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Galaxy October 23, 2012 Distribution & News Brief
by Jennifer Jackson 24 Oct '12

24 Oct '12

*Galaxy Oct 23, 2012 Distribution & News Brief */http://wiki.g2.bx.psu.edu/2012_10_23_DistributionNewsBrief/* * * * *Highlights: * /http://wiki.g2.bx.psu.edu/News/ * *Important Security Fix <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_23#Compute_Tool_Security_Fix>* - upgrade *NOW*. * *New Trello Issue Board <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_23#New_Trello_Issue_Board>* - Learn how to submit, vote, and comment on tickets. * *http://wiki.g2.bx.psu.edu/Tool Shed <http://wiki.g2.bx.psu.edu/Tool%20Shed>* direct updates and changes in Galaxy <http://usegalaxy.org> improve metadata updating, repository management, and more control over tool config. * Updates to the *Visualization <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_23#Visualization_framework>* tool set cover *Trackster*, *Circster*, and new *Scatter Plot* tool. That's an example plot below. scatterplot-partialscreen <http://usegalaxy.org> * New *API <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_23#API>* fixes, tuneups, and brand-new methods to control libraries. * Multiple *Admin <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_10_23#Source>* changes enable better access to user data to solve problems. *http://getgalaxy.org* *http://bitbucket.org/galaxy/galaxy-dist* new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r 12fcd068b12e *Thanks for using Galaxy!* Jennifer Jackson <http://wiki.g2.bx.psu.edu/JenniferJackson> & the Galaxy Team <http://wiki.g2.bx.psu.edu/Galaxy%20Team>

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Ion Torrent data analysis
by Xu, Jianpeng 23 Oct '12

23 Oct '12

Hi All, I am trying to use Galaxy to analyze the Ion Torrent data. I have uploaded my data to the galaxy. However, when I try to use FASTQ Quality Trimmer and Trim sequences to trim my fastq files, my file does not show in the FASTQ File menu. Do you know why ? How to fix it? Do these programs work on Ion Torrent data ? Thanks, Jianpeng ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Transfection Reagent for Primary Cells
by Jim Hall＠KeraFAST 23 Oct '12

23 Oct '12

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Fastq to Bam conversion on paired end reads picard
by Kevin L 22 Oct '12

22 Oct '12

Hi I was trying to enter the 2nd fq file into the second dialog box for this tool but then the selection automatically changes to be the same as the filename in the first dialog. is this a known issue? NGS: Picard (beta) CONVERSION FASTQ to BAM<https://main.g2.bx.psu.edu/tool_runner?tool_id=picard_FastqToSam> creates an unaligned BAM file

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Re: [galaxy-user] Export to file
by Jennifer Jackson 22 Oct '12

22 Oct '12

Hi Dave, Yes, if your Galaxy instance is on the internet, for entire history transfer, you can skip the curl download and just enter the URL from the public Main Galaxy server into your Galaxy directly. To load large data over 2G that is local (datasets, not history archives), you can use the data library option. The idea is to load into a library, then move datasets from libraries into histories as needed. Help is in our wiki here: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files Take care, Jen Galaxy team On 10/17/12 3:21 PM, Dave Corney wrote: > Hi Jen, > > Thanks for your response and suggestion. Just so that it is clear, for > your second method, where I export to file and then use curl, I will > download to my computer as an intermediate stage? Is there a simple way > to take the history and datasets from PSU galaxy to our Princeton galaxy > directly (without downloading to my computer first)? Unfortunately, we > don't have FTP on our own galaxy, which is why I was looking for > alternatives (each file is >2GB, so uploading through the browser won't > work either). It seems that to import from file, the file needs to have > a URL and I'm not sure how to go about that if the file is store locally > on my computer. > > Thanks, > Dave > > > > On Wed, Oct 17, 2012 at 6:12 PM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hi Dave, > > To export larger files, you can use a different method. Open up a > terminal window on your computer and type in at the prompt ($): > > $ curl -0 '<file_link>' > name_the_output > > Where <file_link> can be obtained by right-clicking on the disc icon > for the dataset and selecting "Copy link location". > > If you are going to import into a local Galaxy, exporting entire > histories, or a history comprised of datasets that you have > copied/grouped together, may be a quick alternative. From the > history panel, use "Options (gear icon) -> Export to File" to > generate a link, then use curl again to perform the download. The > "Import from File" function (in the same menu) can be used in your > local Galaxy to incorporate the history and the datasets it contains. > > Hopefully this helps, but please let us know if you have more questions, > > Jen > Galaxy team > > > On 10/17/12 2:37 PM, Dave Corney wrote: > > Hi list, > > Is there a currently a known problem with the "export to file" > function? > I'm trying to migrate some data from the public galaxy to a > private one; > the export function worked well with a small (~100mb) dataset, > but it > has not been working with larger datasets (>2GB) and I get the > error: > Server Error. An error occurred. See the error logs for more > information. (Turn debug on to display exception reports here). > Is there > a limit on the file size of the export? If so, what is it? > > Thanks in advance, > Dave > > > _____________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org <http://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 > <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/ > > > -- > Jennifer Jackson > http://galaxyproject.org > > -- Jennifer Jackson http://galaxyproject.org

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Annotation tool for prokaryotic genome
by Bernardo Bello 22 Oct '12

22 Oct '12

Hello Galaxy community, I would like to know if there is any available tool in Galaxy for automated gene annotation. I need gene annotation in GTF or GFF3 format to run CuffDiff on a RNA-Seq project that we are. If not, do you recommend me any software or utility. We have the genome annotated in GenBank format, but searching in the web I've seen that is not possible to convert GenBank format to GTF or GFF3. I appreciate your opinions. Thank you, Bernardo -- *Bernardo Bello Ortí* Becario predoctoral FPI CReSA-IRTA Campus de Bellaterra-Universitat Autònoma de Barcelona Edifici CReSA 08193 Bellaterra (Barcelona) Tel.: 647 42 52 63 *www.cresa.es * * *

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adding references
by mark.rose＠syngenta.com 22 Oct '12

22 Oct '12

Hello I'm trying to learn how to install my own references for alignment in galaxy. I've found posts citing the following link as being helpful https://bitbucket.org/galaxy/galaxy-central/wiki/NGSLocalSetup This however link appears broken. Can anyone redirect me? Thanks Mark This message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited.

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help
by Jennifer Jackson 21 Oct '12

21 Oct '12

Hello Pranathi, Sorry that you are having problems. Instead, use this Galaxy tool and the links directly between Galaxy and SRA to add the fastq data to your history: 1 - Get Data -> EBI SRA ENA SRA 2 - Enter "SRR192339" into the query box and click on search 3 - At the far right in the bottom table, under the "Fastq" tab, find a column named Galaxy, and under it a link for this data "Fastq file#1". Click on this, and the dataset should start loaded into the current active history. When you import data, be sure to note the other information about the experiment on the SRA form, so that you will know how to prepare the data for use in Galaxy. Note that you cannot load HTML data into Galaxy, so the index itself cannot be transferred directly. However you could copy and paste this into a plain text file (plain .txt, not .html), and upload that, if you wanted to keep a tracking history with the data. This particular data was generated by the Illumina Genome Analyzer IIx technology, which creates data that is compatible with ".fastqsanger" format in Galaxy. It is also single end. This simplifies the data prep - simply assign the datatype as ".fastqsanger" and it is ready to use with tools. Starting with "FastQC" is generally considered a good idea. Good luck with your project, Jen Galaxy team ps: Please note the corrected mailing list address "galaxy-user(a)bx.psu.edu". http://wiki.g2.bx.psu.edu/MailingLists On 10/19/12 11:31 PM, pranathi pappu wrote: > Dear Sir /Madam , > > > I have been i have been trying to upload NGS Datasets from NCBI protein > database onto the "Galaxy" website so that i could go on with my > work but then i have been getting a result like this : > 33: SRR192339.sra > empty > format: txt, database: > ?<https://main.g2.bx.psu.edu/datasets/543f7c4f13f23152/edit> > Info: The uploaded binary file contains inappropriate content > > This has been the case with almost all the files that i have been > trying to > upload . Please help me with this and i would be greatful if you > could direct me to the right person who can help me sort this matter out . > Thanking you > Pranathi Pappu -- Jennifer Jackson http://galaxyproject.org

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Create GTF or GFF3 file from draft genome
by Bernardo Bello 21 Oct '12

21 Oct '12

Hello Galaxy community, I recently entered in RNA-Seq world, I’m a second year PhD. We have recently sequenced a bacterial transcriptome. I would like to create the GTF or GFF3 file from the bacterial genome in order to add it to Cufflinks. The draft genome is still unpublished. We have run the PGAAP [URL="http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html"] http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html[/URL] pipeline to annotate it, but PGAAP do not gives GTF or GFF3 file. Instead, PGAAP gives you GenBank File. If someone could advise me how to do it I will be very grateful. Maybe Artemis can do it. Last, say that I'm a biologist, so I need GUI to work, no programming experience, sorry. Thank you very much, Bernardo -- *Bernardo Bello Ortí* Becario predoctoral FPI CReSA-IRTA Campus de Bellaterra-Universitat Autònoma de Barcelona Edifici CReSA 08193 Bellaterra (Barcelona) Tel.: 647 42 52 63 *www.cresa.es * * *

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More help neeeded
by Kshama Aswath 19 Oct '12

19 Oct '12

Hello , I tried everything possible according to the reply I got from Jen , helping me fix my problem but is not working.Please see below . Is it possible that because the usage shows 91% I am not able to retrieve anything back to display? Might sound ridiculous but have no clue !! I still have no output back and none of the hidden datasets or deleted datasets are showing so I can purge them. When I chose the "purge deleted datasets" from the gear icon , I got back a message indicating "0 datasets purged". Please hlep as this is tremendously delaying my analysis process. I have answered some of the steps Jen asked me to take ,please see below: here is what Jen wrote to help me with my problem on galaxy : We would like to help. I looked for an account under your email address "kaswath(a)masonlive.gmu.edu" on the public Main Galaxy instance at http://main.g2.bx.psu.edu (http://usegalaxy.org) and did not find one, so I will tell you how to check for the data yourself, then you can share your account email address if you are still stuck. I am registered under compugene(a)gmail.com, that is why u could not find me on my school ID. 1 - For unexplained data counting towards your quota: Check for datasets in histories that are deleted, but not permanently deleted. Inside a history, select "Options (gear icon) -> View Deleted Datasets" to bring up those that were deleted. Each will note if permanently deleted or not and give the option to purge. I tried this and it did not show the deleted datasets Also check for complete histories that may be deleted, but also not permanently deleted (or purged). Select "Options (gear icon) -> Saved Histories", then view "all" to see active and deleted. The table will note if the data is deleted, but not purged. The option to purge/permanently delete will also be given. The show all option showed what I currenlty have bt not the deleted datasets 2 - To locate the output of workflow that seems to be missing: Check for hidden datasets. From within a history (the history that launched the job, if no other history was created), select "Options (gear icon) -> View Hidden Datasets" to bring up those that were hidden by the workflow. (Hiding intermediate datasets is a workflow option). Perhaps there was an error early on in the workflow, before the stage where a result would be written to a new history. I would also recommended that you experiment with a test run where the output is not written to a new history (if you have not already done so), just to rule out any problems central to the workflow (or the inputs), independent of the new history issue. Tried this but the hidden datasets did not show up ! Help is also in this wiki: http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets See Hidden & Delete_vs_Delete_Permanently Hopefully this helps, but please let us know if you need more assistance, Jen Galaxy team On 10/17/12 7:20 PM, kaswath wrote: > Hello Galaxy, > > I have a dataset about *20.8GB *to work with using the NGS analysis. I > FTPd the dataset and created a workflow for the analysis and ran the job > on the entire 20.8GB on Galaxy main around september 27th. > > I waited on about two to four days .....no output of any sort ! > I had requested the results be saved in a different history. I checked , > but no new history with results was created ! > > I reran the job again after a week or so and still no results ! > > I had tried running this on small dataset and it had worked earlier ! > Anyhow, getting back to this proble,m I have NOT receive any error > message however , my USAGE bar on the top right is at 90% !! So I went > back and deleted the old copies of my history I had , even so the usage > bar is still at 90%! > Before I ran my workflow I had the usage bar being way less ! > > Please can u let me know what is happening? Why I have not received any > results on my analysis yet? I really need to get this done ASAP ! > > Thanks so much for all your help ! > > Regards > > Kshama. > > > > ___________________________________________________________ > 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/ > -- Jennifer Jackson http://galaxyproject.org Reply Reply to all Forward Click here to Reply, Reply to all, or Forward Why this ad?Ads – Business Analytics Guide Simple Interactive Visualization. Visual Drag & Drop UI. Quick & Easy Pentaho.com/Business-Analytics 128 22% full Using 2.2 GB of your 10.1 GB ©2012 Google - Terms & Privacy Last account activity: 19 minutes ago DetailsPeople (3)Jennifer Jackson jen(a)bx.psu.edu Show details Ads – Why these ads? The Hartfordhartfordauto.com Save on Car Insurance You Could Save $443* on Car Insurance from The Hartford. 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SAS Datasets » SAS Programming » SAS Job Opportunities » SAS Data Analysis » Business Analytics Guide Simple Interactive Visualization.22% fullUsing 2.2 GB of your 10.1 GB ©2012 Google - Terms & Privacy Last account activity: 19 minutes agoDetailsYou have one new message. -- Kshama Aswath Graduate Student-(PhD) Bioinformatics and computational Biology Prince Williams Campus George Mason University Manasses,VA-20110

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