galaxy-dev November 2014

galaxy-dev@lists.galaxyproject.org

61 participants
91 discussions

GMOD user talks at PAG
by Scott Cain 10 Nov '14

10 Nov '14

Hello, I'm looking for some people to give talks about how you've used GMOD tools at your site at the Plant and Animal Genomes meeting in San Diego this January. If you're already going to PAG, or are looking for an excuse to go to San Diego in January, I encourage you to send me a brief note with a title for your talk. If you haven't registered for PAG but will give a talk, you can register at early bird pricing (a savings of $100 dollars I think). Unfortunately, I'm running a little late with this announcement, so if you'd like to give a talk, please get back to me by November 13 (Thursday). Thanks and I hope to see you in San Diego in a few months, Scott -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research

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ulimit problems after update
by Ido Tamir 10 Nov '14

10 Nov '14

Hi, I updated to the latest galaxy distribution (after one year). And now every job fails with: /home/imba/solexa/.profile.sh: line 118: ulimit: virtual memory: cannot modify limit: Operation not permitted The limit is ridiculously high: ulimit -v 60000000 Its just to prevent some badly programmed in house galaxy tools to crash the server. I think the problem happens after the set_metadata stage. Any advice? thank you very much, ido

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tools version (eg: cufflinks) and bowtie indices file
by Elizabeth Chia 10 Nov '14

10 Nov '14

Hi there 1. Why is it that even after installing cufflinks 2.1.1 from the toolshed, it doesn't get reflected when I clicked on the tool from the side panel? It still shows 0.0.5 and 0.0.7. Think it's the same with others too (eg: bowtie) 2. I've modified the bowtie_indices.loc file under tool-data but the entries doesn't get reflected on the Map with Bowtie for Illumina (select a reference genome). I did the same for the bowtie2_indices.loc file and this one got reflected under Bowtie2. Been a little frustrating. Can anyone please advise? Many thanks. Best regards liz

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bowtie2: no stderr output
by Elizabeth Chia 09 Nov '14

09 Nov '14

Dear all Usually the alignment statistics from bowtie2 will be printed to the stderr file, however, on the local instance, the stderr file is empty after alignment. It still does the alignment, but the statistics are not printed out. This is my hg summary: parent: 13802:f7dd0060c296 latest_2014.06.02 Merged in dannon/galaxy-central-prmaker/stable (pull request #404) branch: stable commit: 288 modified, 357 added, 18 unknown (new branch head) update: 27 new changesets (update) Will updating to the latest version help? Or are there any patches available? Thanks. Regards liz

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data_columns
by Jorrit Boekel 07 Nov '14

07 Nov '14

Dear list, I tried to make a tool that takes tsv input and have some data_columns selection parameters in the xml definition. It seems to work, but I get ‘invalid option was selected’ in the browser interface for each of the data_columns. No logging errors or stacktraces. Digging a bit, I found out that the legal_values of the ColumnParameter (in lib/galaxy/tools/parameters/basic.py ) is empty. It is returned empty by get_column_list when this does if not dataset.metadata.columns: on line 1184 of the above mentioned file. Now I’m a bit at a loss, how do I set these columns, or where are those columns set on the metadata? Is it stored, generated from the input file? My files are not official formats, just tsv subclasses. I’m on changeset 14567:007f6a80629a in galaxy-dist. cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden

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Galaxy Not Displacing History
by Jeremy Liu 07 Nov '14

07 Nov '14

Hi Galaxy Dev, I just pulled the latest updates for galaxy-dist with hg pull -u and then migrated over the postgres database with: sh manage_db.sh -c ./universe_wsgi.ini upgrade After restarting the server, my Galaxy instance would not show the history of datasets. The history was still there, since I could see it when I clicked "Saved Datasets" -> "View" -> "Show Structure" and jobs would be executed normally. However the history toolbar was entirely missing. Is there any fix for this other than dropping the database, deleting galaxy and clean install galaxy? (then reinstall the tools that I had downloaded from the toolshed). Note: After running sh run.sh --reload, Galaxy noted that some of the tools were not moved over, so I tried running sh ./scripts/migrate_tools/0012_tools.sh and sh ./scripts/migrate_tools/0012_tools.sh install_dependencies but I was unable to locate the scripts. Thanks, Jeremy Liu

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DecoRNAi error
by Rossella Rispoli 07 Nov '14

07 Nov '14

Hello, I'm trying to analyse a 384-plate screen genome data set(67 plate size)with DecoRNAi tool to discover the over represented seed family, and I got this error: An error occurred running this job: Error: cannot allocate vector of size 617.8 Mb. Any idea of why? Is there a limit on the input size dataset? Thanks in advances, Rossella ------------------------------------------------------ Rossella Rispoli, High Throughput Screening Cancer Research UK 44 Lincoln's Inn fields London WC2A 3LY UK Tel No. +44 (0)207 269 3151 Fax No. +44 (0)207 269 3581 ------------------------------------------------------ NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103) A company limited by guarantee. Registered company in England and Wales (4325234) and the Isle of Man (5713F). Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.

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strange issue with .RData files
by Lukasse, Pieter 07 Nov '14

07 Nov '14

Hi, When I upload any .RData file to my Galaxy server it seems to be unpacking/changing it. The resulting file in my history is different and around 2x larger than the uploaded file. The tool that needs to use it also aborts with an error due to this erroneous file. What are the workarounds? 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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Integrating Docker-based tools within Galaxy failed
by Weiyan Shen 06 Nov '14

06 Nov '14

Hi, I integrated Docker-based tools‍ SMALT whin my local Galaxy by the guid:https://github.com/apetkau/galaxy-hackathon-2014/tree/master/smalt, I found my Galaxy failed to integrate‍ with my docker. My docker images‍: => docker images REPOSITORY TAG IMAGE ID CREATED VIRTUAL SIZE smalt-galaxy shenweiyan bae67dfe69b5 2 hours ago 401.9 MB ubuntu 14.04 5506de2b643b 12 days ago 197.8 MB fedora latest 7d3f07f8de5f 4 weeks ago 374.1 MB‍ My job_conf.xml‍: => cat job_conf.xml <?xml version="1.0"?>  <job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> </plugins> <handlers> <handler id="main"/> </handlers> <destinations default="docker_local"> <destination id="local" runner="local"/> <destination id="docker_local" runner="local"> <param id="smalt-galaxy">true</param> </destination> </destinations> </job_conf>‍ SMALT can run successfuly by the command line: $ docker run -v /App/Docker/smalt:/App/Docker/smalt:rw -w /App/Docker/smalt -i -t smalt-galaxy:shenweiyan smalt_wrapper.py -r /App/Docker/smalt/reference -f /App/Docker/smalt/reads.fastq -u /App/Docker/smalt/smalt.out‍ The SMALT in my Galaxy seems to work with my local samlt_x86_64 only,rather than in my smalt-galaxy image . Could you give me some advices on how to solve these problems? Thanks very much! ‍ Best regards Weiyan Shen‍

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Unable to connect two tools in workflow editor
by David Kelly 05 Nov '14

05 Nov '14

Hello, I'm working with two custom tools in my local galaxy instance: The first tool outputs a single aceb file. aceb is a custom datatype I've added that describes a crop experiment. The second tool takes three files as inputs, one of which is an aceb file. I can successfully run these two tools together in Galaxy outside of a workflow. But for some strange reason I cannot connect these two tools in the workflow editor. The connection never turns green and links. Here are the relevant lines in the tool wrappers: Outputs of first tool: <outputs> <data format="aceb" name="acebData" label="Experiment data with unified format" /> </outputs> Inputs of second tool: <inputs> <param name="acebData" type="data" format="aceb" label="Inut Survey aceb Data" /> <param name="domeData" type="data" format="dome" label="Input Strategy DOME Data" /> <param name="linkData" type="data" format="txt" label="Input Linkage between field overlay and survey" /> </inputs> Any ideas for what could be causing this? Thanks. David

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galaxy-dev November 2014