- galaxy-dev - lists.galaxyproject.org

dramm.py error
by Le-shin Wu 05 Feb '16

05 Feb '16

Hi, I was trying to setup a galaxy server and connect to our UGE cluster. If I setup the default job runner as "local", our galaxy server works properly. But if I change the default job runner as "drmaa", our galaxy server throws out the following error message. It looks like drmaa.py has unicode decoding issue. I wonder does someone have the same problem before and how can I fix it. The python version we are using is 2.7.10. Thank you. galaxy.jobs.runners ERROR 2016-02-04 10:49:44,689 (3) Unhandled exception calling queue_job Traceback (most recent call last): File "/home/c226089/galaxy/lib/galaxy/jobs/runners/__init__.py", line 103, in run_next method(arg) File "/home/c226089/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 135, in queue_job job_name = ''.join( map( lambda x: x if x in ( string.letters + string.digits + '_' ) else '_', job_name ) ) File "/home/c226089/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 135, in <lambda> job_name = ''.join( map( lambda x: x if x in ( string.letters + string.digits + '_' ) else '_', job_name ) ) UnicodeDecodeError: 'ascii' codec can't decode byte 0xaa in position 52: ordinal not in range(128) Best LW

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Upload issue in local installation
by Batsal Devkota 05 Feb '16

05 Feb '16

I installed galaxy locally in a linux server. However, I cannot upload the files (no matter how small, I have tried few kb size fasta files). When I try to upload, the link to the file shows up in the History and gets a new number (purple box). When I click on the link I get 'Dataset is uploading' forever. In the terminal window where I start galaxy, I get the following error report: 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /root/tool_menu HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:33 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:40 -0400] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://redhat:8080/root/tool_menu" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /tool_runner/upload_async_create HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/tool_runner/upload_async_message" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:34:04 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:34:08 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" The last line keeps going for ever... writes new line every 4 secs. I am stuck and don't know where to look. Please help. Batsal.

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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 02 Feb '16

02 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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