April 2014 - galaxy-user - lists.galaxyproject.org

Help with Summary Statistics
by D. A. Cowart 23 May '14

23 May '14

Hello, I am attempting to use Galaxy to calculate the mean sequence read length and identify the range of read lengths for my 454 data. The data has already been organized and sorted by species. The format of the data is as follows: >HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC >HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT etc...for each species I have attempted to use the "Summary Statistics" button, however it appears to only be for numerical data and not sequence data. Is this tool/task available via Galaxy? Thank you, Dominique Cowart User name: dac330

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When will megablast be working again
by Scott W. Tighe 28 Apr '14

28 Apr '14

Dear NCBI and Galaxy Team I have sent a note to determine when the Megablast option will be active again. Whether you use Galaxy or NCBI directly, it is inoperative. Scott -- Core Laboratory Research Staff Advanced Genome Technologies Core Deep Sequencing (MPS) Facility Vermont Cancer Center 149 Beaumont Ave University of Vermont HSRF 303 Burlington Vermont USA 05045 802-656-AGTC 802-999-6666 (cell)

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Megablast database identity
by Scott W. Tighe 28 Apr '14

28 Apr '14

Jennifer I am megablasting a simple 500,000 line dataset that is certainly in galaxy fasta. For a week i have been seeing numerous errors. So i have reprocesed the data multiple times. The error message is "could not find specified database directory" Is there an alternative approach? I did try ncbi directly and that failed too. They say they have a database issue Scott Tighe Core Laboratory Research Staff Advanced Genome Technologies Core Deep Sequencing (MPS) Facility Vermont Cancer Center 149 Beaumont Ave University of Vermont HSRF 303 Burlington Vermont USA 05045 802-656-AGTC 802-999-6666 (cell)

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"Intersect multiple sorted BED files" / tool-data/shared/ucsc/chrom/genome_test.len) could not be opened
by Sarah Maman 25 Apr '14

25 Apr '14

Hello, I try to use "Intersect multiple sorted BED files" tool without success. A genome_test have been added in galaxy (genome_test.len in galaxy-dist/tool-data/shared/ucsc/chrom/, .fa and .dict added in .loc fils in tool-data/) but "Intersect multiple sorted BED files" gives this error message : An error occurred running this job: /Epilog : job finished at lun. mars 24 15:55:04 CET 2014 Error: The requested genome file (/..../galaxy-dist/tool-data/shared/ucsc/chrom/genome_test.len) could not be opened. Exiting! So, /I have integrated the code modification submitted in Galaxy Central (https://bitbucket.org/galaxy/galaxy-central/commits/7105c53139d4b8649e6a371…): - chrom_info = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey ) + chrom_info = os.path.join( trans.app.config.len_file_path, "%s.len" % input_dbkey ) But I always have the same error message. Could you please help us ? Thanks in advance, Sarah // -- --*-- Sarah Maman INRA - GenPhySE - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*--

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BioStar integration - merging accounts
by Peter Cock 25 Apr '14

25 Apr '14

Hi all, I see that https://biostar.usegalaxy.org is live now, with lots of content mined from the galaxy-user mailing list (which may or may not result in this email starting a new question? We shall see...). Is it possible for an admin to merge accounts? e.g. there are all me: https://biostar.usegalaxy.org/u/333/ - old ISP based email address https://biostar.usegalaxy.org/u/337/ - old ISP based email address https://biostar.usegalaxy.org/u/394/ - my Google mail address Thanks, Peter

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'filter pileup' not working on 'generate pileup' output
by Matthew 25 Apr '14

25 Apr '14

I used Bowtie2 on a fastq file. Then, generate pileup on the output of Bowtie2. When I try to use 'Filter pileup', there is no file recognized as input even though I have the output from the 'Generate pileup'. Matthew

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Is the Server Down?
by Scott Tighe 25 Apr '14

25 Apr '14

Jennifer I have been trying to megablast some sequences for a few days now but it seems that the server is down. Can you advise? Scott -- Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core NextGen Sequencing/Flow Cytometry University of Vermont and Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2482 (AGTC)

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Announcing the Galaxy Biostar Forum
by Jennifer Jackson 23 Apr '14

23 Apr '14

Dear Galaxy Community, Galaxy has teamed up with Biostar to create a Galaxy User support forum at https://biostar.usegalaxy.org! We want to create a space where researchers using Galaxy can come together and share both scientific advice and practical tool help. Whether on usegalaxy.org, a Cloudman instance, or any other Galaxy, if you have something to say about Using Galaxy, this is the place to do it! Current integration with usegalaxy.org * We imported the whole history of galaxy-user(a)bx.psu.edu mailing list into Biostar * If you access Galaxy Biostar from usegalaxy.org (menu Help/Galaxy Biostar) you will be automatically logged in. * A Galaxy Biostar account will be created for you if it did not previously exist. To obtain this account’s password please use the password reset feature of Galaxy Biostar (https://biostar.usegalaxy.org/accounts/password/reset/). * When you have a question, search Biostar directly from any Galaxy tool page. Read more about how to get started at https://wiki.galaxyproject.org/Support/Biostar Roll-out phase * Galaxy Biostar is available at http://biostar.usegalaxy.org and will be our primary avenue for support * The galaxy-user(a)bx.psu.edu mailing list will continue to be supported during the transition but starting now please use the biostar.usegalaxy.org forum to ask all questions about using Galaxy. * Please do not double post to both Galaxy Biostar and galaxy-user(a)bx.psu.edu * Send us feedback through the forum's post "Welcome to Biostar" to tell us what you think. What’s next * Notice will be given when the galaxy-user(a)bx.psu.edu mailing list is retired. * Archives of galaxy-user(a)bx.psu.edu will remain accessible. We hope you will like the change and look forward to any feedback you may have. Thank you for using Galaxy! The Galaxy team

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Announcing the Galaxy Biostar Forum
by Jennifer Jackson 23 Apr '14

23 Apr '14

* Dear Galaxy Community, Galaxy has teamed up with Biostar to create a Galaxy User support forum at https://biostar.usegalaxy.org <https://biostar.usegalaxy.org/>! We want to create a space where researchers using Galaxy can come together and share both scientific advice and practical tool help. Whether on *usegalaxy.org <http://usegalaxy.org>*, a***<https://usegalaxy.org/cloud>**Cloudman <http://usegalaxy.org/cloud> *instance, or any other <https://wiki.galaxyproject.org/PublicGalaxyServers> *Galaxy <http://getgalaxy.org>*, if you have something to say about Using Galaxy, this is the place to do it! Current integration with usegalaxy.org * We imported the whole history of galaxy-user(a)bx.psu.edu mailing list into Biostar * If you access Galaxy Biostar from *usegalaxy.org* <http://usegalaxy.org> (Top*m*enu: "Help ->Galaxy Biostar")you will be automatically logged in. A Galaxy Biostar account will be created for you if it did not previously exist. To obtain this account's password please use the password reset feature of Galaxy Biostar (https://biostar.usegalaxy.org/accounts/password/reset/). * When you have a question, search Biostar directly from any Galaxy tool page. Read more about how to get startedat https://wiki.galaxyproject.org/Support/Biostar Roll-out phase * Galaxy Biostar is available at *http://biostar.usegalaxy.org*and will be our primary avenue for support * The galaxy-user(a)bx.psu.edu mailing list will continue to be supported during the transitionbut starting now please use the biostar.usegalaxy.org <http://biostar.usegalaxy.org>forumto ask all questions about using Galaxy. * Please do not double postto both Galaxy Biostar and galaxy-user(a)bx.psu.edu * Send us feedback through the forum's post *"Welcome to Biostar"* to tell us what you think. What's next * Notice will be given when the galaxy-user(a)bx.psu.edu mailing list is retired. * Archives of galaxy-user(a)bx.psu.edu will remain accessible. We hope you will like the change and look forward to any feedback you may have. Thank you for using Galaxy! *Galaxy Team <https://wiki.galaxyproject.org/GalaxyTeam>* *

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GCC2014 Poster Abstracts due April 25, THIS FRIDAY
by Dave Clements 21 Apr '14

21 Apr '14

Hello all, This is just a reminder that poster abstracts for the 2014 Galaxy Community Conference (GCC2014) *are due this Friday. * Abstracts can be submitted at https://wiki.galaxyproject.org/Events/GCC2014/Abstracts Note that posters are reviewed and accepted on a rolling basis, until all slots are full. The deadline is this Friday but sooner may be better. In other news: - We are delighted to have Steven Salzberg as the keynote speaker<https://wiki.galaxyproject.org/Events/GCC2014#Keynote_Speaker> . - Registration for the GCC2014 hackathon<https://wiki.galaxyproject.org/Events/GCC2014/Hackathon>is now open - Early registration<https://wiki.galaxyproject.org/Events/GCC2014/Register>for the GCC2014 Training Day and Meeting<https://wiki.galaxyproject.org/Events/GCC2014/Program>are also open - Abstracts <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts>for accepted talks will start showing up on the website this week. Thanks, and hope to see you in Baltimore, Dave C On Fri, Feb 14, 2014 at 1:33 PM, Dave Clements <clements(a)galaxyproject.org>wrote: > Hello all, > > *We are pleased to announce that Early Registration > <https://wiki.galaxyproject.org/Events/GCC2014/Register> and Talk and > Poster Abstract Submission > <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts> are now open for > the 2014 Galaxy Community Conference (GCC2014) > <https://wiki.galaxyproject.org/Events/GCC2014>.* > > GCC2014 <https://wiki.galaxyproject.org/Events/GCC2014> will be held at > the Homewood Campus<http://webapps.jhu.edu/jhuniverse/information_about_hopkins/campuses/homewo…>of Johns > Hopkins University <http://jhu.edu>, in Baltimore, Maryland<http://visitors.baltimorecity.gov/>, > United States, from June 30 through July 2, 2014. GCC2014<https://wiki.galaxyproject.org/Events/GCC2014>starts with a Training > Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> featuring > four *five* parallel tracks, each with three, two and half hour long > workshops. There are 13 different topics spanning the full Galactic > spectrum of topics. Take a look!<https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> > > *Early registration > <https://wiki.galaxyproject.org/Events/GCC2014/Register>* is now open. > Register early and *avoid paying 70% more for regular registration costs.* Early registration is very affordable, with combined registration (Training > Day <https://wiki.galaxyproject.org/Events/GCC2014/TrainingDay> + main > meeting) starting at $140 for post-docs and students. Registration is > capped this year at 250 participants, *and we expect to hit that limit*. > Registering early assures you a place at the conference and also a spot in > the Training Day workshops you want to attend. > > You can also book affordable conference housing at the same time you > register. See the conference Logistics page<https://wiki.galaxyproject.org/Events/GCC2014/Logistics>for details on this and other housing options. > > *Abstract submission > <https://wiki.galaxyproject.org/Events/GCC2014/Abstracts>* for both oral > presentations and posters is also open. Abstract submission for oral > presentations closes April 4, while poster submission closes April 25. > Poster authors will be notified of acceptance status within two weeks of > submission, while presentation authors will be notified no later than May2. > *Please consider presenting your work. If you are dealing with big > biological data, then this meeting wants to hear about your work.* > > The *GigaScience <http://www.gigasciencejournal.com/>* "Galaxy: Data > Intensive and Reproducible Research" series announced for the last > conference has published its first papers<http://www.gigasciencejournal.com/series/Galaxy>, > *and is continuing to take submissions for this year's meeting and beyond*. > BGI is also continuing to cover the article processing charges until the > end of the year, and for more information see their latest update<http://blogs.biomedcentral.com/gigablog/2014/02/06/rewarding-reproducibilit…>. > > > Thanks, and hope to see you in Baltimore! > > The GCC2014 Organizing Committee<https://wiki.galaxyproject.org/Events/GCC2014/Organizers> > > -- > http://galaxyproject.org/ > http://getgalaxy.org/ > http://usegalaxy.org/ > http://wiki.galaxyproject.org/ > -- http://galaxyproject.org/GCC2014 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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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 11 Apr '14

11 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 11 Apr '14

11 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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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 10 Apr '14

10 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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Can not delete data from my local galaxy
by Nishant THAKUR 10 Apr '14

10 Apr '14

Hello, I am using local galaxy server. I have disc storage problem and I noticed that galaxy is utilizing most of the space. I deleted old projects permanently, but they are appearing again in the saved history with one message which says "datasets were not removed from disk because that feature is not enabled in this Galaxy instance". Any suggestions how to enable this feature or delete dataset permanently from history. Galaxy installed on ubuntu 12.04 LTS, 3.5.0-44-generic, 64bit. Best regards Nishant Thakur

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server problem?
by Sarah Schaack 10 Apr '14

10 Apr '14

Hi there! I am teaching a workshop in East Africa, right this second, and we are trying to use a tool in galaxy (not too complex, files are not huge) to illustrate RNA-seq analysis. The server is SOOOOOOO slow-- is there a problem? Should we abandon ship and teach them Tophat using the command line? Please advise, at your earliest convenience-- I have a room full of impatient newbie hackers ;) Thank you! --Sarah **************************************** Sarah Schaack, PhD *Assistant Professor, Reed College* *Fulbright Scholar, Centre for Bioinformatics and Biotechnology, University of Nairobi**and Biosciences Eastern and Central Africa Hub, Int'l Livestock Research Institute* Email: schaackmobile(a)gmail.com Website: https://sites.google.com/site/schaackwork/ Phone (Kenya): +254 7 29 470 027 Workshop Info: https://sites.google.com/site/bioinfogenomicswrkshpea/

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Trackster error on dbkeys
by Aarthi Mohan 10 Apr '14

10 Apr '14

Hi all, I am setting up galaxy on a server running CentOS 6.5. I found that Trackster application hits me with an error "Could not load chroms for this dbkey: PF3D7", when I try "add new track" from Visualization. I am working with Plasmodium falciparum (PF3d7) genome, and I followed the instruction for setting visualization from " https://wiki.galaxyproject.org/Visualization%20Setup" and placed the 2bit, len files in the appropriate path. I have also made sure the genome build is present in the builds.txt under tool-data/shared/ucsc. For a test, I have the human chromosomes len files and Trackster loads it without any problem. Any suggestion would greatly help me. Thanks RT Log file: ----------- 127.0.0.1 - - [10/Apr/2014:12:29:44 +0800] "GET /visualization/trackster HTTP/1.1" 200 - "http://127.0.0.1:8081/" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" 127.0.0.1 - - [10/Apr/2014:12:29:45 +0800] "GET /api/genomes?chrom_info=True HTTP/1.1" 200 - " http://127.0.0.1:8081/visualization/trackster" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" 127.0.0.1 - - [10/Apr/2014:12:29:51 +0800] "GET /api/genomes/PF3D7?low=0&num=100 HTTP/1.1" 500 - " http://127.0.0.1:8081/visualization/trackster" "Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0" Error - <type 'exceptions.IndexError'>: list index out of range URL: http://127.0.0.1:8081/api/genomes/PF3D7?low=0&num=100 File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__ app_iter = self.application(environ, sr_checker) File '/data/maarthi/Galaxy/Test/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__ return self.application(environ, start_response) File '/data/maarthi/Galaxy/Test/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__ return self.handle_request( environ, start_response ) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request body = method( trans, **kwargs ) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 78 in decorator return to_json_string( func( self, trans, *args, **kwargs ) ) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/webapps/galaxy/api/genomes.py', line 42 in show rval = self.app.genomes.chroms( trans, dbkey=id, num=num, chrom=chrom, low=low ) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/visualization/genomes.py', line 292 in chroms rval = genome.to_dict( num=num, chrom=chrom, low=low ) File '/data/maarthi/Galaxy/Test/galaxy-dist/lib/galaxy/visualization/genomes.py', line 153 in to_dict chroms[ fields[0] ] = int( fields[1] ) IndexError: list index out of range CGI Variables ------------- CONTENT_LENGTH: '0' HTTP_ACCEPT: 'application/json, text/javascript, */*; q=0.01' HTTP_ACCEPT_ENCODING: 'gzip, deflate' HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5' HTTP_CONNECTION: 'keep-alive' HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603abc74375a63eca6a53211ad8efeb084140a6e95d9de0824b221b12b4bbc465351' HTTP_HOST: '127.0.0.1:8081' HTTP_REFERER: 'http://127.0.0.1:8081/visualization/trackster' HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64; rv:24.0) Gecko/20100101 Firefox/24.0' HTTP_X_REQUESTED_WITH: 'XMLHttpRequest' PATH_INFO: '/api/genomes/PF3D7' QUERY_STRING: 'low=0&num=100' REMOTE_ADDR: '127.0.0.1' REQUEST_METHOD: 'GET' SERVER_NAME: '0.0.0.0' SERVER_PORT: '8081' SERVER_PROTOCOL: 'HTTP/1.1' WSGI Variables -------------- application: <paste.recursive.RecursiveMiddleware object at 0x6b37cd0> is_api_request: True paste.cookies: (<SimpleCookie: galaxysession='c6ca0ddb55be603abc74375a63eca6a53211ad8efeb084140a6e95d9de0824b221b12b4bbc465351'>, 'galaxysession=c6ca0ddb55be603abc74375a63eca6a53211ad8efeb084140a6e95d9de0824b221b12b4bbc465351') paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x748eed0> paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x795c310> paste.parsed_querystring: ([('low', '0'), ('num', '100')], 'low=0&num=100') paste.recursive.forward: <paste.recursive.Forwarder from /> paste.recursive.include: <paste.recursive.Includer from /> paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from /> paste.recursive.script_name: '' paste.throw_errors: True request_id: 'c1be491ec06811e39ed60025905a9e10' webob._parsed_query_vars: (MultiDict([('low', '0'), ('num', '100')]), 'low=0&num=100') wsgi process: 'Multithreaded' ------------------------------------------------------------

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Re: [galaxy-user] Filtering PhiX
by Jennifer Jackson 08 Apr '14

08 Apr '14

Hi Scott, Sorry to hear that you are having trouble. These are exact match hits to both? Contamination isn't out of the question with public databases, but I would start with filtering results first to see if that helps. If you still have concerns, a test versus the line-command version is the definitive answer. As you may have seen on the public Galaxy instance, the Megablast tool happens to have the ' phiX174' genome as a specific target, so you could use that. Most NGS mappers have a custom reference database option (however not Megablast, for resource reasons) and a local/cloud Galaxy can be configured to use any Galaxy-wrapped mapper (there are many, check the tool shed). Combined, these provide many options. Please send "reply-all" to keep questions on list going forward. Thanks! Jen Galaxy team On 4/8/14 10:26 AM, Scott Tighe wrote: > Jennifer > > Not in the case of Megablast. So sounds like there is no PhiX filter. > Also I noticed that when I selected megablast, all the reads went to > Bovine, but when I hand selected from galaxy a bunch of the sequences, > that blasted (using NR) to Pseudomonas and other bacteria which is > correct. I think your Megablast is not working properly. > > > > Scott > > Scott Tighe > Senior Core Laboratory Research Staff > Advanced Genome Technologies Core > NextGen Sequencing/Flow Cytometry > University of Vermont and Vermont Cancer Center > 149 Beaumont ave > Health Science Research Facility 303/305 > Burlington Vermont 05405 > 802-656-2482 (AGTC) > > On 4/8/2014 10:23 AM, Jennifer Jackson wrote: >> Hi Scott, >> >> This genome is available in most mapping tools, so a positive match >> could be used to identify the control. But if you just want to leave >> it behind, control should fall out during mapping against the >> sample's target genome (if available). >> >> Best, >> >> Jen >> Galaxy team >> >> On 4/4/14 12:33 PM, Scott Tighe wrote: >>> Dear Team Galaxy >>> >>> Is there a simple way to filter PhiX control from a sample set? >>> >>> S >>> >> > -- Jennifer Hillman-Jackson http://galaxyproject.org

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Filtering PhiX
by Scott Tighe 08 Apr '14

08 Apr '14

Dear Team Galaxy Is there a simple way to filter PhiX control from a sample set? S -- Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core NextGen Sequencing/Flow Cytometry University of Vermont and Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2482 (AGTC)

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setting dbkey in a workflow
by William Holtz 07 Apr '14

07 Apr '14

I'm working on making my first workflow in Galaxy, using a local server. A high level overview of the workflow is: 1) take a fasta file as input with dbkey set to organism1 2) blast input fasta file against organism2 database 3) manipulate the blast output into bed format 4) extract genomic DNA from organism2 based on the bed data I can't find a way to set the dbkey on the bed data to organism2. This results in the extract genomic DNA step failing, as it seems to default to the only dbkey that exists in my workflow, the dbkey from the input fasta file. (The names and intervals are not present in the organism1 genome, and thus the extract step fails.) I have found that if I set my the dbkey of my input fasta file to be organism2 (even though the sequences contained in it are actually from organism1), then my workflow successfully completes with the desired output. But this is a bit of a hack. I'd like to share my workflow with some coworkers and make it as easy to use as possible. Therefore I don't want to have to explain this hack to them. Is it possible to set the dbkey within a workflow? thanks in advance for your help! -Will

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illogical results in Tophat2 analysis
by Si Naftaly 07 Apr '14

07 Apr '14

Hello, I used a Tophat 2 analysis and got 99.2% discordant in the summary, while in fact I checked the distance between the reads and got 170 with std of 35 (this is the data i filled in the Tophat2). Why did the Tophat2 test found 99.2% discordant when it should have been much lower? The starting reads was 16665209, in a Bowtie2 test i got a logical outcome of 16567482, while on the other hand i got from Tophat2 35066991 and 34816158 - not logical. I tried to do the same test number of times with another data and got resemblance in the results. In all of the tests in Tophat2 i got discordant 99% and higher. What am i doing wrong? What is the correct way to feed data into the test? Thank you Si.

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Invitation to connect on LinkedIn
by Zhandong Liu 07 Apr '14

07 Apr '14

LinkedIn ------------ I'd like to add you to my professional network on LinkedIn. - Zhandong Zhandong Liu Assistant professor at Baylor College of Medicine Greater Philadelphia Area Confirm that you know Zhandong Liu: https://www.linkedin.com/e/psdo7u-htpaphru-20/isd/5858801440302051328/NhMsq… -- You are receiving Invitation to Connect emails. Click to unsubscribe: http://www.linkedin.com/e/psdo7u-htpaphru-20/7wF3Dvdrn6R4dvztTwX5DLGm1Z4fwH… (c) 2012 LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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known name outputs shown in /database/files but not in galaxy windows
by ANGELICA GOMEZ ROIG 04 Apr '14

04 Apr '14

I have made a wrapper that has a tool that giving it an input file, gives you two output files with known extension: .gem and .log I call the tool with a python file, and I pass it the input file and the two output file names for galaxy to show them, but when I look into de database/files/000/ i get four files: dataset_54.dat (my first declared output that it's empty) dataset_54.dat.gem (the output that throws the tool) dataset_54.dat.log (the other output file that throws the tool) dataset_55.dat (my second declared output that it's empty) So,what I'm getting in the galaxy interface is _54.dat and _55.dat, both empty, instead of _54.dat.gem and _54.dat.log that are the good ones. How can I fix these? Thanks

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GMOD Online Training 2014
by Amelia Ireland 03 Apr '14

03 Apr '14

Greetings GMOD community! Applications are now open for the 2014 GMOD online training course, to be held from May 19th - 23rd 2014. The course will cover the installation, configuration, and usage of core GMOD software, including GBrowse and JBrowse, Galaxy, MAKER, Tripal, WebApollo, Canto, and the Chado database. The course is taught by experienced instructors and developers with deep knowledge of the tools. Although the course will be run online, students will be able to interact with the tutors and fellow attendees, ask questions, and so on. For more information and to apply, please see http://gmod.org/wiki/GMOD_Online_Training_2014 If you have any questions, please contact the GMOD help desk at help(a)gmod.org. Thanks! -- Amelia Ireland GMOD Community Support Generic Model Organism Database project http://gmod.org || @gmodproject

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question history
by Liesbeth Van Rompay 01 Apr '14

01 Apr '14

Hi, Although I am occupying 91% of my space on the Galaxy platform, since Galaxy was out, I cannot access my history anymore. No error message appears. What can I do? Best regards, Liesbeth

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galaxy-user April 2014