galaxy-user April 2014

galaxy-user@lists.galaxyproject.org

25 participants
31 discussions

Galaxy 101 tutorial
by Carrie Gaut 21 Apr '14

21 Apr '14

I'm working my way through the Galaxy 101 tutorial. I've run into a discrepancy when trying to "Get Data" from the USC Main table browser. When trying to follow directions and choose the group, "variations and repeats," it doesn't exist. I can choose variations OR I can choose repeats. This makes several of the results not come out exactly as it shows they should and it makes steps further on in the tutorial confusing. For me to get the correct tutorial results, which should I choose? Variations or repeats? It may be that the tutorial was updated at some point but the tutorial directions and pictures were not. I hope I've posted this in the correct mailing list... Sincerely, Carrie Sent from my iPhone

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How many registered users are there at galaxy?
by Peng Yu 19 Apr '14

19 Apr '14

Hi, I'm wondering how many registered users there are at galaxy. Is there a way to check? Thanks. -- Regards, Peng

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bedtools error
by Tamara Simakova 16 Apr '14

16 Apr '14

Hello! I'm using BedTools on the main Galaxy server. I try to use multiinter function to compare two bed files, but there is an error in the resulted file. Some coordinates that are present in both files are marked as they present only in one file. The bed-files format is correct. What could be the problem? Thanks, Tamara Simakova

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Base Recalibration tool on usegalaxy
by KS 15 Apr '14

15 Apr '14

Dear all, I can't find either of Table Recalibration or Base Recalibrator on usegalaxy public server. I am defident this is right place to ask, but seqanswers is clouded with many other pipelines. Is there an update of base recalibration tool on usegalaxy? Best, Kaz

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April 14, 2014 Galaxy Distribution News Brief
by Jennifer Jackson 15 Apr '14

15 Apr '14

*April 14, 2013 Galaxy Distribution News Brief* Distribution Summary 2014_04_14 <https://wiki.galaxyproject.org/News/2014_04_14_Galaxy_Distribution> * Highlights:* * Visualization framework updates and Trackster updates * Tool Shed updates to repos, test frameworks, and documentation * Over 100 genomes with updated content on our rsync server * UI Dataset action controls expanded and overall unification of design * API functionality additions and new job control/admin abilities * Administrator, Configuration, Job control, and Egg features and updates * 18 new community contributions added Get Galaxy getgalaxy <http://getgalaxy.org/> *getgalaxy.org <http://wiki.galaxyproject.org/Admin/Get%20Galaxy>* *galaxy-dist.readthedocs.org <http://galaxy-dist.readthedocs.org/>* *bitbucket.org/galaxy/galaxy-dist <http://bitbucket.org/galaxy/galaxy-dist>* *new*: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable *upgrade*: $ hg pull $ hg update release_2014.04.14 Upgrades * *Review instructions for core build:Getting the Stable Distribution <http://getgalaxy.org/>* * *Review reset for Tool Shed repos:Resetting Metadata For Installed Repositories <http://wiki.galaxyproject.org/ResettingMetadataForInstalledRepositories>* Data 1. New and updated reference genomes added toRsych <https://wiki.galaxyproject.org/Admin/UseGalaxyRsync>server that mirrors contents of the public Mainhttp://usegalaxy.org <http://usegalaxy.org/>instance * New/updated genomes: 115 o includes hg38 o note: all available in tool "Extract Genomic DNA" * New bowtie indexes: 60 * New bowtie2 indexes: 115 * New BWA indexes: 54 * New lastz indexes: 54 * New sam indexes: 64 * New picard (srma) indexes: 59 * New liftOver mappings: 163 2. MAF hg19 100waymultiz conservation alignment sourced fromUCSC <http://genome.ucsc.edu/> 3. Replaced: The sam index for hg_g1k_b37 was updated to use "samtools faidx" with version 0.1.18 (original from GATK 1.4 bundle used 0.1.13). The older index lead to some issues with BAM<->SAM conversion using the newer SAMTools version. Visualizations 1. Framework tuninghttps://trello.com/c/kdhJ1Dit 2. /Trackster/: * Sow complete read/feature across tile boundaries, in all tileshttps://trello.com/c/Q03dC1QC * Better handling of deep coverage regions in read trackshttps://trello.com/c/TxxzqWNx Workflows 1. Prep for dataset collections: Refactor out common logic for running workflows across controllershttps://trello.com/c/pdGNjllH UI 1. New/Updated Dataset Action Controls: * Located at the top of the history pane * Ability to select: all, none, or check individual datasets * Actions: Hide, Unhide, Delete, Undelete, Permanently delete (Purge) * https://wiki.galaxyproject.org/Learn/Managing%20Datasets#Searching_Datasets * Additional actions pending review/implementation * https://trello.com/c/8gLGPzxV,https://trello.com/c/mq1m6X5M, 2. When multiple tool versions installed, default to the latest versionhttps://trello.com/c/zRBZ9nvD 3. Better handling when one of many versions of a tool repo is uninstalledhttps://trello.com/c/BmdG2201 4. Unify the places where histories are shown and used: UI view and in core codehttps://trello.com/c/7cN0nmKH 5. Configure workflow menu, improve buttons and stylinghttps://trello.com/c/xFzp3lt6 6. Handle disabled sessionStorage/localStorage more gracefully in the history panehttps://trello.com/c/V2VCxzmx 7. RemoveBaseViewfrom base-mvchttps://trello.com/c/xUV4qvIc 8. Do not serve non-HTML content that may containJavaScriptin such a way that web browsers execute ithttps://trello.com/c/G67ELiMI 9. There are now 2 interfaces to data libraries (the original and new Beta) and feedback is welcomedhttps://trello.com/c/d3muKvqr 10. Wiki page on how to compile the css.https://wiki.galaxyproject.org/Develop/CSShttps://trello.com/c/gLI6hUjN API 1. New functions: * Make histories importable and/or published via the API is now implimented (sharing with individual users a pending feature update)https://trello.com/c/Bcsadi1q * History export/importhttps://trello.com/c/qhu1KdWU * Ability to extract workflow from a history to workflowshttps://trello.com/c/ZTehdMZH 2. Improved history payload and returned error consistencyhttps://trello.com/c/fWC7WgQf 3. Checkftypeattribute (if defined) on test output datasetshttps://trello.com/c/hFFlM4gY 4. Published histories contents now fully accessible (no permissions issue)https://trello.com/c/KME3ZRRY 5. Correct exception formats used in history & HDAhttps://trello.com/c/bS9wY4Ri Core 1. Admin: History view, allow importing purged datasetshttps://trello.com/c/tbhpQdMF 2. Admin: User list, show 'activated' and 'create_time' columnshttps://trello.com/c/C6MhEHWo 3. Admin: Setting user quota at zero is now permitted (noZeroDivisionError <http://moinmo.in/ZeroDivisionError>)https://trello.com/c/38NoBtlL 4. Admin: Admin user now has permissions to copy datasets from any history to a libraryhttps://trello.com/c/Ed91qIUC 5. Admin: Improvements to 'Impersonate User' implementationhttps://trello.com/c/lny2me4u 6. Config: Renametool-data/shared/ucsc/ucsc_build_sites.txttoucsc_build_sites.txt.sample 7. Jobs: Prevent 'unicode' strings being sent to pbs library as hostnamehttps://trello.com/c/NlFXYDta 8. Jobs: Fix Torque CLI runner to recognize complete ('C') state as 'ok'https://trello.com/c/vSO52k17 9. Jobs: Are now cancelled if a running history item is deleted (via API).https://trello.com/c/PDmUdtbw 10. LWR: Several updates including communication via message queue, more plannedhttps://trello.com/c/6DcXqXNt 11. LWR: Introduce and extend along withComputeEnvironment, to eliminate string based path rewritinghttps://trello.com/c/dL0poowc 12. Egg Update: Guppy 0.1.9+https://trello.com/c/zeSnHEav 13. Egg Update: Boto 2.25 to facilitate launching into VPChttps://trello.com/c/QXfJQhlS 14. Egg Addition: PyYAML 3.10 to be used initially withCloudlaunchfor parsingpersistent_data yamlhttps://trello.com/c/JMZkqBtH 15. Lib: package_libpng_1_6_7 deprecated, replaced with package_libpng_1_6_8https://trello.com/c/Wr5U8laVhttps://trello.com/c/65DOL… Pull Requests Merged Thanks to our Galaxy community contributors! 1. 309 - Job module for API (list and inspect jobs). Kyle Ellrott.https://trello.com/c/s2Gk6QlH 2. 312 - Remove unused imports and unused variables. Fix spacing. Nicola Soranzo.https://trello.com/c/iWaf1ak4 3. 316 - Fixing non-string parameter selection for job searches. Kyle Ellrott.https://trello.com/c/ZXZ9lEkN 4. 317 - Web API: safer and cleaner workflow parameter passing. Simone Leo.https://trello.com/c/JaC2EBM8 5. 318 - Adding deleted field to 'to_dict' and search selection of Workflows. Kyle Ellrott.https://trello.com/c/lv9q67nF 6. 315 - Allow jobs to be filtered by tool_id and history_id as well as by state. The tool_id is compared with the like operator. James Johnsonhttps://trello.com/c/dvLvPUmK 7. 322 - Added "ignore lines starting with specific characters" to group tool. Clayton Turner.https://trello.com/c/j6TP6M7m 8. 323 - API methods to access Workflow Usage. Kyle Ellrott.https://trello.com/c/UetzHj64 9. 325 - Useplaceholderinstead ofvaluein html5 - editor.mako. Trevor Wennblom.https://trello.com/c/PIZAXsOS 10. 326 - Specify third-party cookies must not be blocked - repository.py. Trevor Wennblom.https://trello.com/c/XsAUr6wl 11. 331 - Code housekeeping: standardize whitespace in various locations. Trevor Wennblom.https://trello.com/c/WtWdxP2n 12. 341 - Workflows API enhancements (pull request #337 corrected). Nicola Soranzo and Simone Leo.https://trello.com/c/zizGdqy1 13. 338 - Patch to expose the actual dataset id in the LDDA and HDA to_dict calls (in addition to the instance id). Kyle Ellrotthttps://trello.com/c/BrOscqTJ 14. 339 - Strip trailing slashes in tool IDs. Björn Grüning.https://trello.com/c/bpKNn66u 15. 334 - Optional Input Datasets Not Compatible with Parallelism Tag. Michael Lihttps://trello.com/c/WMgr8Xx0https://trello.com/c/Muw6fd8h 16. 346 - Tool panel label bug correction. Nicola Soranzo.https://trello.com/c/8NpgYM3U 17. 353 - Add BCF datatype sniffing, so BCF files are not uncompressed during upload. Nicola Soranzo.https://trello.com/c/FVKZhlsU 18. 355 - Workflow API: show also workflow owner, so a user can check it before importing. Nicola Soranzo.https://trello.com/c/cMiaYcCI Fixes 1. Fix issue with tool panel display when the tool_conf.xml has only a single entryhttps://trello.com/c/6nJIhOdJ 2. Fix issue when multiple versions of the same tool installed results in separate entries in the tool panelhttps://trello.com/c/SlNI79mR 3. Fix Published Page's JS errorhttps://trello.com/c/yGw1DwwM 4. Fix error in Babel egg utf-8, OSX 10.7https://trello.com/c/PUdh6SWw 5. Fix failures when using unicode in History name editable_text fieldshttps://trello.com/c/MTdotrHR 6. Fix tool form image display for toolshed installed toolshttps://trello.com/c/5G6jlB4B 7. Fix to improve link format in user activation emailshttps://trello.com/c/JALX9DL3 8. Fix problem with rerun of tools havingDataToolParameter <http://moinmo.in/DataToolParameter>set as optionalhttps://trello.com/c/pzHcSGzK 9. Fix bug in Tool Panel when installing repositorieshttps://trello.com/c/AiUefffC Tool Shed Documentation 1. Reorganization of the Tool Shed wiki is underway! See current changeshttps://wiki.galaxyproject.org/ToolShedand what is next uphttps://trello.com/c/Gg0jnll7 2. Data Manager documentation specific to toolshedhttp://wiki.galaxyproject.org/Tool%20Shed#The_contents_of_your_tool… Repositories 1. New Tool Shed categorieshttps://trello.com/c/niCdaARH * Genome-Wide Association Study * Imaging * RNA 2. Eliminate the use of fabric as the installation process for repositorieshttps://trello.com/c/zJoRROvv 3. Enhancements for updating a repositoryhttps://trello.com/c/c4Y9t7db * Will now trigger the install of new dependencies * Handles newly defined repository dependencies included in updates to installed repositories 4. Add support for the new repository type: Repository suite definitionhttps://trello.com/c/sxXMmfLs 5. Defined a base set of utilities that can be expected to be on systems into which tool dependencies are being installedhttps://trello.com/c/gYlRdqwr, related to project-in-planninghttps://trello.com/c/7VTlX9rD 6. Dependency ez_setup.py added to keep package_pysam_0_7_7 from failing on tool shedhttps://trello.com/c/AkACDWix 7. Update Main Tool Shed Picard repo that contained invalid toolshttps://trello.com/c/mxxHWxLY 8. UpdateFreeBayesrepo so that it specifies precompiled binaries in dependency definitionhttps://trello.com/c/zYoVHKoV 9. Update EMBOSS repo so that it downloads a precompiled platform-specific binaryhttps://trello.com/c/iW3Amhl5 Install and Test Framework 1. Tool shed install and test framework now works with API driven tool testshttps://trello.com/c/vfr7b0VK 2. Test script to provide coverage for recently discovered scenario that produced a white ghost upon Galaxy installhttps://trello.com/c/JICmJueB 3. Test script to provide coverage for recently introduced repository administration featurehttps://trello.com/c/vjTrhIST 4. Test script to check toolshed dependency files for broken/invalid download URLshttps://trello.com/c/i4GVgZwS Tool Shed Fixes 1. Fix setup_r_environment broken in central repohttps://trello.com/c/zyCzlgzo 2. Fix scenario where by uninstalling and reinstalling a repository that has been updated creates database entries for repositories that are persistently in the New statehttps://trello.com/c/iUDUM4Ut 3. Fixes in automated test frameworkhttps://trello.com/c/QWgsgll8 4. Fix bug in install and test framework related to samtools migrationhttps://trello.com/c/sN2iLCCn Project Updates 1. News <http://wiki.galaxyproject.org/News> 2. Events <http://wiki.galaxyproject.org/Events> 3. Videos on Vimeo <https://vimeo.com/galaxyproject> 4. /April 2014 Galaxy Update <http://wiki.galaxyproject.org/GalaxyUpdates/2014_04>/ 5. /March 2014 Galaxy Update <http://wiki.galaxyproject.org/GalaxyUpdates/2014_03>/ ------------------------------------------------------------------------ About *GalaxyProject.org <http://galaxyproject.org/>* The*Galaxy Team <http://wiki.galaxyproject.org/GalaxyTeam>*is a part of the*Center for Comparative Genomics and Bioinformatics <http://www.bx.psu.edu/>*at*Penn State <http://www.psu.edu/>*, and the*Department of Biology <http://www.bio.jhu.edu/>*at*Johns Hopkinis University <http://www.jhu.edu/>*. *Galaxy <http://usegalaxy.org/>*is supported in part by*NSF <http://www.nsf.gov/>*,*NHGRI <http://www.genome.gov/>*, the*Huck Institutes of the Life Sciences <http://www.huck.psu.edu/>*, and*The Institute for CyberScience at Penn State <http://www.ics.psu.edu/>*, and*Johns Hopkins University <http://www.jhu.edu/>*. The/public Main instance <https://wiki.galaxyproject.org/Main>/of*Galaxy*at*http://usegalaxy.org <http://usegalaxy.org/>*utilizes infrastructure generously provided by the*iPlant Collaborative <http://www.iplantcollaborative.org/>*at the*Texas Advanced Computing Center <https://www.tacc.utexas.edu/>*, with support from the*National Science Foundation <http://www.nsf.gov/>*. Follow us on*Twitter@galaxyproject <http://twitter.com/galaxyproject>*or read our tweets at*Galaxy on Twitter <https://wiki.galaxyproject.org/GalaxyOnTwitter>* Have a suggestion? Please see*Using the Galaxy Issue Board <http://wiki.galaxyproject.org/Issues>*, and be sure to up vote the issues important to YOU. -- Jennifer Hillman-Jackson http://galaxyproject.org

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trouble visualizing data
by Jennifer Jackson 12 Apr '14

12 Apr '14

Hi Lindsey, I see a few potential problem areas here. Double check these things: 1. when uploading, if the files are over 2G, or close to that, use FTP instead of a browser upload. Here is how: https://wiki.galaxyproject.org/FTPUpload 2. do not use the option to convert spaces to tabs. I doubt this does anything to a compressed format like BAM, but you almost never want to use this. Really is only for hand entered or pasted in data. 3. Try to convert the file to SAM to see if that functions. This will do two things: confirm basic BAM format is intact and permit you to examine the sequence identifiers on the header. Or try a tool like Picard's 'BAM Index Statistics'. 4. There could be an identifier mismatch problem between your data and our internal reference genome. The only ways to check are to either run some type of job that will list out our genome's sequences in the UI (like a small mapping job that creates a Galaxy-native BAM/SAM file) or obtain our version of the genome by rysnc and compare your files against it locally (before uploading to Galaxy). Both have advantages. The rsync server instructions are here, and I happened to use the genome question from yesterday to fill in the example last night, so you have near-exact instructions! https://wiki.galaxyproject.org/Admin/UseGalaxyRsync 5. If all else fails, consider loading the genome that you used to do the mapping up to Galaxy as a Custom reference genome: https://wiki.galaxyproject.org/Support#Custom_reference_genome https://wiki.galaxyproject.org/Support#Reference_genomes There have been some UI delays, but these are transient. Resubmitting the action has been working, so try that if buttons do not respond the first time. Let us know if you continue to have problems, Jen Galaxy team On 4/11/14 9:20 AM, Lindsey Fallis wrote: > Hi Jennifer, > > I’m a post doc working with Brenda Oppert (she contacted you yesterday with some problems). I too have been having some problems getting visualizations to work. My goal is to show the Tribolium genome as a Circster plot with my RNA-seq data laid on top. My RNA-seq data is currently in .bam format. So far what I have a attempted to do is upload my .bam files into Galaxy using the Get Data, upload file from computer functions. Then I choose my file, check the ‘convert spaces to tabs’ box and set the genome to Tcas. It uploads correctly. Then I ask it to visualize as Circster and nothing happens… Then I tried viewing in trackster and nothing happens OR I get an error message saying one of my sequences isn’t in the genome file. Any suggestions to get the visualizations to work so that I have the Tcas chromosomes as the Circster backbone and my RNA-seq data showing around it? > > Thank you! > Lindsey > > > -- Jennifer Hillman-Jackson http://galaxyproject.org

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trouble visualizing data
by Jennifer Jackson 12 Apr '14

12 Apr '14

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Cuffdif output NOTEST
by Meike.Latz＠mdc-berlin.de 11 Apr '14

11 Apr '14

Dear all, I have Illumina RNAseq data and want to look for differences in gene expression between male and female rats and transgenic vs. wildtype; for each condition I have triplicates. I mapped with TopHat for Illumina, using the reference genome rn5 and default settings. I did Cuffdiff afterwards and used the GTF-file Rattus norvegicus.Rnor_5.0.72.gtf as transcript. As result I got no significant changes in expression and it always says "NO TEST" (or sometimes "LOW DATA"). I found that lowering or raising the -c option might control the cuffdiff behavior, but I do not know what it is and how to control it. Can you explain me how to do it? And would you advise me to use another transcript for Cuffdiff? And when yes, where can I get it? Lots of questions. Thanks in advance for your answer. Best, Meike

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Re: [galaxy-user] Add Tribolium genome
by Jennifer Jackson 11 Apr '14

11 Apr '14

Hi Brenda, The examples below are labeled by the tool/user interface location where the two menus are located. Which tool are you using under "Get Data"? Perhaps "UCSC Main"? Any tool other than "Upload File" accesses an external data source and the available data can vary. It is important to know that the data content included on externally hosted sites is managed by that sites owners. If you are using "Get Data -> UCSC Main", then you are correct in that they do not provide data for this genome, just the ones you list. When you do locate data for this species that you wish you use (try searching for "Tribolium castaneum" with the tool " EBI SRA ENA SRA"), and import it, the Galaxy locally cached reference genome for Tcas_3.0 is available with several, but not all, mapping tools. It is likely to be added to Bowtie2/Tophat2 sometime in the future. Thanks! Jen Galaxy team On 4/10/14 2:27 PM, Brenda Oppert wrote: > > Hi Jen, > > > When I go to "get data" and I put "insect" the only pull downs are > some Drosophila and Anopheles spp. Is it somewhere else? > > > Thanks, > > > Brenda > > ------------------------------------------------------------------------ > *From:* Jennifer Jackson <jen(a)bx.psu.edu> > *Sent:* Thursday, April 10, 2014 4:18 PM > *To:* Brenda Oppert; galaxy-user(a)lists.bx.psu.edu > *Subject:* Re: [galaxy-user] Add Tribolium genome > Hello Brenda, > > Are you working at http://usegalaxy.org? I just checked and it is > still there. Please give this another look. > > Thanks! > > Jen > Galaxy team > > > On "Get Data -> Upload File" tool: > > > Under "Edit Attributes" (found by clicking on a dataset's pencil icon): > > > On 4/10/14 11:06 AM, Brenda Oppert wrote: >> I thought that the genome sequence for Tribolium castaneum (Tcas3.0) was in the genome pull-down, but I don't see it. Can it be added? >> >> Thanks, >> >> Brenda >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org. Please keep all replies on the list by >> using "reply all" in your mail client. For discussion of >> local Galaxy instances and the Galaxy source code, please >> use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, >> please use the interface at: >> >> http://lists.bx.psu.edu/ >> >> To search Galaxy mailing lists use the unified search at: >> >> http://galaxyproject.org/search/mailinglists/ > > -- > Jennifer Hillman-Jackson > http://galaxyproject.org -- Jennifer Hillman-Jackson http://galaxyproject.org

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Add Tribolium genome
by Brenda Oppert 10 Apr '14

10 Apr '14

I thought that the genome sequence for Tribolium castaneum (Tcas3.0) was in the genome pull-down, but I don't see it. Can it be added? Thanks, Brenda

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galaxy-user April 2014