November 2014 - galaxy-dev - lists.galaxyproject.org

Job wrapper object
by Alexandre Defelicibus 18 Dec '14

18 Dec '14

Hi all, I'm developing some tools on my Galaxy instance and I need to get some information about the job that a tool creates. The question is, how can I have a job_wrapper object in my tool wrapper? I tried to use the reserved variable $__app__, but I got errors. I couldn't import and use the galaxy lib in order to get the job information. Could someone show me the correct way to do that, with some examples? I appreciate all the help. Best regards, -- Alexandre Defelicibus Mestrando em Bioengenharia Programa de Pós-Graduação em Bioengenharia Universidade de São Paulo - USP

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HOWTO share tool parameter settings?
by Lukasse, Pieter 18 Dec '14

18 Dec '14

Hi, Do we have a way (or plans) for sharing tool parameter settings in Galaxy? I know the following workarounds : * Share a history with all users: so users can import your step and do "rerun" to run on their own file with your settings * Wrap the step in a workflow with all parameters set and publish this workflow: users can run this "workflow" * Have a dummy tool to produce a settings file and allow the users to choose this file when running the real tool * Use a conditional and many macros that are basically a copy of each other, only differing in the parameter values But what I would like to have is a way to define bindings between a settings file and the parameters in the tool form. Any plans, ideas? Thanks, Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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Stop autoselecting in drop-down menus
by Aleksey Jironkin 18 Dec '14

18 Dec '14

Hi, I was wondering if there is a way to prevent auto-selecting an option for Running a workflow? Quiet often users (especially novices) would re-run workflows without checking much the data that goes in thinking it will be the same as before. But because the options in drop down menus are auto-populated it seems the top option is always selected by default. For example, previously we had a single fasta file as reference and in the process of a workflow few other fasta files get generated. they appear above the previous fasta in the selection, so without paying attention people skip the input without really checking it. Can we manually add a "blank" selection at the top to force users to select something? Alex -- Dr Aleksey Jironkin Bioinformatician Bioinformatics Unit Infectious Disease Informatics Microbiologicy Services, Colindale Public Health England 61 Colindale Avenue London NW9 5EQ Aleksey.Jironkin(a)phe.gov.uk Tel: 020 83 276610 www.gov.uk/phe Follow us on Twitter @PHE_uk Protecting and improving the nation’s health

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Strange issue with datatypes in Galaxy version of last week
by Lukasse, Pieter 12 Dec '14

12 Dec '14

Hi, Apparently a new datatypes bug has been introduced in the Galaxy version of last week: I have a tool that generates a csv file. Tool configuration is like this: <outputs> <data name="simOut" format="msclust.csv" label="${tool.name} on ${on_string} - SIM file"/> The datatypes has this entry: <datatype extension="msclust.csv" type="galaxy.datatypes.tabular:Tabular" mimetype="text/csv" display_in_upload="true" subclass="true"/> At first Galaxy output seems fine: [cid:image001.png@01CF4847.DE4A1A70] But when I download the file, the downloaded file name will be : Galaxy40-[MsClust_on_data_1_-_SIM_file]- When I go to "edit attributes" and just click "save", then upon downloading again, the file name is correct... Galaxy40-[MsClust_on_data_1_-_SIM_file].msclust.csv . Anyone faced this issue? Thanks and regards, Pieter. Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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Unable to add tools from tool shed
by Ryan G 10 Dec '14

10 Dec '14

I'm following the guide on https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial to add a tool from the tool shed. The tutorial uses 'bwa_base', but I don't see that. So instead, I'm using 'bwa_mem'. I choose 'Preview and Install', then 'Install to Galaxy'. I then select to have it installed in 'NGS: Mapping' tool panel, then click Install. The page then shows two tools: bwa_mem, and package_bwa_0_7_7. Both of which show 'Error' as the status. Clicking on 'bwa_mem' shows some information with "This repository is not installed correctly (see the Repository Installation Error below)...." What does this mean? And how do I fix it?

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Tool Shed Categories
by Alam, Khalid K. (MU-Student) 09 Dec '14

09 Dec '14

Hi; I’m getting ready to submit several (5) tools for processing data related to combinatorial selection technologies (aptamer and (deoxy)ribozyme selections, phage display, etc.) and would like to propose a new category for the Tool Shed entitled “Combinatorial Selections” where these repositories can be published. Khalid Kamal Alam University of Missouri Department of Biochemistry 415 Life Sciences Center 1201 Rollins St. Columbia, MO 65211 <mailto:khalidkalam@mail.missouri.edu>KhalidKAlam<mailto:KhalidKAlam@mail.missouri.edu>@mail.missouri.edu<mailto:kkafy3@mail.missouri.edu> @BiochemPhD

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how to use api to log into Galaxy?
by xlwang 03 Dec '14

03 Dec '14

Hi, I will integrate Galaxy with another system. When I logged into this system, and clicked a link jump to Galaxy, I hope this user has already logged into Galaxy. How to use api to deliver a session or somthing else to Galaxy? Now, I can use api to create a new user in this system and also in Galaxy.

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Help testing Galaxy - new release is coming soon
by Björn Grüning 01 Dec '14

01 Dec '14

Hi! As far as I know the Galaxy team is preparing a new release for next week with a ton of great new features, like Interactive Environments, multiple History view, Dataset collections and many more ... If you want to help testing, trying out the latest features or just give feedback we have put together a Galaxy Docker Image with all this stuff included. Install Docker, run the following command and report any issues! docker run -p 8080:80 -p 8800:8800 --privileged bgruening/galaxy-stable:dev Happy testing and Thanksgiving to everyone! The Galaxy Docker Team

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Trimmomatic wrapper for Galaxy
by Peter Cock 01 Dec '14

01 Dec '14

Hi Simon, I was looking for a Trimmomatic wrapper for Galaxy (which I have thus far only used at the command line outside of Galaxy), and while there does not seem to be one in the main Tool Shed, I see you have been working on this over on the Test Tool Shed: https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/trimmomatic_0_22 https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/trimmomatic_032 Note that according to http://www.usadellab.org/cms/?page=trimmomatic the Trimmomatic authors have been given permission to redistribute the Illumina adapter sequences now :) It would be nice to have functional tests, but other than that, what status is the wrapper? Are there some issues blocking releasing this via the main Tool Shed for wider use? Thanks, Peter

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Deleted tool temp dir
by Pandori n 01 Dec '14

01 Dec '14

Hi all. Config: - galaxy-dist stable (changeset: 11247:a9a0ac9c1afa) [Dec/18/2013] - NFS - Cluster (torque) When i start my WF, on step 2, in 'job_working_directory' created temp (intermediate) dir (for tool step 3). But when step 2 is completed, temp dir (in 'job_working_directory') removed(via galaxy) and step 3 failed. In 'universe_wsgi.ini' 'cleanup_job = never'. Why galaxy.jobs deleted temp dir....? Any help is appreciated. Thanks.

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