a directory other than /tmp" ? Our cluster is made with small tmp dirs on all its nodes. The actual attempts are : ------------------ data_manager_gatk_picard_index_builder.py line 40 : args = [ 'java', '-Xmx5120m', '-Djava.io.tmpdir=/local', '-jar', jar, 'R=%s' % gatk_sorted_fasta_filename, 'O=%s.dict' % sequence_id ] ------------------ job_conf.xml : <destination id="java_heavy" runner="drmaa"> <param id="nativeSpecification">-p kosmos --mem-per-cpu=5120 --ntasks-per-node=4 --nodes=1</param> <env id="_JAVA_OPTIONS">-Xmx5120m -Djava.io.tmpdir=/local</env> </destination> ------------------ Regards, Laurent Fournier. --- Laurent FOURNIER IT Specialist University of Liège, GIGA +1 laurent.fournier(a)ulg.ac.be +32 4 366 34 53 +32 497 87 96 46 www.giga.ulg.ac.be

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Pause queued jobs
by Lachlan Musicman 02 Oct '17

02 Oct '17

Hi, I'm new to Galaxy and have been tasked with learning how to admin it. We are running commit 407da92f88ac859d3f9b259be83640516159fe15 I notice there is a screen called "Manage Jobs". How to I re-order, re-prioritise or pause jobs in that list? It seems to only have the options to stop (which I presume cannot be restarted because it's called stop not pause), and Job Lock, which I presume controls if users can or cannot submit jobs, rather than locking individual jobs. Are my assumptions incorrect - is one of these options a "pause" option? cheers L. ------ "The antidote to apocalypticism is *apocalyptic civics*. Apocalyptic civics is the insistence that we cannot ignore the truth, nor should we panic about it. It is a shared consciousness that our institutions have failed and our ecosystem is collapsing, yet we are still here — and we are creative agents who can shape our destinies. Apocalyptic civics is the conviction that the only way out is through, and the only way through is together. " *Greg Bloom* @greggish https://twitter.com/greggish/status/873177525903609857

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October News: Hacktoberfest, Pubs and Pub News, Events, Openings, Servers, ....
by Dave Clements 02 Oct '17

02 Oct '17

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show tool errors admin interface
by Previti 28 Sep '17

28 Sep '17

Dear all, Does anybody know how to configure galaxy to actually show errors under the "show tool errors" section of the admin interface? I can't find any infos about this...we're running version 17.05. Thanks and best regards, 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 42-4434 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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Docker Galaxy & HISAT2: ValueError: Parameter index requires a value, but has no legal values defined.
by Peter van Heusden 28 Sep '17

28 Sep '17

I'm trying to use HISAT2 using a Docker-ized Galaxy (bgruening/galaxy-rna-seq:dev - Galaxy 17.05). I installed the HISAT2 index builder from the toolshed and built an index for the dm3 genome (resulting in an index in /galaxy-central/tool-data/dm3/hisat2_index/dm3). When I try and run HISAT2 with this newly created genome, I get the following error: Traceback (most recent call last): File "/galaxy-central/lib/galaxy/jobs/runners/__init__.py", line 170, in prepare_job job_wrapper.prepare() File "/galaxy-central/lib/galaxy/jobs/__init__.py", line 878, in prepare tool_evaluator.set_compute_environment(compute_environment, get_special=get_special) File "/galaxy-central/lib/galaxy/tools/evaluation.py", line 72, in set_compute_environment visit_input_values(self.tool.inputs, incoming, validate_inputs) File "/galaxy-central/lib/galaxy/tools/parameters/__init__.py", line 106, in visit_input_values visit_input_values(input.cases[values['__current_case__']].inputs, values, callback, new_name_prefix, label_prefix, parent_prefix=name_prefix, **payload) File "/galaxy-central/lib/galaxy/tools/parameters/__init__.py", line 112, in visit_input_values callback_helper(input, input_values, name_prefix, label_prefix, parent_prefix=parent_prefix, context=context) File "/galaxy-central/lib/galaxy/tools/parameters/__init__.py", line 77, in callback_helper new_value = callback(**args) File "/galaxy-central/lib/galaxy/tools/evaluation.py", line 70, in validate_inputs value = input.from_json(value, request_context, context) File "/galaxy-central/lib/galaxy/tools/parameters/basic.py", line 858, in from_json raise ValueError("Parameter %s requires a value, but has no legal values defined." % self.name) ValueError: Parameter index requires a value, but has no legal values defined. (also at: https://gist.github.com/pvanheus/f463b4a60b064c6f45dd99c1bf883480) The "index" parameter is the one used in selecting between the genome from the History and the built-in genome options. Curiously if I spend some time changing this selection before running the tool the HISAT2 run completes successfully. This looks like a bug though - any workarounds or suggestions? Thanks! Peter

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Re: [galaxy-dev] upload file format is data - type not recognized in, galaxy
by Evan Clark 27 Sep '17

27 Sep '17

Good afternoon, Which environment file did you modify we are having a similar issue and need to change the $galaxy_lib environment variable. galaxy-dev-request(a)lists.galaxyproject.org wrote: > Re: upload file format is data - type not recognized in > galaxy

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resubmission on out of memory
by Matthias Bernt 27 Sep '17

27 Sep '17

Dear list, I recall that its possible to configure a tool can such that out of memory conditions (and run time) can be recognized (by regexp matching on stadout/stderr). Can this be used to trigger job resubmission on the cluster? Could someone please point me to some kind of documentation, if this is the case? 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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Changing $galaxy_lib Variable
by evan clark 27 Sep '17

27 Sep '17

Where is it possible to change the $galaxy_lib env variable? We moved our galaxy instance and this variable we are unable to change the path to the new location.

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Cron Job Tool
by Mohamed Kassam 26 Sep '17

26 Sep '17

Dear all, I made a tool that is doing analysis every two days and send me a notification by email when the analyis is completed. I would like to know if I can run this kind of job and how to integrate this tool in Galaxy tools panel in Galaxy ? If someone has this experience can help me. Thanks in advance, Mohamed

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