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

visualization in anonymous mode ?
by Loraine Guéguen 18 Dec '14

18 Dec '14

Hi, I'd like to use the visualization in anonymous mode, but the visualize icon on the dataset is not available in anonymous mode (although it works fine when connected). Is it possible to activate the dataset visualization in anonymous mode ? Thanks, Loraine -- Loraine Guéguen Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) Service Informatique et Bioinformatique Station Biologique de Roscoff FR 2424 CNRS UPMC Place Georges Teissier CS 90074 29688 Roscoff cedex tel: ++33 (0)2 98 29 56 46 (interne : 415) http://abims.sb-roscoff.fr/ http://www.sb-roscoff.fr/

1 0

"join" produces an import error
by Wang, Yu 17 Dec '14

17 Dec '14

Hi, I am testing Basic Protocol 1 on my local galaxy instance. But Join didn't work. What did I do wrong? I installed join from galaxy main tool shed, bx_python_0_7 was installed but with installation Status "missing tool dependencies". Thanks. ----------------------------------------------------------------------------- job id: 49 tool id: toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/1.0.0<http://toolshed.g2.bx.psu.edu/repos/devteam/join/gops_join_1/1.0.0> tool version: 1.0.0 job pid or drm id: 46018 job tool version: ----------------------------------------------------------------------------- job command line: python /home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_join.py<http://toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_joi…>/local/galaxy/database/files/000/dataset_45.dat /local/galaxy/database/files/000/dataset_46.dat /local/galaxy/database/files/000/dataset_50.dat -1 1,2,3,6 -2 1,2,3,6 -m 1 -f none ----------------------------------------------------------------------------- job stderr: Traceback (most recent call last): File "/home/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_join.py<http://toolshed.g2.bx.psu.edu/repos/devteam/join/de21bdbb8d28/join/gops_joi…>", line 13, in <module> from bx.intervals import * ImportError: No module named bx.intervals Cheers, Yu di29her wang(a)lrz.de<mailto:wang@lrz.de>

6 11

Re: [galaxy-dev] disk space does not add up...
by Dooley, Damion 17 Dec '14

17 Dec '14

Just a small question about this - you have purge_datasets.sh, and then delete_datasets.sh . Shouldn't it be the other way around, since purging only works on the deleted datasets? (I realise this doesn't address your main issue, since running it twice should have maximized free space.) Damion On 12/17/2014 01:05 PM, Langhorst, Brad wrote: > My glaaxy user data area is using 40T > > But the repots server only show usage of about 16T… > > Im nearly out of space and I’m not sure how to resolve the disparity. > I have run the clearnup_datasets.py and other > > > > I’m running mainenance scripts like this: > > #!/bin/sh > > echo 'running galaxy maintenace scripts' > #runs galaxy maintenance scripts > GALAXY_PATH=/mnt/galaxy/data/galaxy/galaxy-dist > SCRIPT_PATH=${GALAXY_PATH}/scripts/cleanup_datasets > sh ${SCRIPT_PATH}/delete_userless_histories.sh > sh ${SCRIPT_PATH}/purge_histories.sh > sh ${SCRIPT_PATH}/purge_libraries.sh > sh ${SCRIPT_PATH}/purge_folders.sh > sh ${SCRIPT_PATH}/purge_datasets.sh > sh ${SCRIPT_PATH}/delete_datasets.sh > > > -- > Brad Langhorst, Ph.D. > Applications and Product Development Scientist >

2 1

Functional tests using gzipped inputs have broken
by Peter Cock 17 Dec '14

17 Dec '14

Hi all, Using gzipped input files in tool functional tests (which would be decompressed by the upload tool) used to work, e.g. https://travis-ci.org/peterjc/pico_galaxy/builds/42395911 https://github.com/peterjc/pico_galaxy/blob/539260fa4348ed454ce464e48c9dbbc… But with more recent versions of Galaxy this has broken, e.g. https://travis-ci.org/peterjc/pico_galaxy/builds/44038046 https://github.com/peterjc/pico_galaxy/blob/e3064cc8f42253efd1f8eed56844d4c… According to the TravisCI failure, the command run was: python /home/travis/build/peterjc/pico_galaxy/galaxy-central-master/tools/seq_filter_by_mapping/seq_filter_by_mapping.py -i "None" -f "data" -m lax -p /tmp/tmpaCsMm5/tmpEpBIX1/database/files/000/dataset_50.dat /tmp/tmpaCsMm5/tmpEpBIX1/database/files/000/dataset_49.dat In this case the -i argument was $input_file, and -f was its extension/datatype. Somehow the gzipped FASTQ was not found, which is why the filename is just "None" and its datatype the default "data". My tool is sensibly returning error code 1, and: Missing input file: 'None' I have made some minor changes to this tool between those TravisCI tests, but the test is the same: <tests> <test> <param name="input_file" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> <param name="mapping_file" value="SRR639755_sample_by_coord.sam" ftype="sam" /> <param name="pair_mode" value="lax" /> <param name="output_choice" value="pos" /> <output name="output_pos" file="SRR639755_sample_lax.fastq" ftype="fastqsanger" /> </test> <test> <param name="input_file" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> <param name="mapping_file" value="SRR639755_sample_by_coord.sam" ftype="sam" /> <param name="pair_mode" value="strict" /> <param name="output_choice" value="pos" /> <output name="output_pos" file="SRR639755_sample_strict.fastq" ftype="fastqsanger" /> </test> </tests> -- I could reproduce this on my development machine running an older Galaxy: $ hg log | head changeset: 16732:212e1d5e9be5 branch: stable tag: tip parent: 16716:2db0fb9594d6 parent: 16731:7adac1842adf user: John Chilton <jmchilton(a)gmail.com> date: Wed Dec 10 12:20:55 2014 -0500 summary: Merged in dannon/galaxy-central/stable (pull request #602) And again updating to the current tip, $ hg log | head changeset: 16850:e614c7c1e0e9 tag: tip parent: 16848:1cf0af0a6324 parent: 16849:d13f2b265dbf user: Dannon Baker <dannon.baker(a)gmail.com> date: Tue Dec 16 15:48:44 2014 -0500 summary: Merged in nitesh1989/galaxy-central3 (pull request #615) I can "fix" it by swapping the gzipped test input_file SRR639755_mito_pairs.fastq.gz to the uncompressed SRR639755_mito_pairs.fastq instead, as in this commit: https://github.com/peterjc/pico_galaxy/commit/126e3e716965016808ec2ba3a4be3… https://travis-ci.org/peterjc/pico_galaxy/builds/44317785 I would like to revert this workaround since the uncompressed FASTQ file is a bit large to bundle as a test case - so I hope this is simply due to an accidental regression in Galaxy itself. Thanks, Peter

2 2

disk space does not add up...
by Langhorst, Brad 17 Dec '14

17 Dec '14

My glaaxy user data area is using 40T But the repots server only show usage of about 16T… Im nearly out of space and I’m not sure how to resolve the disparity. I have run the clearnup_datasets.py and other I’m running mainenance scripts like this: #!/bin/sh echo 'running galaxy maintenace scripts' #runs galaxy maintenance scripts GALAXY_PATH=/mnt/galaxy/data/galaxy/galaxy-dist SCRIPT_PATH=${GALAXY_PATH}/scripts/cleanup_datasets sh ${SCRIPT_PATH}/delete_userless_histories.sh sh ${SCRIPT_PATH}/purge_histories.sh sh ${SCRIPT_PATH}/purge_libraries.sh sh ${SCRIPT_PATH}/purge_folders.sh sh ${SCRIPT_PATH}/purge_datasets.sh sh ${SCRIPT_PATH}/delete_datasets.sh -- Brad Langhorst, Ph.D. Applications and Product Development Scientist

2 1

param name="type"
by Jorrit Boekel 17 Dec '14

17 Dec '14

Hi all, Just a heads-up, I had a tool.xml file in which a command line was called with a parameter called —type. I therefore set <param name=“type” type=“select > etc etc. to do: command —type $type Big mistake. This lead to errors as soon as the tool was modified in the workflow (set as runtime triggered an error for me), due to the fact that the workflow module type was not one of tool, data input, data collection, but was instead the value of the type param which was currently filled in. Now I know not to do this, hope you already did. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden

2 1

When do tool tests run on main & test toolsheds?
by Peter Briggs 16 Dec '14

16 Dec '14

Hello all When do the tool tests run on the main and test toolsheds? In Greg's blog about the toolshed: http://gregvonkuster.org/galaxy-tool-shed-certifying-repositories-install-t… it's implied that the tests run daily for both, but it doesn't look like any tests have run for tools that I've pushed to either toolshed over the last few days. I wondered if was because my tests are broken somehow, but the links to "Latest revision: missing tool tests" etc don't bring anything up either. I'm interested because I'd like to check that the tests run on the test toolshed before I push the tool to the main toolshed - so any advice or suggestions 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

3 3

How galaxy workflow work ?
by Weiyan Shen 15 Dec '14

15 Dec '14

Hi , As we know galaxy tools work with the python,perl,and other tools script in galaxy-dist/tools,but are there any workflow scripts will be created when we edit or import it to run and where they saved? Are there some details about how galaxy workflow work? Thank you very much.

4 3

server datacache.g2.bx.psu.edu unreachable
by Sarah Maman 15 Dec '14

15 Dec '14

Hello, The server datacache.g2.bx.psu.edu <rsync://datacache.g2.bx.psu.edu/indexes/oviAri1> isn't reachable since 2/3 days, so we can't access to banks provided by Galaxy Project (https://wiki.galaxyproject.org/Admin/UseGalaxyRsync) Could you please give us some informaiton to solve this problem? The error message is the following : /*En essayant d'accéder à l'URL http://datacache.g2.bx.psu.edu/ l'erreur suivante a été rencontrée :*/ /*La connexion 128.118.250.10 a échouée.*/ /*Le système a retourné : *//*(111) Connection refused */ / /Thanks in advance for your help, Sarah Maman -- --*-- Sarah Maman INRA - GenPhySE - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - CS 52 627 - 31326 Castanet Tolosan cedex 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*--

3 6

Assertion errors when starting Galaxy
by Lance Parsons 12 Dec '14

12 Dec '14

After updating my local instance of Galaxy to latest_2014.10.06 I get a number of similar errors relating to DisplayApplications. It seems that others have run into this problem as well (see http://dev.list.galaxyproject.org/Assertion-errors-when-starting-Galaxy-td4…) but as of yet I haven't figured out the cause (or a workaround or solution). An example is below: galaxy.datatypes.registry ERROR 2014-12-11 10:57:01,183 Error loading display application (./display_applications/igv/vcf.xml): Filename and id attributes required for dynamic_links Traceback (most recent call last): File "/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/registry.py", line 576, in load_display_applications display_app = DisplayApplication.from_file( config_path, self ) File "/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/display_applications/application.py", line 170, in from_file return cls.from_elem( parse_xml( filename ).getroot(), datatypes_registry ) File "/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/display_applications/application.py", line 183, in from_elem for link in DynamicDisplayApplicationBuilder( dynamic_links, rval, datatypes_registry.build_sites ): File "/data/galaxy-dev/galaxy-dev/lib/galaxy/datatypes/display_applications/application.py", line 91, in __init__ assert filename is not None, 'Filename and id attributes required for dynamic_links' AssertionError: Filename and id attributes required for dynamic_links Note: Cross posted on Galaxy Biostars site: https://biostar.usegalaxy.org/p/9944/ -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University

2 1