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Follow the 2011 Galaxy Community Conference on Twitter
by Dave Clements 24 May '11

24 May '11

Hello all, The 2011 Galaxy Community Conference starts in about 10 hours with the sold out Introduction to Galaxy session, and then gets fully rolling Wednesday morning with the main meeting. See the schedule ( http://galaxy.psu.edu/gcc2011/Programme.html) for full details. If you want to follow the meeting on Twitter, we are encouraging copious tweeting by participants using the #usegalaxy hashtag. You can follow at https://twitter.com/#!/search/%23usegalaxy or http://galaxy.psu.edu/gcc2011/Home.html In addition, NBIC, the conference host, is also sponsoring the videotaping of all 23 talks. These will be placed online after the conference and will be open to anyone. We have 148 registered attendees (about twice as many as last year) form 19 countries (6 continents!) Well over 100 different organizations will have representatives at the meeting. I'm expecting great things. Thanks, Dave C -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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(no subject)
by Aaron Jex 24 May '11

24 May '11

Hi, Can't seem to find an answer to this on your wiki site and it's not in the tutorial. I would like to filter my 454 reads for high quality regions, rename the resulting sequence fragments AND relink the new reads (fragments) to the original quality data so that I can take these filtered reads and assembly them using MIRA. Is there a way to do this with Galaxy? So basically all I want to do is take the new read fragments I get from converting the tabular file to the fasta file as shown in your metagenomics tutorial, and generate a corresponding qual file for these 'new' reads. Best regards, Aaron Aaron Jex, BSc, PhD Senior Research Officer, Department of Veterinary Science, The University of Melbourne, 250 Princes Highway, Werribee, Victoria, 3030 tel: +61 3 9731 2294

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May 20, 2011 Galaxy Development News Brief
by Jennifer Jackson 20 May '11

20 May '11

May 20, 2011 Galaxy Development News Brief http://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_… Prior releases: https:bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBriefs ------------ 2011_04_08 Highlights Picard FastQC NBIC Galaxy Hackathon Results Multiple-Input Workflows ------------ How to get this distribution https:bitbucket.org/galaxy/galaxy-dist/ new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r 8c11dd28a3cf ------------ Key Upcoming Galaxy Event: GCC 2011 May 24-26, 2011 Galaxy Community Conference Lunteren, The Netherlands http://galaxy.psu.edu/gcc2011 ------------ What's New = NBIC Galaxy Hackathon Results = Two new features (so far) were created and added to Galaxy from the May conference. Hackaton: tool_conf.xml Autogeneration Work from the NBIC Galaxy Hackathon by Rob Hooft, Henk van den Toorn, and Wil Koetsier which adds new optional tags to tool configuration files, and a script which uses these tags to automatically generate tool_conf.xml. The scripts can be found at: * scripts/build_toolbox.py * scripts/extract_toolbox_sections.py Documentation on the new XML tags and how to use the scripts has not yet been prepared. Hackathon: Tool Tags Work from the NBIC Galaxy Hackathon by Freek de Bruijn, Alex Bossers, and Nate Coraor which enables associating tags with tools. This feature requires 'enable_tool_tags = True' since there are some inefficient database operations performed during tool loading to support this feature. Tool authors can specify tags directly in tool configuration files with the new optional <tags> tagset: <tags> <tag>ngs</tag> <tag>mapping</tag> </tags> If used with the tool_conf.xml autogeneration scripts, this will create <tool> tags containing a new "tags" attribute: <tool file="example/example.xml" tags="ngs,mapping"/> Upon startup, Galaxy associates these tags with the tools and presents them in a cloud at the top of the tool menu when unhidden via the tool panel's "Options" menu. = Picard = http://picard.sourceforge.net|http://picard.sourceforge.net New Galaxy tools wrapping the most commonly used **Picard** functions related to metrics and repair of mapped short read sequencing. Metrics include * BAM index statistics (count of mapped reads by reference chromosome) * Alignment summary * Hybrid selection (for targeted data) * Insert size (for paired reads) * Library complexity Repair tools include * Fix mate pair, mark optical/pcr duplicates * Add or replace read groups * SAM/BAM: replace headers and/or reorder based on a different reference = FastQC = http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/|http://www.bioinform… New tool wrapper generates a comprehensive and useful QC report. Inputs and Outputs * This wrapper will accept any FASTQ, SAM, or BAM file as primary input. It will also take an optional file containing a list of contaminants information, in the form of a tab-delimited file with 2 columns, name and sequence. * The tool produces a single HTML output file that contains all of the results, including the following basic statistics: ** Per base sequence quality ** Per sequence quality scores ** Per base sequence content ** Per base GC content ** Per sequence GC content ** Per base N content ** Sequence Length Distribution ** Sequence Duplication Levels ** Overrepresented sequences http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011… = Workflows & Multiple datasets = Workflows can now be run on multiple datasets at the same time. The run workflow page will now show a new stacked dataset icon. http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011… Upon clicking that, the selection box changes to a multi-select, and an independent workflow execution will occur for each of these input dataset steps. The rest of the parameters of the workflow will be identical. Combining this functionality with the existing "Send results to a new history" option will send the results of *each* workflow execution to a separate history, numbered sequentially "<name> 1", "<name> 2", etc., where <name> is whatever text you put in the new history name box. http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011… Please note that this new type of "multiple-input dataset" step can currently be used only once in any individual workflow. ------------ Updated & Improved = Current Tools = * BAM to SAM tool can now optionally output headers. * GFF,GFF3,GTF related ** Gracefully handle parsing errors in GFFReader and accurately compute raw size of GFF features. ** Enable GFF and GFF3 attributes to be written in GTF format. ** Make Operate on Genomic Intervals (GOPS) intersect and subtract tools compatible with GFF features rather than GFF lines. ** Enable GFF filter attributes tool to accept arbitrary conditions. * Datasource tools: Remove hard-coded special-case handling of UCSC Table Browser and GBrowse datasource tools; functionality remains, but is now a part of the individual tool's XML configuration files. Auto-detect is now available by providing data_type=auto parameters. * Make Cufflinks, Cuffcompare, and Cuffdiff wrappers compatible with v1.0.1 (new option implementation pending). * BWA wrapper enhancement ** The Galaxy BWA wrappers (for Illumina and for SOLiD) were updated for version 0.5.9 of BWA. Three new options have been added to them: Maximum number of alignments to output in the XA tag for reads paired properly (samse/sampe -n); Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons) (sampe -N); and Specify the read group (samse/sampe -r). ** If read groups are to be specified, the following aspects MUST be set: *** Read group identifier (ID) *** Library name *** Platform/technology used to produce the reads sample ** And the following can be set: *** Sequencing center that produced the read *** Description *** Date that run was produced *** Flow order *** Array of nucleotide bases that correspond to the key sequence of each read *** Programs used for processing the read group *** Predicted median insert size *** Platform unit ** Formerly, when sampse/sampe -n was specified, it would cause BWA to output a format other than SAM. This is no longer the case. The BWA manual can be found at http://bio-bwa.sourceforge.net/bwa.shtml|http://bio-bwa.sourceforge.net/bwa… * SAM header ** For several wrappers where SAM header suppression was optional (BWA, BFAST, Bowtie, SRMA), the default was changed to NOT suppress, however it is still optional. ** Bam-to-sam now keeps the header in the BAM file. * Setting of output dbkey ** Outputs for the following now are correctly set to the relevant dbkey (for reference dbkey whether using built-in or one from history): Freebayes, SRMA, Mosaik, BFAST, Bowtie, BWA, sam-to-bam, and bam-to-sam. = New Tools = * GATK ** note: These tool integrations should be considered alpha. Changes are not necessarily backwards-compatible with workflows or re-run functionality. ** Realigner Target Creator ** Indel Realigner ** Count Covariates ** Table Recalibration ** Analyze Covariates ** Unified Genotyper * Add tool Filter GTF by attribute values list. Tool filters a GTF based on a list of attribute values. The tool is especially useful as a downstream analysis tool for filtering GTF files based on Cuffdiff outputs. = Trackster = * Greatly improve LineTrack performance to fetch optimal amount of data for display. * Add support for Operate on Genomic Intervals (GOPS) intersect and subtract tool. * Enable users not logged in to use tools in shared visualizations. * Add support for static tool select parameters. * Enable datasets that cannot be indexed to be used as tool inputs. * Ensure that reads are drawn in squish and pack modes even when view area is large by setting a minimum width of 1px. * Add histogram mode to feature tracks so that user can generate coverage histogram at any level of data. * Use user preferences when drawing summary tree. * Enable a tool to be run on complete dataset or a visible region. = User Interface (UI) = * Show rerun and info buttons in dataset previews for additional states (e.g. running, queued). * Show details button functional for all tools run within a history, even if currently retired. * Show inheritance chain for datasets expanded to note if source was another history or a library. = CloudMan = * Cloud instance sharing: now share your entire cloud instance deployment (including data, analyses, and/or customizations) with the world or specific users with a click of a button. http://bytebucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011… = Source = * Reserved/predefined tool template values ** Tool command line templates may make use of certain variables pre-defined by the Galaxy framework. Some of these already existed but were undocumented. All have been changed to use a common (pythonic) naming scheme, but the old names are retained for backwards compatibility: *** new name = old name (if any) = value description *** __new_file_path__ = universe_wsgi.ini new_file_path value *** __tool_data_path__ = GALAXY_DATA_INDEX_DIR = universe_wsgi.ini tool_data_path value *** __root_dir__ = GALAXY_ROOT_DIR = Top-level Galaxy source directory made absolute via os.path.abspath() *** __datatypes_config__ = GALAXY_DATATYPES_CONF_FILE = universe_wsgi.ini datatypes_config value *** __user_id__ = userId = Email's numeric ID (id column of galaxy_user table in the database) *** __user_email__ = userEmail = User's email address *** __app__ = The galaxy.app.UniverseApplication instance, gives access to *** __app__.config and much more. Should be used as a last resort, may go away in future releases. = Tool Framework = * When label text for a static option in a SelectToolParameter is not provided, default to using the 'value'. * Fix for dynamic options when referencing a DataToolParameter that has already been wrapped. * Only allow a user to rerun if they have access permissions on the dataset. = Test Framework = * Add a "contains" compare type to functional tests. Enables simple checking for substrings in a test output file, on a line-by-line basis. * Fix for expand grouping to allow toolbox tests to use the default parameter value. = Bug Fixes = * Have MACS peak caller wrapper use return code to set error state. Fixes issues seen when MACS was be green, despite encountering fatal errors. * Fix hyperlinks in Cuffcompare and Cuffdiff documentation. * Add support for comment handling to gff_to_interval_index tool. * Workflow Parameter bugfix for the improperly handled case when a parameter isn't used in any workflow step, but should still be available for PJAs. * Bugfix for workflow run not reloading history. * SGE/DRMAA runners did not respect the value set in cluster_files_directory. * Galaxy did not set a public username when 'use_remote_user = True' and did not provide an interface to set it. Upon account creation, Galaxy will now automatically create a public username matching the username portion of the user's email address, with any non-alphanumeric characters replaced with a '-'. If the username is not unique, a '1' is appended, and then incremented until the username is unique. Users may modify their public username via the User menu in the masthead. ------------ = About Galaxy = The Galaxy team is a part of http://www.bx.psu.edu/|BX at http://www.psu.edu/|Penn State, and the http://www.biology.emory.edu/|Biology and http://www.mathcs.emory.edu/|Mathematics and Computer Science departments at http://www.emory.edu/home/index.html|Emory University. Galaxy is supported in part by http://www.nsf.gov/|NSF, http://www.genome.gov/|NHGRI, the http://www.huck.psu.edu/|Huck Institutes of the Life Sciences, and http://www.ics.psu.edu/|The Institute for CyberScience at Penn State, and http://www.emory.edu/home/index.html|Emory University. http://bitbucket.org/galaxy/galaxy-central/wiki/GalaxyTeam|GalaxyTeam http://usegalaxy.org|Use Galaxy! http://galaxyproject.org|GalaxyProject.org Join us at Twitter #usegalaxy http://twitter.com/#!/search/galaxyproject|http://twitter.com/#!/search/gal… ------------ Galaxy Team

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Workflows with conditional statements
by Florent Angly 18 May '11

18 May '11

Hi all, I was wondering if there is a way to put conditional statements in a Galaxy workflow. This would be useful, for example, in the case of a workflow that has an optional advanced option that the user can click. This advanced option would add some extra steps to the data processing. Another example of how this could be useful is if inside a workflow, the data needs to be processed differently based on the results of previous workflow steps. Say, you have a worflow that takes some sequences, and calculate their average length. Using a conditional statement, the workflow would put the data through DeBruijn assembler if the reads are small, but through a traditional Overlap-Layout-Consensus assembler if the reads are long. Are conditional statements possible in Galaxy workflows and I just don't know how to use them? Best, Florent

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Calling SNP's
by sukeerthi teja Rallapalli 17 May '11

17 May '11

Hi, Is it possible to convert a fasta file to sam/bam format using galaxy. ? OR Is is possible to call SNP's using Blast 2.2.25 (Stand Alone Blast) Thank you Teja

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Reload ".loc" files without restarting the Galaxy server?
by Luobin Yang 17 May '11

17 May '11

Hi all, I am wondering if it's possible to to reload a ".loc" file without restarting the Galaxy server? Thanks, Luobin

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problem with filter RNA-seq
by shamsher jagat 17 May '11

17 May '11

I have tried to follow the steps: File 33 in my history is generated by using filter GTF data by attributes. Two files used were file 29 which is a splicing diff file filtered for yes and file 2 is combined GTF. I used TSS-id for filtering. the out put file file 32 is empty. Any suggestion? Jagat, It depends what filter tool you're using and what dataset you're filtering. There is a generic filter tool that can be used to filter Cuffdiff tabular files for either FPKM values and differential expression tests. There is also a tool for filtering GTF files based on a Cuffdiff expr dataset. It sounds like you may be confusing either the tools or the inputs. If after double-checking you're still having problems with filtering, please put together a short list of your analysis steps and share your history with me, and I can take a look. Thanks, J. Further to my question, It appear that there is some problem with the filter option: When I use the isoform/gene exp file as such it work fine but when I filter these files with either parameter such as status if test was successful or on p value it return me empty file. The way am saving the file is - expr file filter save as txt file and upload back in Galaxy. Any suggestion? Jagat

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Re: [galaxy-user] Calling SNP's
by Jennifer Jackson 16 May '11

16 May '11

Hello Teja, Exploring the "Pages" tutorials is recommended as many have SNP-specific analysis examples. I am not sure if your data is RNA or DNA or if you have quality scores available, but there are tutorials that cover most common-use cases. http://main.g2.bx.psu.edu/page/list_published It is recommended to start with these: http://main.g2.bx.psu.edu/u/aun1/p/screencasts http://main.g2.bx.psu.edu/u/james/p/exercises http://main.g2.bx.psu.edu/u/aun1/p/galaxy101 Good luck with your research! Best, Jen Galaxy team ps: For next time, please keep the galaxy-user cc so that our entire team can contribute to replies. This would be especially helpful when you have a new question. On 5/16/11 11:53 AM, sukeerthi teja Rallapalli wrote: > Jen, > > Thank you so much. In the NGS toolbox what option should i choose. > > Regards > Teja -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

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finding Conserved non coding region
by De Kumar, Bony 16 May '11

16 May '11

Hi all , I have a set of 1500 sequence obtained from my Chip_Seq experiment. I am interested to Know how many of them are within Conserved non coding Region. My definition of conserved Non coding region is as follows 1. Atleast a 200bp region with 80% conservation between Human , Mice and Chicken 2. Atleast a 200bp region with 70% conservation between Human , Mice , Chicken and Fish If someone can suggest me how to use galaxy for this purpose. Thanks in advance. Bony

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Phylogenetic tree viewer ?
by Luobin Yang 16 May '11

16 May '11

Hi, Do you guys know any phylogenetics tree viewer that works well with Galaxy system? Thanks, Luobin

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