- galaxy-user - lists.galaxyproject.org

Installing new tools from the tool shed
by David Joly 13 Feb '13

13 Feb '13

Hi! Ok, I know many people had the same issue, but I just can't figure what's going on. I'm quite new about using a local instance of Galaxy and I'm trying to figure how to install a tool from the tool shed. Reading the tutorial (Installing Galaxy tool shed repository tools into a local Galaxy instance) looked pretty simple, but maybe I missed something. First, I modified the universe_wsgi.ini file by removing the "#" before the tool_config_file and tool_path lines. Then, I created a shed_tools folder in my $HOME directory before modifying the shed_tool_conf.xml file <?xml version="1.0"?> <toolbox tool_path="$HOME/shed_tools"> </toolbox> Finally, I log as the Admin, and select "Search and browse tool sheds", select one tool (trinityrnaseq for example), click "Preview and install" and then "Install to Galaxy". However, that's where I get an error message: The tool_config_file setting in universe_wsgi.ini must include at least one shed tool configuration file name with a <toolbox> tag that includes a tool_path attribute value which is a directory relative to the Galaxy installation directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name shed_tool_conf.xml whose <toolbox> tag is <toolbox tool+path="..shed_tools">). Any idea? Thanks, DJ

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Reference Genome in Lastz
by Murphy, Caitlin N 13 Feb '13

13 Feb '13

I'm trying to map a series of short sequencing reads from a clinical isolate of Klebsiella pneumoniae to the Klebsiella pneumoniae MGH 78578 genome which is found on NCBI. This reference genome is not listed under mapping Lastz, which it says I should contact the galaxy team if that is the case. I'm new at all this and trying to upload the reference genome myself, but I am new at all this and any help would be amazing. Thanks, Caitlin Murphy

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Galaxy on one computer not showing latest runs in history
by Dikla Aharonovich 13 Feb '13

13 Feb '13

Hi I am running galaxy and am working both from home and work. Last night at home, my history had up to 35 items in it, that all ran. At work today, I can only see 30. This includes number 27 in my history, which shows that it is still running, while I already saw the results for it at home last night. I tried logging in and out, and pressing the refresh button. Please let me know what else may be causing this Many thanks, Dikla

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hg19 reference gnome for Tophat2
by Sachit Adhikari 13 Feb '13

13 Feb '13

I downloaded the entire directory of UCSC for the reference gnome of Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference gnome. I found a directory: Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index with the files: genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2 genome.rev.1.bt2 genome.rev.2.bt2 While adding the reference gnome, I need to edit bowtie2_indices.loc Shall I replace: /orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 with hg19 hg19 hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index Thanks, Sachit

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cufflinks output for cummeRbund
by Mike Shamblott 12 Feb '13

12 Feb '13

I have been using cufflinks on Galaxy Main. I have downloaded the files generated but they do not correspond to the file names expected by cummeRbund. For example: cummeRbund expects 4 tracking files (e.g isoforms.fpkm_tracking) , 4 .diff files (e.g isoform_exp.diff). Here is a trimmed version of the output I download, grouped by what Im guessing is the tracking, diff and usage files: TRACKING ...Galaxy109_transcript_FPKM_tracking.tabular ...Galaxy107_gene_FPKM_tracking.tabular ...Galaxy105_TSS_groups_FPKM_tracking.tabular ...Galaxy103_CDS_FPKM_tracking.tabular .DIFF ...Galaxy108_transcript_differential_expression_testing.tabular ...Galaxy106_gene_differential_expression_testing.tabular ...Galaxy102_CDS_FPKM_differential_expression_testing.tabular USAGE ...Galaxy99_splicing_differential_expression_testing.tabular ...Galaxy100_promoters_differential_expression_testing.tabular ...Galaxy101_CDS_overloading_differential_expression_testing.tabular Given that cummeRbund is a common next step in the workflow, is there an option to save the output in the expected format, perhaps with a galaxy history number prepend? I'm not sure which files are to be renamed and to what name and it seems that one file is missing. If there were a cummeRbund implementation on Main it probably wouldn't matter as much but until that happens, I (and i'm guessing other newcomers) would appreciate the help! Thanks, mike

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Galaxy Join takes too long?
by Milad Bastami 12 Feb '13

12 Feb '13

I'm trying to joint two large intervals (one with 800,000 intervals and the other with about 350,000 intervals) using operates on intervals > join tool . I have no idea how long it should takes normaly. Two days have past and it is still runnig. Is there any limitation in file size for this tool? Any help would be appreciated. Regards, Milad Bastami PhD student of Medical Genetics Department of Medical Genetics Shahid Beheshti's university of Medical Science

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Discrepancy between Intersect and Join
by Aaron Quinlan 09 Feb '13

09 Feb '13

Dear list, I have a student that found an unexplained discrepancy between the results produced by the "Operate on Genomic Intervals" (OGI) intersect operation versus the OGI join operation. In particular, we know for certain that there are exactly 1105 intersection of at least 1bp between the two files we are testing, as we have confirmed this with our own bedtools and the ucsc table browser. An example intersection (intersecting positions: 10012008 - 10012013): file 1: chr1 10012008 10012021 5.6186 file 2: chr1 10011813 10012013 5_Strong_Enhancer 0 + 10011813 10012013 250,202,0 However, OGI intersect find 0 intersections between the files (settings: return overlapping intervals, >= 1bp). In an effort to make sure we didn't goof up on file formats (BED) or genome builds (hg19), we tested the exact same two files with the OGI join operation and found 1105 intersections as expected. I also tested the files with the bx-python bed_intersect.py and bed_intersect_basewise.py scripts and get the expected results. Does anyone have a suggestion for how to resolve this? Thanks for your help and for providing such a fantastic resource to the genomics community. Best, - Aaron quinlanlab.org

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Galaxy February 8, 2013 Distribution & News Brief
by Jennifer Jackson 09 Feb '13

09 Feb '13

Galaxy Feb 8, 2013 Distribution & News Brief <http://wiki.galaxyproject.org/News/2013_02_08_GalaxyNewsBrief> *Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2013_02_08> * *Highlights:* * /Improvements/ to our release process <http://wiki.galaxyproject.org/DevNewsBriefs/2013_02_08#Improvements_to_Rele…>. *Release tag must be used in the hg update command to upgrade*. More at *usegalaxy.org <http://wiki.galaxyproject.org/Admin/Get%20Galaxy>*. * Tool Shed /Complex repository dependencies/ <http://wiki.galaxyproject.org/DefiningRepositoryDependencies#Complex_reposi…> are introduced, streamlining core dependency use across individual tools. * Also updated in the Tool Shed: multiple repository installation, dependency installation (when defined), and many usability enhancements and fixes. * New /Bedgraph-to-bigwig/ <http://wiki.galaxyproject.org/Learn/Datatypes#BedGraph> tool plus /Filter/ tool updated. * /Workflows/ now include option to export an image and the core /Framework/ now allows more unified reference genome usage and access. * /Ten Community Pull-Requests/ incorporated, plus another contribution to the tool Shed, addressing general usability, API, tools, error handling, workflows, and more. Thanks!! * Review highlights from the latest monthly */Galaxy Update/* <http://wiki.galaxyproject.org/GalaxyUpdates> newsletter and Galaxy Project Stats <http://wiki.galaxyproject.org/Galaxy%20Project/Statistics>! * Plus bug fixes and related enhancements for visualizations, histories, workflows, and tools. *http://getgalaxy.org* *http://bitbucket.org/galaxy/galaxy-dist* *http://galaxy-dist.readthedocs.org * new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull $ hg update release_2013.02.08 To ensure that you continue to receive updates about *Galaxy Distributions and News Briefs* <http://wiki.galaxyproject.org/DevNewsBriefs>, be sure to subscribe to the Galaxy-Announce mailing list <http://wiki.galaxyproject.org/MailingLists#The_lists>, a low-volume list dedicated to News Items <http://wiki.galaxyproject.org/News> and priority messages from the Galaxy community <http://wiki.galaxyproject.org/Community> and project core team <http://wiki.galaxyproject.org/Galaxy%20Project>. /Thanks for using Galaxy,/ The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team>

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Why SGE needed for galaxy ?
by Zeeshan Ali Shah 08 Feb '13

08 Feb '13

Hi, It seems that cloud man need SGE for scaling . Does SGE need also when run cloud on private cloud ? Zeeshan

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gather results from multiple histories
by mark.rose＠syngenta.com 07 Feb '13

07 Feb '13

Hi All Let's say that I have results produced from a step in multiple different histories and that I now want to gather these results into a new history so that they can be joined. Is there a way to do this without exporting results to my desktop and then uploading? Thanks Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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