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

Error while trying to bootstrap the toolshed
by Anmol Hemrom 05 Feb '16

05 Feb '16

Hi, I was trying to bootstrap the main toolshed but it threw me error message. Is it a bug? *The command was this:-* * # sh run_tool_shed.sh -bootstrap_from_tool_shed http://toolshed.g2.bx.psu.edu <http://toolshed.g2.bx.psu.edu>* *The error message was the following:-* *Activating virtualenv at /home/centos/galaxy/.venvBootstrapping from tool shed at http://toolshed.g2.bx.psu.edu <http://toolshed.g2.bx.psu.edu>.Creating database... done.Creating user 'admin' with email address 'admin(a)test.org <admin(a)test.org>'...Traceback (most recent call last): File "lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py", line 15, in <module> from .bootstrap_util import admin_user_infoValueError: Attempted relative import in non-package done.Starting tool shed in order to populate users and categories... done.Retrieving admin user's API key from http://127.0.0.1:9009... done.Creating users... usage: create_users.py [-h] -a API -f FROM_TOOL_SHED -t TO_TOOL_SHEDcreate_users.py: error: unrecognized arguments: (most recent call last):\n File \done.Creating categories... usage: create_categories.py [-h] -a API -f FROM_TOOL_SHED -t TO_TOOL_SHEDcreate_categories.py: error: unrecognized arguments: (most recent call last):\n File \done.Bootstrap complete, shutting down temporary tool shed process. A log has been saved to tool_shed_bootstrap.log* Thanks Anmol

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Rscript run under Tools Directory cannot see Datafile in History
by rbrown1422＠comcast.net 04 Feb '16

04 Feb '16

Good morning team, I have an Rscript tool that is trying to read a file I uploaded into the history beforehand. Galaxy is running with the same user and privileges as the dataset directory. <command>Rscript --slave --vanilla --file=$GALAXY_ROOT_DIR/tools/Foo/Foo.R --args $inputFile1 ..... </command> Why would this be? Error in file(file, "rt") : cannot open the connectionCalls: performDataOrdering -> read.table -> fileIn addition: Warning message:In file(file, "rt") : cannot open file '--file=/home/rbrown/hmgalaxy/database/files/000/dataset_162.dat': No such file or directoryExecution haltedWhen I try to run as R versus Rscript - I get a syntax error about unexpected '(' on function call that works fine in R window.ThanksBob

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planemo reports test failure when test succeeds
by Peter van Heusden 04 Feb '16

04 Feb '16

Hi there When testing the latest trimmomatic tool (from https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmom…, planemo test reports an error on the last test, but according to the test report the test has succeeded (see attached HTML and JSON). For the test setup you need to set some environment variables: TRIMMOMATIC_DIR - the location of the trimmomatic jar TRIMMOMATIC_JAR - the name of the jar file TRIMMOMATIC_ADAPTERS_DIR - location of adapters This is with planemo 0.22.2 and a fresh $HOME/.planemo. Any ideas? Peter

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Trimmomatic doesn't recognise pair collection
by Peter van Heusden 04 Feb '16

04 Feb '16

Hi there I've got Trimmomatic installed (from the toolshed) into our local Galaxy server (server is latest commit on the dev branch from GitHub). It refuses to see a dataset pair as a valid input, however. I've tested this with two types: firstly a pair made out of 2 individual datasets (both fastqsanger) and then also a list of pairs. I've tested this with 'planemo serve' and the tool works, but for some reason it is not working on our server. Any ideas? Thanks, Peter

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Galaxy sending jobs to multiple clusters
by Nikolay Aleksandrov Vazov 04 Feb '16

04 Feb '16

Hi, John, Dan, Carrie and all others, I am considering a task of setting up a Galaxy instance which shall send jobs to more than on cluster at a time. In my case I am using drmaa-python and I was wondering if it was possible to configure multiple drmaa runners each "pointing" at a different (slurm) control host, e.g. local drmaa1 drmaa2 Thanks a lot for your advice Nikolay =============== Nikolay Vazov, PhD Department for Research Computing, University of Oslo

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February 2016 Galaxy News: GCC2016 Registration and Abstract Submission are Open
by Dave Clements 02 Feb '16

02 Feb '16

Hello all, The *February 2016 Galactic News <https://wiki.galaxyproject.org/GalaxyUpdates/2016_02>* is hot off the presses: *GCC2016 <https://wiki.galaxyproject.org/GalaxyUpdates/2016_02#GCC2016> early registration and abstract submission are now open.* - Register early <https://wiki.galaxyproject.org/GalaxyUpdates/2016_02#GCC2016_Early_Registra…> and save up to 40% off regular registration costs. Early bird prices start at less than $45 / day for post-docs and students. - Abstract submission is open <https://wiki.galaxyproject.org/GalaxyUpdates/2016_02#GCC2016_Abstract_Submi…> as well. If you are doing work in data-intensive biology then you are strongly encourage to present your work at the conference. Oral presentations, poster presentations, and the new Visualization Showcase & Software Demos are all opportunities to share your work. - And, we have two new sponsors: Please welcome Lenovo and Globus Genomics <https://wiki.galaxyproject.org/GalaxyUpdates/2016_02#Sponsors> to GCC2016. *And lots of new, new, new, new:* - New Tutorials ... and Interactive Tours! <https://wiki.galaxyproject.org/GalaxyUpdates/2016_02#New_Tutorials_..._and_…> - 156 new publications, including 8 highlighted pubs <https://wiki.galaxyproject.org/GalaxyUpdates/2016_02#New_Papers> - New jobs <https://wiki.galaxyproject.org/GalaxyUpdates/2016_02#Who.27s_Hiring> - New releases <https://wiki.galaxyproject.org/GalaxyUpdates/2016_02#Releases> - New Galaxy servers <https://wiki.galaxyproject.org/GalaxyUpdates/2016_02#New_Public_Galaxy_Serv…> - New ToolShed Contributions <https://wiki.galaxyproject.org/GalaxyUpdates/2016_02#ToolShed_Contributions> *And other cool bits too:* - Galaxy Goes Mobile <https://wiki.galaxyproject.org/GalaxyUpdates/2016_02#Galaxy_Goes_Mobile.21> - Galaxy on Windows and OS X using Kitematic <https://wiki.galaxyproject.org/GalaxyUpdates/2016_02#Galaxy_on_Windows_and_…> - Ten upcoming events <https://wiki.galaxyproject.org/GalaxyUpdates/2016_02#Upcoming_Events> Happy February! Dave Clements and the Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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REST API - Tool input information
by Koehorst, Jasper 01 Feb '16

01 Feb '16

Is it possible to get tool input information through the REST api? For example, I would like to know for a specific tool to retrieve the inputs needed and the types of inputs being either integer, dataset, string, etc… Kind regards, Jasper Koehorst

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Get data via the cloud?
by Scott Szakonyi 01 Feb '16

01 Feb '16

Hi all, Of course, we need to upload large data files. I understand that the common way to achieve this is with an FTP server, but due to our situation setting one up is problematic. Does Galaxy have any mechanism for retrieving data from cloud resources such as Dropbox, Box, or Google Drive? Thanks in advance, -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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Working on the admin interface: JS vs Mako
by Peter van Heusden 01 Feb '16

01 Feb '16

Hi there Zipho and I'd would like to make some changes to the admin pages, including the tool info page and the local data page. These are currently rendered from mako templates - should we change these or is the interface going to be rewritten in client side / javascript in the near(ish) future? Thanks, Peter

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Picard tools don't include CreateSequenceDictionary?
by Scott Szakonyi 01 Feb '16

01 Feb '16

Hello all, I have some biologists here at Notre Dame who use the Picard Tools CreateSequenceDictionary application as part of their workflow. I've tried to locate it in the toolshed but all the Picard Tools versions that are available don't seem to include it. Does anyone know where I might find this tool to add to Galaxy? Thanks! -- Scott B. Szakonyi Research Programmer *Center for Research Computing* 107 Information Technology Center Notre Dame, IN 46556 http://crc.nd.edu

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