October 2013 - galaxy-user - lists.galaxyproject.org

SFTP for local galaxy instance?
by Alicia Linford 31 Oct '13

31 Oct '13

Hi, I have been using the Main galaxy instance for analysis of ChIP-Seq data. My university has recently installed a local instance of Galaxy and we have an SFTP server available. Is there an easy way to upload fastq files to Galaxy by SFTP rather than FTP? Thanks

2 1

Re: [galaxy-user] Tool XML form building bug with <options from_data_table="..."> ?
by damion＠learningpoint.ca 31 Oct '13

31 Oct '13

Darn, never mind. Discovered the " />" at end of <options from_data_table="bccdc_blast_fields" /> was of course causing all the <filters> that followed to be ignored. Thanks to those who may have chipped in on this one. (I get digest mode). d. ---------------------------------------- From: "damion(a)learningpoint.ca" <damion(a)learningpoint.ca> Sent: 30 October 2013 14:24 To: galaxy-user(a)lists.bx.psu.edu Subject: Tool XML form building bug with <options from_data_table="..."> ? Has anyone run into this? I'm building a general-purpose filter control on my galaxy tool xml template for enabling numeric fields to be filtered by > < etc. parameters - in a user friendly way. I have a select list <para> driven by a data table: ... <param name="filter_column" type="select" label="Col"> <options from_data_table="bccdc_blast_fields" /> </param>...

1 0

'Could not connect to server'
by Leontovich, Alexey A., Ph.D. 30 Oct '13

30 Oct '13

I successfully uploaded files to the main Galaxy server a month ago using ftp. However, any attempts to upload files today have failed. I get a 'Could not connect to server' error when trying to connect to main.g2.bx.psu.edu<http://main.g2.bx.psu.edu> uisng FileZilla. Any suggestions? Thank you. Alex Alexey Leontovich, Ph.D. | Assistant Professor of Medical Informatics | Biomedical Statistics and Informatics |Phone: 507-284-4850 | Fax: 507-538-0850 | leontovich.alexey(a)mayo.edu Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | mayoclinic.org<http://www.mayoclinic.org>

2 2

Re: [galaxy-user] [galaxy-dev] Bam File
by Jeremy Goecks 29 Oct '13

29 Oct '13

Hello, First, I've moved this question from the Galaxy development mailing list to the Galaxy user mailing list; in the future, please send questions about using Galaxy to the galaxy-user list. To answer your question, files larger than 2GB must be uploaded via FTP to Galaxy. This is necessary due to Web browser limitations. Help to use FTP is on this wiki. The screencasts both show the two step process. The first is to FTP the data to the server, the second is to move the data from the "Get Data -> Upload Data" tool form into your history. http://wiki.galaxyproject.org/FTPUpload Best, J. On Oct 28, 2013, at 11:55 AM, Arshad Rafiq <arshadrafiq68(a)gmail.com> wrote: > I am trying to upload a bam file for my data analysis (size is about 9GB) I am trying URL method to up load and getting error message, can you please help me to sort out this problem. I am seeing following message > "An error occurred setting the metadata for this dataset. You may be able to set it manually or retry auto-detection" > > Thanks > *********** > Arshad > > -- > Muhammad Arshad Rafiq, PhD > Research Associate > Laboratory of Dr. R. Hamilton > Physiology and Experimental Medicine > Research Institute > The Hospital for Sick Children > McMaster Building, Room 7005 > 88 Elm St. > Toronto, ON > M5G 1X8 > Canada > 647-237-4915 > arshadrafiq68(a)gmail.com > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. 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/

1 0

inconsistant error messages on disk quota?
by Francis Ouellette 26 Oct '13

26 Oct '13

I'm on cloudman, trying to upload files, and I'm getting this error message: "No space left on device" transferring a 1 GB file to my instance, but the cloudman console says I have more than 5 GB left? Is this a bad error message? Is there some other file you want to see? @bffo [cid:BF845074-1348-4A8F-87D2-6AACAD1313E7@wtgc.org] [cid:11E8AB13-A630-4638-8A1F-BF9E3AE526DF@wtgc.org] -- B.F. Francis Ouellette http://oicr.on.ca/person/francis-ouellette

3 5

posting supplementary information on galaxy server
by Jainy Tharun 24 Oct '13

24 Oct '13

Hello, I would like to know whether I can post my supplementary data for an article in the galaxy server. I have .docx files and .xlsx files. I am planning to upload these data in a folder and share the link at first and later publish it. When I tried uploading xlsx file, it is getting automatically converted to .xml files. Please let me know if it is possible provide the supplementary information through galaxy that includes doc and excel sheets.. Thank you so much for your help Jainy

3 2

problems in transitioning from Tophat to Cuffdiff
by Elwood Linney 22 Oct '13

22 Oct '13

After successfully using RNAseq software in Galaxy online for about 10 different datasets to just get gene expression differences between replicates from control versus exposed zebrafish embryos, I am having no luck getting cuffdiff to work with the "moved" Galaxy. I had this problem with histories developed before the move and histories developed after the move. I have had this problem using an order cuffmerge gtf file that worked in the past in Cuffdiff, with a new cuffmerge file developed from cufflinks of the files and by just using a ref file gtf from UCSC. I don't know if this is just some interface problem with a different version of the software that was included with the move, or a reference genome that does not interface with Cuffdiff. It has happened with about 5 different histories. Is anyone else having this problem? And found a solution? Elwood Linney

4 5

Issues on RNAseq since the changeover
by Elwood Linney 18 Oct '13

18 Oct '13

My histories seem to be stopping their processing around the Tophat-cuffmerge steps since the change over of Galaxy online. Sometimes a red box appears over my history name but disappears in a minute or less. I am wondering, given the way the Toolshed now looks different for RNAseq work, if some changes have been made that are disallowing the procedures I used previously. For example: I run larger Fastq files (100 million to 200 million 50bp single-ended reads per sample). I have been grooming my illumina fastq's, using Tophat (not Tophat2) for alignment, then Cuffmerge, then Cuffdiff. This worked in the past but my history are just getting thru Tophat or Cuffmerge and stalling. Should I be doing this in a different manner? This has been my second time around with these datasets after it was suggested that I delete and start all over again. Elwood Linney

2 1

Re: [galaxy-user] Registration is Open for December Bioinformatics Bootcamps at UC Davis!
by Dave Clements 18 Oct '13

18 Oct '13

Hello everyone, There will be 4 days of Galaxy-based training at UC Davis, December 10-13. See below for details. These do sell out, so if you are interested, please think about registering sooner, rather than later. Thanks, Dave C On Thu, Oct 17, 2013 at 8:35 PM, training ucdbio <training.ucdbio(a)gmail.com>wrote: > Registration is now open for Bioinformatics Bootcamps in December! > > We’re excited to announce our next offering of Bioinformatics Bootcamps, > which will be held on the UC Davis campus December 10-13. > > These focused one-day courses are perfect for the student, postdoc, > faculty, or industry professional looking to get up to speed quickly on the > latest technologies and techniques in bioinformatics. Students will work on > their own laptops and have continued access to software and example data > used in the exercises through our public Amazon Web Services virtual > machine (details here <http://bioinformatics.ucdavis.edu/software/>). The > first three bootcamps will use the Galaxy <http://galaxyproject.org/>platform, and the final bootcamp will use both Galaxy and the command-line. > The Alignment and Assembly bootcamps (Dec. 11th & 12th) require you to know > Galaxy, so if you are unfamiliar with Galaxy, you should also take the > Introduction bootcamp on Dec. 10th. > > Tuesday, December 10: > > Introduction to Next-Generation Sequence Analysis with Galaxy<http://training.bioinformatics.ucdavis.edu/2013/10/16/bootcamp-introduction…> > > Wednesday, December 11: > > Next-Generation Sequence Alignment and Variant Discovery<http://training.bioinformatics.ucdavis.edu/2013/10/16/bootcamp-next-generat…> > > Thursday, December 12: > > Genome Assembly using Next-Generation Sequence Data<http://training.bioinformatics.ucdavis.edu/2013/10/16/bootcamp-genome-assem…> > > > Friday, December 13: > > Introduction to the Amazon Cloud for Galaxy and the Command-Line<http://training.bioinformatics.ucdavis.edu/2013/10/16/bootcamp-introduction…> > > > Daily instruction will run from 9am until 5pm. Lunch, light breakfast, and > snacks will be provided. Enrolment for each bootcamp will be capped at 24 > students. Please enroll early to be assured of a seat, as these bootcamps > usually fill up quickly! > > More information, including full descriptions of each bootcamp can be > found at https://training.bioinformatics.ucdavis.edu/bootcamps/ > > > Pricing and Payment > > The cost for each bootcamp is $200 (academic/government) or $250 > (non-academic/industry). We now accept credit cards. UC Davis attendees can > also charge their registration directly to a DaFis account. > > Questions > > If you have any questions, please don’t hesitate to contact us: > > > - > > Training email: training.ucdbio(a)gmail.com > - > > Core email: ucdbio(a)gmail.com > - > > Core main telephone line: 530-752-2698 > > > > We hope to see you in December! > > - The UC Davis Bioinformatics Core Team > > http://training.bioinformatics.ucdavis.edu > > http://bioinformatics.ucdavis.edu/ > <http://bioinformatics.ucdavis.edu/> > > Email List Note: We have now consolidated our contacts into one mailing > list, bioinformatics(a)ucdavis.edu, run by Sympa (lists.ucdavis.edu/sympa/) > If you received this email directly from training.ucdbio(a)gmail.com and > do not want to continue to receive emails from the Bioinformatics Core, you > can unsubscribe by sending an email to sympa(a)ucdavis.edu with the > following in the subject: unsubscribe bioinformatics > > > -- > UC Davis Bioinformatics Core > University of California, Davis > Genome and Biomedical Sciences Facility > 451 Health Sciences Dr. > contact email: ucdbio(a)gmail.com > contact phone: 530-752-2698 > www.bioinformatics.ucdavis.edu > training.bioinformatics.ucdavis.edu > > [image: Inline image 2] > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

1 0

Re: [galaxy-user] Need your helps about Galaxy
by Lei Yan 17 Oct '13

17 Oct '13

Thanks Jen and James so much. Now it looks like I have fixed the problem about tophat_indexes_color, because "Tophat for SOLiD" tool is running in my account (still running, but not finished yet). Here is a summary: - The hg19 index files for colorspace have been there, so I don’t need to build or download. /mnt/galaxyIndices/genomes/Hsapiens/hg19/bowtie_color/hg19 - Change the tool_data_table_conf.xml file, add this: < <table name="tophat_indexes_color" comment_char="#"> < <columns>value, dbkey, name, path</columns> < <file path="/mnt/galaxyIndices/galaxy/tool-data/bowtie_indices_color.loc" /> < </table> /mnt/galaxy/galaxy-app/tool_data_table_conf.xml - Yes, both Bowtie and Tophat use the same indexes. - bowtie_indexes and tophat_indexes use this loc file: /mnt/galaxyIndices/galaxy/tool-data/bowtie_indices.loc - bowtie_indexes_color and tophat_indexes_color use this loc file: /mnt/galaxyIndices/galaxy/tool-data/bowtie_indices_color.loc Hope this can help somebody. Lei Yan Center for Integrative and Translational Genomics The University of Tennessee Health Science Center On Wed, Oct 16, 2013 at 3:21 PM, Jennifer Jackson <jen(a)bx.psu.edu> wrote: > Hi Lei, > > You can download all at once or in two parts (for slower connections): > > > > iGenomes has been pretty good about using the exact same build as released > by the source with no changes for the GTF files, but I do not know about > the indexes - so do a test run once in place. Just to let you know, > creating these may be easier than downloading, is just a single line > command and you have a server to run this on, but the choice is yours. > > Jen > Galaxy team > > > > On 10/16/13 1:11 PM, Lei Yan wrote: > > Hi James, > > I found this: http://bowtie-bio.sourceforge.net/manual.shtml > There are some Pre-built indexes in the right side of this page. > If I just need an hg19 index for colorspace, which index file can work for > us? > Thanks again. > > > Lei Yan > Center for Integrative and Translational Genomics > The University of Tennessee Health Science Center > > > On Wed, Oct 16, 2013 at 2:54 PM, Lei Yan <leiyan2000(a)gmail.com> wrote: > >> Hi Jen and James, >> >> Thanks for your info. >> Yes, we are already running a cloud instance ( >> http://galaxyclass.genenetwork.org/) >> So if I can build the index for colorspace, then how to configure it? >> And I didn’t find the “tophat_indexes_color” record in the Admin - “View >> data tables registry”. Please see attachment. >> >> >> Lei Yan >> Center for Integrative and Translational Genomics >> The University of Tennessee Health Science Center >> >> >> On Wed, Oct 16, 2013 at 2:35 PM, James Taylor <james(a)jamestaylor.org>wrote: >> >>> They are already running a local instance. >>> >>> I didn't realize that bowtie required a different index for colorspace >>> alignment. So Lei, you will have to build the index using bowtie-build >>> -C. >>> >>> -- >>> James Taylor, Associate Professor, Biology/CS, Emory University >>> >>> >>> On Wed, Oct 16, 2013 at 3:31 PM, Jennifer Jackson <jen(a)bx.psu.edu> >>> wrote: >>> > Hello Lei, >>> > >>> > If genomes are not listed, that means that they are not indexed for >>> use with >>> > the tool. The test server is primarily for demonstration or test use >>> > besides, and there could be other unexpected issues even if genomes are >>> > listed (we really do test here). Also, the quotas are very small >>> (10G). If >>> > you want to use this tool, a local, cloud, or slipstream Galaxy is >>> > recommended. Full choices with details are listed here: >>> > http://wiki.galaxyproject.org/BigPicture/Choices >>> > http://usegalaxy.org/toolshed >>> > >>> > Help for setup is here, with the galaxy-dev(a)bx.psu.edu mailing list >>> > available for further support. Tools will need to be installed, and >>> indexes >>> > created. You can rsync the genome, but most genomes will not have loc >>> file >>> > entries and indexes for SOLiD already created - see the Tophat manual >>> for >>> > the command to create these: >>> > >>> http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uni… >>> > http://wiki.galaxyproject.org/Admin/Data%20Integration >>> > http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup >>> > >>> > Hopefully this helps! >>> > >>> > Jen >>> > Galaxy team >>> > >>> > >>> > On 10/16/13 11:57 AM, Lei Yan wrote: >>> >> >>> >> Hi all, >>> >> >>> >> We are trying to use “Tophat for SOLiD”. >>> >> But this tool (Tophat for SOLiD) does not seem to be linked to the >>> >> reference genomes that are installed. I can see those genomes on the >>> Tophat >>> >> for illumina tool and the other tools that require a reference genome. >>> >> Please see attachments. >>> >> Does anybody have any ideas for this? Thanks a lot. >>> >> >>> >> >>> >> Lei Yan >>> >> Center for Integrative and Translational Genomics >>> >> The University of Tennessee Health Science Center >>> > >>> > >>> > -- >>> > Jennifer Hillman-Jackson >>> > http://galaxyproject.org >>> > >>> >> >> > > -- > Jennifer Hillman-Jacksonhttp://galaxyproject.org > >

3 2