- galaxy-dev - lists.galaxyproject.org

Conflicting conda dependencies for Galaxy tool
by Peter Briggs 15 Jun '18

15 Jun '18

Dear devs I'm currently trying to update a tool developed to wrap an in-house scripted pipeline written by a local researcher, so that it gets its dependencies from conda. The pipeline uses a variety of third-party software packages (many of which are now at "legacy" versions), and I've hit a problem where two of these packages turn out to have conflicting dependencies. Specifically the issue is with qiime=1.8.0, which it turns out is not compatible with any version of R which is available in the channels used by Galaxy. So when Galaxy builds the conda environment for the tool at execution time, it fails with an error from conda: UnsatisfiableError: The following specifications were found to be in conflict: - cairo==1.14.10=0 -> freetype==2.8.1 - cairo==1.14.10=0 -> pixman=0.34 - py2cairo==1.10.0=py27_1 -> cairo==1.12.2 -> freetype=2.4 - py2cairo==1.10.0=py27_1 -> cairo==1.12.2 -> pixman==0.26.2 (The py2cairo requirement comes from an older version of matplotlib that qiime 1.8.0 pulls in.) It's a long shot, but: does Galaxy offer any options for working around conflicting conda dependencies like these? Or is the only option to try and resolve them at the conda packaging level (which might not be practical, or even possible)? Thanks in advance for any advice, 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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python: error while loading shared libraries
by Floreline TOUCHARD 14 Jun '18

14 Jun '18

Dear Galaxy community, I'm currently testing cross-platform compatibility with our Galaxy instance (15.10) : - [on PROD environment] Galaxy service runs on a RedHat 6.5 server (using python2.6 installed in a virtualenv) and submits jobs on cluster nodes also in RedHat 6.5/python2.6 (default version installed on the system). - [on TEST environment] I changed the configuration of our Galaxy TEST instance (still RedHat 6.5 / python 2.6) to submit jobs on cluster nodes in CentOS7/python2.7 (default version installed on the system). - Galaxy installations (test and prod) and virtualenv folders are located in a volume mounted on Galaxy servers and all cluster nodes. On TEST environment python tools (like the internal Galaxy tool "upload1", or the NCBI BLAST toolkit) if submitted on the cluster failed with the following message : "python: error while loading shared libraries: libpython2.6.so.1.0: cannot open shared object file: No such file or directory" I guess the problem lies in the shared library libpython2.6.so.1.0 located in /usr/lib64/libpython2.6.so.1.0 on the Galaxy server and absent from the cluster nodes (it should be something like /usr/lib64/python2.7/libpython2.7.so.1.0). Is it possible to integrate this shared library in the Python virtualenv and use a specific configuration to indicate Galaxy to use it when submitting jobs on the cluster ? Thanks in advance, Floreline.

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job deletion
by Matthias Bernt 14 Jun '18

14 Jun '18

Dear list, i stumbled over a little problem in the implementation of my univa/drmaa job runner (https://github.com/galaxyproject/galaxy/pull/4857) which gets its information from qacct. The problem is that jobs that are deleted before they start are not stored in the job accounting data base which is used by qacct. Is there a way to determine that a job was deleted from the Galaxy job properties? It seems that in the stop_job method of the drmaa runner does not record anywhere that the job was deleted... 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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galaxy upgrade 18.05 problem
by Matthias Bernt 11 Jun '18

11 Jun '18

Dear list, after upgrading to 18.05 I get an empty page when opening the galaxy website. The proxy logs say: [Mon Jun 11 15:20:10 2018] [error] [client 141.65.5.81] File does not exist: /data/galaxy_server/galaxy/static/scripts/packed, referer: https://galaxy.intranet.ufz.de/root/login?redirect=%2F Which is true, ie. the file/directory does not exist. Any ideas which step I forgot during the upgrade? 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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Permanently deleting users from a Galaxy instance
by Peter Briggs 11 Jun '18

11 Jun '18

Hello I'm wondering if there is an option to permanently delete a user account from a Galaxy instance, for example to comply with GDPR (for those of us running public Galaxy instances). The admin interface provides "delete" and "purge" options for user accounts, but neither of these seems to permanently remove an account - the deleted accounts are still visible and can be undeleted (at least, in Galaxy 17.09). It's also unclear to me what "purge" does in this case - I wasn't able to find any documentation on these user management options. As I understand it, under GDPR a person can request to have all their personal data removed from a database, but neither of the above options would be sufficient to leave the database compliant with GDPR in this case (as at the very least the email address - which I understand constitutes personal information in this context - would remain in the database). Is there any way within Galaxy to truly permanently remove a user account? Thanks in advance for any advice on this, 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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problem with Visualization 'Scatterplot' in 18.05
by Hans-Rudolf Hotz 09 Jun '18

09 Jun '18

Hi all I am in the process of upgrading our servers to 18.05. And I have encountered an issue with the Visualization tool "Scatterplot, Creates a 2D-scatterplot from tabular datapoints" I am starting with a simple bed file for chromosome 15 (downloaded with UCSC table browser tool). When I click on the Visualization icon, followed by "Scatterplot", I end up with an near empty page. I only get the title: Scatterplot of 'UCSC Main on Human: ncbiRefSeq (chr15:20010162-22868384)' UCSC Main on Human: ncbiRefSeq (chr15:20010162-22868384) This happens with our development server (after being upgraded from 17.09). It is the same using a new clone of 18.05 code. It also happens on usegalaxy.eu but it does work on usegalaxy.org As a side note: on usegalaxy.org, each visualization has its little icon (see: 'usegalaxy.org.png'), while on usegalaxy.eu, each visualization just has an eye (see: 'usegalaxy.eu.png') I hope there is an easy fix for this.... Regards, Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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Uploads via Nginx proxy fail after upgrade to current release
by Hans-Georg Sommer 07 Jun '18

07 Jun '18

Hi, after updating Galaxy to 18.05 (from 17.05) the file upload doesn't work anymore, but shows an Internal Server Error (500) in the status column of the upload form. We use a nginx proxy also for uploads, configured as described in [1], galaxy.ini contains the line 'nginx_upload_path = /_upload'. The nginx access logs show, that the upload requests seem to go to the wrong location ('/api/uploads' instead of '/_upload'): 0.0.0.0 - - [06/Jun/2018:10:44:43 +0200] "POST /api/uploads HTTP/1.1" 500 193 "https://galaxy.gwdg.de/" I searched the release notes and the github issues, but wasn't able to find anything besides [2], which sounds similar but does not give much information. Thanks for your help, Hans-Georg [1] https://docs.galaxyproject.org/en/latest/admin/nginx.html [2] https://biostar.usegalaxy.org/p/25870/ -- ------------------------------------------------------------------------ Hans-Georg Sommer Arbeitsgruppe "Anwendungs- und Informationssysteme" E-Mail: hans-georg.sommer(a)gwdg.de ------------------------------------------------------------------------ Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen (GWDG) Am Faßberg 11, 37077 Göttingen, URL: http://www.gwdg.de Tel.: +49 551 201-1510, Fax: +49 551 201-2150, E-Mail: gwdg(a)gwdg.de Service-Hotline: Tel.: +49 551 201-1523, E-Mail: support(a)gwdg.de Geschäftsführer: Prof. Dr. Ramin Yahyapour Aufsichtsratsvorsitzender: Prof. Dr. Norbert Lassau Sitz der Gesellschaft: Göttingen Registergericht: Göttingen, Handelsregister-Nr. B 598 ------------------------------------------------------------------------ Zertifiziert nach ISO 9001 ------------------------------------------------------------------------

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Job Script Integrity
by John Letaw 05 Jun '18

05 Jun '18

Hi all, I’m installing via GalaxyKickStart… I’m getting the following error: galaxy.jobs.runners ERROR 2017-11-06 19:14:05,263 (19) Failure preparing job Traceback (most recent call last): File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/galaxy/jobs/runners/__init__.py", line 175, in prepare_job modify_command_for_container=modify_command_for_container File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/galaxy/jobs/runners/__init__.py", line 209, in build_command_line container=container File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/galaxy/jobs/command_factory.py", line 84, in build_command externalized_commands = __externalize_commands(job_wrapper, external_command_shell, commands_builder, remote_command_params) File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/galaxy/jobs/command_factory.py", line 143, in __externalize_commands write_script(local_container_script, script_contents, config) File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/galaxy/jobs/runners/util/job_script/__init__.py", line 112, in write_script _handle_script_integrity(path, config) File "/home/exacloud/lustre1/galaxydev/galaxyuser/lib/galaxy/jobs/runners/util/job_script/__init__.py", line 147, in _handle_script_integrity raise Exception("Failed to write job script, could not verify job script integrity.") Exception: Failed to write job script, could not verify job script integrity. galaxy.model.metadata DEBUG 2017-11-06 19:14:05,541 Cleaning up external metadata files galaxy.model.metadata DEBUG 2017-11-06 19:14:05,576 Failed to cleanup MetadataTempFile temp files from /home/exacloud/lustre1/galaxydev/galaxyuser/database/jobs/000/19/metadata_out_HistoryDatasetAssociation_16_I8bhLX: No JSON object could be decoded I would like to further understand what it means to not verify integrity of a job script. Does this just mean there is a permissions error? Ownership doesn’t match up? Thanks, John

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tabular data display
by Matthias Bernt 02 Jun '18

02 Jun '18

Dear list, I'm struggling with tabular data in Galaxy. Attached is a tab separated file that is generated by MetaProSIP (an updated - not yet committed -- version). The problem is that it is not shown as table in Galaxy (dev) at all. Also the peek preview is odd, some values of the header and data are omitted. Is this a bug in Galaxy, or of the data in the table? 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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argparse -> tool xml advice
by Matthias Bernt 29 May '18

29 May '18

Dear list, just a question for advice: I plan to wrap a python script (with lots of options) which uses the argparse library. I was wondering if somebody has an idea to generate the tool xml (semi-)automatically? For instance, by subclassing the formatter, parsing the python code, or parsing the command line... 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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