November 2016 - galaxy-dev - lists.galaxyproject.org

problem installing a tool
by Michael Thon 29 Nov '16

29 Nov '16

I installed a tool called heatmap and when I tried to run it I got this error: bash: /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/guru-ananda/heatmap/dbd447fcd3e4/heatmap/heatmap//home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/guru-ananda/heatmap/dbd447fcd3e4/heatmap/r_wrapper.sh: No such file or directory the actual script its trying to call is in: /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/guru-ananda/heatmap/dbd447fcd3e4/heatmap/heatmap <http://toolshed.g2.bx.psu.edu/repos/guru-ananda/heatmap/dbd447fcd3e4/heatma…> so it looks like the tool is not configured correctly. Any ideas on how to fix it? Thanks!

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Moving Galaxy Install From One Server To Another
by evan clark 28 Nov '16

28 Nov '16

Is there a good method for moving a fully functional galaxy install from one machine to another in a different directory?

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Galaxy ToolShed Installation Question
by Yip, Miu ki 28 Nov '16

28 Nov '16

Hi all, When a tool is installed onto Galaxy via the GUI from the ToolShed, where is the tool itself installed on the system? For instance, having installed Bed Tools from the ToolShed, the tool errors out on a run with the following error: Fatal error: Exit code 127 () /galaxy/database/job_working_directory/000/84/tool_script.sh: line 9: bedtools: command not found This means that a path needs to be set somewhere in Galaxy to the tool? Where is the tool installed? Having checked the location below, only the xml files are listed. /shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/bedtools/7b3aaff0d78c/bedtools<http://toolshed.g2.bx.psu.edu/repos/iuc/bedtools/7b3aaff0d78c/bedtools> Is there a configuration that is missing? Thanks! Miuki Yip

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running jobs on Apache Mesos
by Matthias De Smet 28 Nov '16

28 Nov '16

Hi All, We’d like to migrate our Galaxy instance to an Apache Mesos environment. We can use the Galaxy docker image to run the webserver, but I’m wondering if there is any support (or support in the works) the schedule jobs on a Mesos cluster. As far as I’m aware, none of the supported job schedulers has Mesos capabilities. Thanks! Matthias

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"Phantom" tool dependencies when installing from toolshed?
by Peter Briggs 25 Nov '16

25 Nov '16

Hello Galaxians I've been reinstalling some tools and dependencies as a part of relocating our local Galaxy server to a new VM platform, and while the majority of tools seem to be okay for a few I've noticed a baffling problem with what appear to be "phantom" tool dependencies. For example: for package_matplotlib_1_2, I'm now seeing an unsatisfied dependency on "package_libpng_1_6_7" from devteam - but the matplotlib repository in the toolshed no longer has a requirement on this package. So I don't know where this phantom dependency has come from (a hangover from the original installation, which was at an earlier revision of the package?) or more pragmatically, how to clear it. Has anyone else seen this problem before, and if so then can they advise how to fix it? To clarify: -- By "reinstall" I mean: manually uninstall the tool repository via the Admin/Manage installed tools interface, and then perform an install using a Python utility that uses the API via bioblend. -- I'm using Galaxy v15.10.2 but planning to upgrade the code base once the tools are installed. Any help or advice greatly appreciated, 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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Running unit tests on [dev]
by Maximilian Friedersdorff 24 Nov '16

24 Nov '16

-------------------------------------------------------------------- Un o’r 4 prifysgol uchaf yn y DU a’r orau yng Nghymru am fodlonrwydd myfyrwyr. (Arolwg Cenedlaethol y Myfyrwyr 2016) www.aber.ac.uk Top 4 UK university and best in Wales for student satisfaction (National Student Survey 2016) www.aber.ac.uk

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Talk abstracts for Galaxy Australasia Meeting (GAMe 2017) are due 30 Nov
by Dave Clements 23 Nov '16

23 Nov '16

Hello all, This is just a reminder that talk abstracts for the 2017 Galaxy Australasia Meeting (GAMe 2017, https://www.embl-abr.org.au/game2017/) are due Wednesday, 30 November. GAMe 2017 is a series of events in Melbourne, Australia running from 3 February through 11 February. This includes a training day for researchers on *using* Galaxy, a two day meeting, and then a 4 day course on how to set up your own production quality Galaxy server. Oral presentations will be given at the meeting, 4-5 February. The meeting is split into a BIO Day (4 Feb) focusing on biological applications, and an INFO Day (5 Feb) focusing on infrastructure, tools, development and deployment. Participants can register for one or both days, and you can specify a preferred presentation day when you submit your abstract(s). GAMe 2017 will also feature poster presentations, keynotes, birds-of-a-feather meetups, and lots of networking., Poster abstracts are reviewed on a rolling basis and will be accepted until we run out of poster space (so, submitting sooner is better). Early registration ends 31 December. We strongly encourage you to register early can save up to 45% off regular registration rates. We hope to see you in Melbourne! The GAMe 2017 Organising Committee -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Mapping LDAP groups to Galaxy groups/roles
by Ignacio EGUINOA 23 Nov '16

23 Nov '16

Hi all, I'm currently looking for some help to manage groups/roles in Galaxy. The instance I'm working with uses LDAP authentication (all Galaxy registered users are in LDAP) and the datasets that are uploaded have permissions 'patterns' that can be mapped to groups already available in the LDAP server. Current approach is to manually add roles and groups and assign the registered users to them. Since the amount of users and groups is considerable large and can also change, I was hoping to have a more automatic system such that, when a new dataset is added, the required group/roles are already available to be assigned. I guess that, since the LDAP system is only used for authentication purposes, there is no way to directly map all the groups and users to galaxy (and actually it would be an overkill). But, at least I would like to get to map the primary LDAP group in a somehow automatic way. The only approach I could come up with is to manage the group/roles creation through the API, assuming I have a list of the relevant group names at a certain point in time, and then update the link of users to the available groups/roles by using information from LDAP. When I first deployed the instance I added an extra check during user authentication to verify that the user belongs to a specific LDAP group which grants access to the Galaxy instance. To do this, a list of groups the user belongs to is obtained from the server. I was thinking about extending this step to also update the user's Galaxy profile, associating it with the groups that are already created in Galaxy. Since this will require some digging into Galaxy code, I first want ask if there is any alternative solution for this kind of situation or some work was already done.. Thanks in advance Ignacio EGUINOA - Predoctoral fellow Applied Bioinformatics And Biostatistics VIB Department of Plant Systems Biology Ghent University Technologiepark 927 - 9052 Ghent - Belgium Tel. +32(0)9 331 36 95 www.psb.ugent.be

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Error running bedgraph to bigwig on local galaxy
by evan clark 23 Nov '16

23 Nov '16

When attempting to generate a bigwig file I receive this error. hashMustFindVal: 'GL000192.1' not found Fatal error: Matched on Error Error running wigToBigWig. I have added the chrom len files for galaxy and update the location path but an unsure what could be causing this issue.

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Is there demand for rate limiting in Galaxy?
by Maximilian Friedersdorff 23 Nov '16

23 Nov '16

-------------------------------------------------------------------- Un o’r 4 prifysgol uchaf yn y DU a’r orau yng Nghymru am fodlonrwydd myfyrwyr. (Arolwg Cenedlaethol y Myfyrwyr 2016) www.aber.ac.uk Top 4 UK university and best in Wales for student satisfaction (National Student Survey 2016) www.aber.ac.uk

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