galaxy-user April 2014

galaxy-user@lists.galaxyproject.org

25 participants
31 discussions

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-user April 2014