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TopHat paired end
by suzan katie 09 Aug '12

09 Aug '12

Hello, I am trying to do RNAseq analysis on Paired end data Illumina. I have about 4 files for each sample (2 forward and 2 reverse). I want to analyze the data in Galaxy. Do I have to groom and run the QC for each file? Should I join the paired files and run both tools on each pair, or should I combine all of the data for each sample (which I don't know how to do) and then groom and run the QC for all of the reads for the sample. Ultimately, How do I run TopHat for paired-end data. When I select paired end data in Galaxy, it gives an option to upload both files should I upload both forward files once and reverse files once. Or should I combine both the files before running the TopHat. I am all confused. Any kind of help will be appreciated Thanks in advance

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upgrading over several releases
by Robert M. Flight 09 Aug '12

09 Aug '12

Hi Everyone, Our current Galaxy instance is from August 30, 2011. This was our first deployment, and we have never upgraded. We are going to upgrade it, but I am trying to determine whether the best process would be to upgrade incrementally over the six dist releases since then, or to try and do it all in one shot, upgrading to the latest dist. Looking at the news briefs, I'm also considering upgrading in 3 steps, upgrade to before the major changes in the tool shed, then to the first release with major tool shed changes, and then finally to the latest release. I would appreciate any insights and advice on this process. Thank you, -Robert Robert M. Flight, Ph.D. University of Louisville Bioinformatics Laboratory University of Louisville Louisville, KY PH 502-852-1809 (HSC) PH 502-852-0467 (Belknap) EM robert.flight(a)louisville.edu EM rflight79(a)gmail.com robertmflight.blogspot.com bioinformatics.louisville.edu/lab github.com/rmflight/general/wiki The most exciting phrase to hear in science, the one that heralds new discoveries, is not "Eureka!" (I found it!) but "That's funny ..." - Isaac Asimov

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Problem with get data/uploading file
by David Roquis 09 Aug '12

09 Aug '12

Dear Galaxy community, I have a problem with uploading data on Galaxy, using the get data/upload file tool, and I can't figure out where the trouble comes from. Basically, when I try to upload files (size ranging from less than 1 Mo up to 600 Mo), sometimes it works, sometimes it doesn't (keep uploading forever), and I don't get any error message when it doesn't work. I can't find a pattern on when it works or not, it seems pretty random. It don't think it is related to the files I use, because I tried with different files, of different types and format, and the exact same file can sometimes be uploaded, sometimes not. One thing I have noticed is that when the upload is successful, a file is created in /tmp/, and when the upload runs forever, no new file appears in /tmp/. I have tried a couple of basic things to solve the problem: emptying the /tmp/, restarting galaxy, deleting permanently my history, etc. Sometimes I can upload 4-5 files in a row, then it stops working, and some other time I can't even upload one. When one upload keep running forever, even if I cancel it, no further uploads will work. I have to stop the uploads and restart galaxy, but it doesn't work 100% of the time (sometimes I have to try 2-3 times before I can upload again). I am facing this problem on two different instances of galaxy. A development one that I simply installed on my /home/ using mercurial and didn't modified at all, and a production one that I just set up following the Galaxy Team recommendations (using PostgreSQL and nginx with the upload module, and working on a dedicated Galaxy user account). I am a beginner in informatics, and since I get no error message, I don't know where to look for a way to solve this annoying problem. Uploading files using data libraries under the admin menu seems to be working perfectly all the time. Thank you very much for your help and advice. Sincerely David Roquis Ph.D. student University of Perpignan additional info: - I am using the latest version of galaxy, and my OS is Fedora 16 - I tried working with and without virtualenv (made no difference). - I don't know if this is related or not, but it seems quite strange to me. Whenever I try to access "manage jobs" in the admin section (on both instances), I get the following error message: "This Galaxy instance is not the job manager. If using multiple servers, please directly access the job manager instance to manage jobs." How is that possible since I am not using multiple servers (especially for the development instance, which I haven't modified at all)? - debug = False is causing me a server error in the history frame (so I use True instead).

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galaxy-central does not start
by Björn Grüning 09 Aug '12

09 Aug '12

Hi, galaxy-central does not start because of commit 9f790bc90769. The attached patch should fix it. Salve, Bjoern -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruening(a)pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/

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EBI SRA download: connection time out
by Joachim Jacob 09 Aug '12

09 Aug '12

Hi all, I do not succeed in downloading data from SRA. For every dataset I use (from smaller one to bigger ones) I get this error, after running for a few minutes. The remote data source application may be off line, please try again later. Error: [Errno ftp error] [Errno 110] Connection timed out Any idea? cheers, Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

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TopHat for paired end
by suzan katie 09 Aug '12

09 Aug '12

Hello, I am trying to run TopHat for paired end and this is my first time using Galaxy and TopHat and I have a doubt regarding what to mention in Mean Inner Distance between Mate Pairs:The default value is 20. Should I leave the value or should I be changing the value. What is Mean Inner Distance between Mate Pairs:? Thanks

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Bowtie .loc file with fasta.1.ebwt
by Robert Chase 09 Aug '12

09 Aug '12

Hello, I am trying to get the reference genomes to appear in our NGS tools. In my bowtie.loc file for instance I have the following line: hg18 /share/shared/data/genomes/hg18/bowtie/Homo_sapiens_assembly18.fasta.1.eb wt [galaxy@ tool-data]$ cd /share/shared/data/genomes/hg18/bowtie/ [galaxy]$ ls Homo_sapiens_assembly18.fasta.1.ebwt Homo_sapiens_assembly18.fasta.4.ebwt Homo_sapiens_assembly18.fasta.2.ebwt Homo_sapiens_assembly18.fasta.rev.1.ebwt Homo_sapiens_assembly18.fasta.3.ebwt Homo_sapiens_assembly18.fasta.rev.2.ebwt Do the files provided in the .loc file have to be fasta files? Where can these fasta files be obtained? -Rob

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Starting a Cloud Instance
by Jennifer Jackson 09 Aug '12

09 Aug '12

Re-Post to galaxy-dev On 8/7/12 3:01 AM, Mark Lindsay wrote: >> I wondered if you might be able to help. >> >> I have very little computing experience but have been trying to launch >> a cloud instance for the last 24 hrs. >> >> Initially I had problems launching the instance in Sahari i.e. it kept >> saying that it could not connect to the relevant page. >> >> When I have finally got top the CloudMan launch page it is giving the >> following message > > [Critical] Volume 'vol-dd6397db' is located in the wrong availability > zone for this instance. You MUST terminate this instance and start a new > one in zone 'us-east-1a' > >> despite the fact that I am sure I have started in zone 'us-east-1a. >> >> How important are the security codes and keys? >> >> BW >> >> Mark >> > ___________________________________________________________ > 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

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a problem with python version
by Rui Wang 08 Aug '12

08 Aug '12

Hi All, we are installing a local galaxy instance but we met something puzzling. we are running galaxy on cent os 5.x and python 2.6.1. when we tried to upload data, it failed with the message ************************************************************************* Dataset generation errors Dataset 5: brain.fa Tool execution generated the following error message: /usr/usc/python/2.6.1/lib/python2.6/site-packages/pytz/tzinfo.py:5: DeprecationWarning: the sets module is deprecated from sets import Set ************************************************************************* However, when we tried to use the galaxy version tied to the OS, which is 2.4.3, we were able to upload successfully. Did anyone have the same experience? Any advice will be greatly appreciated. Thanks, Rui

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Multi-level conditional output files
by John Patterson 08 Aug '12

08 Aug '12

Hello! The wiki entry on dealing with the <filter> tags is wonderful, but I seem to hit its limitations, unless someone has experience with multi-level conditionals in the input. For example in my XML, <conditional name="Build_Settings"> <param name="SettingsType" type="select" label="Settings to use"> <option value="preSet">Use Defaults</option> <option value="full">Full parameter list</option> </param> <when value="preSet" /> <when value="full"> <conditional name="Bam"> <param name="Bam_Output" type="select" label="Bam Output" > <option value="no">No</option> <option value="yes">Yes</option> </param> </conditional> </when> </conditional> The bam conditional sets an argument in my program to generate bam instead of sam (default) which is the reason for the conditional. There are two cases for sam output, when the option is preset, or when full parameters>bam_output == no. for this reason It wouldnt work to filter this on the bam_output boolean because it would evaluate to false if preset was chosen. I cannot do a simple <change format> for the same reason. Do the filter tags only support one boolean check? How would I actually get past the "settings" parameter and into the bam_output parameter?

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