galaxy-user March 2014

galaxy-user@lists.galaxyproject.org

32 participants
34 discussions

upload data to galaxy using terminal
by do kadya 26 Mar '14

26 Mar '14

Hi, Can I upload data (mostly link the data) using terminal ? MuSiC 2 tool integration is not available in their website nor in tool shed. MuSiC 2 creates folder and files by itself, which is hard to track by Galaxy. So is there any way to link files to galaxy current work space so that I can link those distracted files which are created by MuSiC 2. ex: if you run music2 bmr calc-bmr file_of_input output is 3 files, ./file1.txt ./folder1/file2.txt ./folder2/file3.txt we can not mention that we need this output filename or save file at specific location, we can not give this option. Galaxy will not able to track this output, hence i have to do it manually. So is it possible to upload this files manually by terminal ? Waiting for positive reply. Thank You - Chetan

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GCC2014 Early Registration and Abstract Submission are now OPEN!
by Dave Clements 25 Mar '14

25 Mar '14

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/

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Output file to history
by Sebastian Luna Valero 21 Mar '14

21 Mar '14

Dear All, I am trying to add a new tool in Galaxy and I have the following problem. Let me explain a simplified example. Let's imagine that my script works from CLI as follows: python script.py --input "input-file" --pattern "output-pattern" After processing "input-file", the script writes several output files and their name is given according to "output-pattern". The number of output files depends on the content of "input-file". The output files are written to the current working directory where script.py is located. In the simplest scenario, I get only one output file in the working directory. My problem is that I would like to see the output files in Galaxy's history without modifying the CLI interface. To solve this problem, I have looked at the wiki page: https://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number… and the email here: http://dev.list.galaxyproject.org/Multiple-output-files-do-not-appear-in-hi… However, I think that mine is a different scenario. I do not want to add new output parameters in the CLI. I would like Galaxy to bring these output files to my history without modifying the CLI options, is that possible? Many thanks in advance for your help! Best regards, Sebastian.

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Usegalaxy.org network upgrade this Saturday
by Dave Clements 18 Mar '14

18 Mar '14

Hello all, Access to all TACC resources and services, including UseGalaxy.org<https://usegalaxy.org/>, will be unavailable between 9 a.m. - 5 p.m. (US Central Time) on Saturday, March 22. TACC staff will be performing an upgrade to the networking infrastructure. During this outage, users are encouraged to use the *50+ other public Galaxy servers <https://wiki.galaxyproject.org/PublicGalaxyServers>* that won't be affected by this upgrade. We apologize for any inconvenience this may cause you. Thanks, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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please unsubscribe
by Bogdan Tanasa 17 Mar '14

17 Mar '14

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Re: [galaxy-user] Exome seq work flow
by Mathew Bunj 17 Mar '14

17 Mar '14

No I have not received any feedback as yet. Thanks On Friday, March 14, 2014 7:42 AM, Kristin Kernohan <kristinkernohan(a)gmail.com> wrote: Hi did anyone answer this? Id be curious to know as well thanks Kristin On Thu, Mar 13, 2014 at 10:22 PM, Mathew Bunj <mathewbunj(a)yahoo.com> wrote: I was wondering if Galaxy has any work flow for calling mutations in Exome seq and then annotating. Alignment can be done by BWA. > > >Thanks > > >Mathew >___________________________________________________________ >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/ >

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Unsubscribe
by Elvio Pederzolli 14 Mar '14

14 Mar '14

Hi there can you please unsubscribe me from all Galaxy lists please Thank you Elvio Pederzolli Sent from my iPad

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Re: [galaxy-user] Data Uploading through FTP
by Martin Čech 14 Mar '14

14 Mar '14

Scott: 15GB file is a candidate for a FTP upload because web browsers can't usually handle this size. FTP server address is usegalaxy.org and credentials are the same you use for Galaxy (you have to use some other client outside of web browser to connect to this FTP server and upload this large file successfully e.gg FileZilla). After you finish uploading your file there you will see it in the upload tool (Get Data / Upload File) on Galaxy (when logged in). Then you will be able to start using it in history. There is an awesome screencast that shows the full process here: http://vimeo.com/75938324 Martin On Fri, Mar 14, 2014 at 1:48 PM, Scott Tighe <scott.tighe(a)uvm.edu> wrote: > Martin > > One other thing. I believe you are incorrect about uploading using the > usegalaxy.org page with a 15 gb file. That I believe that is a mistake by > the Galaxy team. Maybe a clear tutorial on how to upload a 15gb file would > be nice. > > Thanks Again > > 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 3/14/2014 12:52 PM, > Martin Čech wrote: > > Hello Scott, > > there is no 'new Galaxy' that has changed the way upload works. If you > were able to upload files before the February release just follow the same > path. The only thing that evolved is that we added another way to upload > files that we are planning to replace the old one with - but that will > happen in the future. > > So to reiterate once more: You can use the 'old upload' that is intact > under Get Data / Upload File on the usegalaxy.org server if you have > trouble using the new one. > > If you have trouble using the new one please post a specific question > about it. > > Please do not reply to other threads with an unrelated question. > > Thank you > > Martin > > > > > On Fri, Mar 14, 2014 at 11:24 AM, Scott Tighe <scott.tighe(a)uvm.edu> wrote: > >> >> Hi Galaxy List >>> >>> If anybody has some insight as to how to upload data to the new Galaxy, >>> I sure would enjoy hearing the trick. >>> >>> 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 3/14/2014 10:25 AM, Jennifer Jackson wrote: >>> >>>> Hi Elvio, >>>> >>>> Peter is correct - you can manage any list membership through the >>>> mailman web pages. >>>> >>>> I found you only on this list and unsubscribed you. If you want to >>>> instead consider the galaxy-announce mailing list (low volume, general >>>> project updates), links for how to sign up are on this wiki: >>>> https://wiki.galaxyproject.org/MailingLists >>>> >>>> Best, >>>> >>>> Jen >>>> Galaxy team >>>> >>>> On 3/14/14 2:58 AM, Elvio Pederzolli wrote: >>>> >>>>> Hi there can you please unsubscribe me from all Galaxy lists please >>>>> >>>>> Thank you >>>>> >>>>> Elvio Pederzolli >>>>> >>>>> Sent from my iPad >>>>> ___________________________________________________________ >>>>> 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/ >>>>> >>>> >>>> >>> ___________________________________________________________ >>> 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/ >>> >> >> ___________________________________________________________ >> 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/ >> > > >

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Exome seq work flow
by Mathew Bunj 13 Mar '14

13 Mar '14

I was wondering if Galaxy has any work flow for calling mutations in Exome seq and then annotating. Alignment can be done by BWA. Thanks Mathew

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adding danrer7 as a reference genome for tophat2
by Elwood Linney 12 Mar '14

12 Mar '14

Can you add danrer7 as a reference genome for tophat2 for online Galaxy? Its there for tophat for Illumina. Elwood Linney

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galaxy-user March 2014