- galaxy-user - lists.galaxyproject.org

Problems with the Groomer
by Felix Hammer 11 Mar '11

11 Mar '11

Hi, I'm experiencing some strange problems with the fastq groomer. Trying to groom my files I get the following error: "Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/tools/fastq/fastq_groomer.py", line 37, in if __name__ == "__main__": main() File "/galaxy/home/g2main/galaxy_main/tools/fastq/fastq_groomer.py", line 18, in main for read_count, fastq_read in enumerate( fastqReader( open( input_filename ), format = input_type ) ): File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 452, in __iter__ yield self.next() File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 448, in next rval.assert_sequence_quality_lengths() File "/galaxy/home/g2main/galaxy_main/lib/galaxy_utils/sequence/fastq.py", line 142, in assert_sequence_quality_lengths assert qual_len == seq_len, "Invalid FASTQ file: quality score length (%i) does not match sequence length (%i)" % ( qual_len, seq_len ) AssertionError: Invalid FASTQ file: quality score length (63) does not match sequence length (36)" I've double checked the file and it should be ok. Any ideas? thx, Felix

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Import data in RGenetics
by BAULANDE Sylvain 211527 Partnerchip 11 Mar '11

11 Mar '11

dear Galaxy users, I would like to import genotyping data in Rgenetics and I can't succeed. I have ped file and map file, I try to import them in lped format but it didn't work ... Anybody with experience can help me to solve this issue ? Many thanks in advance, Best regards, Sylvain

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Fwd: Question about FTP
by Cathy Riemer 10 Mar '11

10 Mar '11

----- Forwarded message from Noushin Ghaffari <noushin.ghaffari(a)gmail.com> ----- Date: Mon, 7 Mar 2011 09:09:13 -0600 From: Noushin Ghaffari <noushin.ghaffari(a)gmail.com> To: dbadmin(a)bio.cse.psu.edu Subject: Question about FTP Dear Galaxy team, Firstly, thank you very much for the great tools. I am working on a large dataset and need to upload it to Galaxy via FTP. I used ftp://main.g2.bx.psu.edu but I cannot login. I used my email, my public name on Galaxy and just simple my name, but none of them worked. Can you please help me to know how can I login to upload my file? Here is my inofrmation: email: noushin.ghaffari(a)gmail.com public name: me-on-galaxy I appreciate you help and time in advance. Noushin ----- End forwarded message -----

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EMBOSS programs with graphical output(s)
by Martin Senger 09 Mar '11

09 Mar '11

Hi, I am new to Galaxy (but not to EMBOSS :-)) - so I may be doing something stupid. Sorry if I do. I am referring to my own local Galaxy installation. 1) I noticed that most of the emboss graphical programs (e.g. plotorf) are executed from/by the perl interpreter, e.g.: perl /home/galaxy/galaxy-dist/tools/emboss_5/ emboss_single_outputfile_wrapper.pl plotorf -sequence ... These programs are working fine. 2) There are few other programs that could produce a graphical output (freak, hmoment, iep) but they don't because the toggle "-plot" is not used in their command line. Therefore, strictly speaking, they are also working fine (producing tables instead of graphs). 3) But there are two programs, prettyplot and pepnet, that are called without any wrapper (no perl interpreter), e.g. pepnet -sequence ... and they produce graph (as PNG), indeed, but this graphical result is not shown in Galaxy. Instead, I am getting there an image showing just the text of a URL (attached). And metadata/report on this result says: 114: prettyplot on data 1 empty format: png, database: ? Info: Created /home/galaxy/galaxy-dist/database/files/000/dataset_116.dat.1.png I do not know why there is an "empty" remark - because the PNG file is created, and it is a PNG file, it is just not shown in the Galaxy. I wonder what I have wrongly configured...? Thanks for any help, Martin -- Martin Senger email: martin.senger@gmail.com,martin.senger@kaust.edu.sa skype: martinsenger

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Problem Adding a Custom Build in Trackster
by Liisa Koski 09 Mar '11

09 Mar '11

Hello, I am trying to 'Add a Custom Build' to my local instance of Galaxy/Trackster. There seems to be a problem when I enter the chromosome length info, both when I paste directly on the screen and when I use the upload button (for the .len file). After I press Submit I can see the Name and Key info that I specified but it always says that the 'Number of Chroms' is 0. Is there a bug or I am doing something wrong? Thanks for you help, Liisa

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Referencing data library directly from tool's input parameter dropdown.
by Rodriguez, Aaron (NIH/NCI) [C] 08 Mar '11

08 Mar '11

Hello all. First of all thanks to Galaxy developers and supporters for this great tool -- I'm experimenting with adding my custom tools to galaxy and I'm very impressed with how simple galaxy makes this process. Some of the tools that I'm adding to my local instance take reference files as a parameter. These files are often large and fairly static. I understand that I can create a data library where users can select the reference file needed and import into "history" for analysis. However, I would like to know if it's possible for a tool's input parameter (dropdown) to enumerate these files from a public data-library (to avoid the steps needed to import from library into history) and have that file pathname become the value for my parameter? As an alternative, would it be possible to load such a drop down from files (of a certain type) existing at some predefined system path? Thanks in advance, -AR

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Re: [galaxy-user] [galaxy-bugs] For small RNA analysis
by Jennifer Jackson 08 Mar '11

08 Mar '11

Hello, Yes, and this tutorial can help to get you oriented: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise Please let us know if we can help more (using galaxy-user(a)bx.psu.edu please for data/tool questions), Best, Jen Galaxy team On 2/16/11 9:10 AM, Jianquan Wang wrote: > Dear Sir/Madam, > > I have one set of small RNA sequence data. I am wondering whether I can use > Galaxy to analyze it. > Thank you. > > Jianquan Wang > > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

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Bowtie Job doesn't start
by Felix Hammer 08 Mar '11

08 Mar '11

Hi, just trying to use Bowtie, but the job does not start. Is there somthing wrong with the server at the moment? Felix

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Re: [galaxy-user] Fwd: Need a generous help regarding uploading
by Jennifer Jackson 08 Mar '11

08 Mar '11

Hi Vasu, Very sorry to hear that you are still having problems. Have you been able to do the update? It was not clear from your email. The latest is: http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r ca0c4ad2bb39 When you reply, could you note which revision you are using (perhaps you are pulling from galaxy-central instead?) Thanks for helping us to diagnose the problem, Jen Galaxy team On 1/3/11 12:05 PM, vasu punj wrote: > NO I am still unable to get it through. Any help in this regard will be > apprceiated. > Vasu > > --- On *Mon, 1/3/11, Jennifer Jackson /<jen(a)bx.psu.edu>/* wrote: > > > From: Jennifer Jackson <jen(a)bx.psu.edu> > Subject: Re: [galaxy-user] Fwd: Need a generous help regarding uploading > To: "vasu punj" <punjv(a)yahoo.com> > Cc: "galaxy-user(a)bx.psu.edu" <galaxy-user(a)bx.psu.edu> > Date: Monday, January 3, 2011, 1:59 PM > > Hello Vasu, > > Are you still having problems? Or did this other reply help? > http://gmod.827538.n3.nabble.com/Bam-file-after-Tophat-run-td2089789.html#a… > > If the problem is persistent, Galaxy needs to be updated to get better > UI support for downloading BAM files. > > Hopefully the problem can be resolved, but please let us know if you > need more help. > > Thanks! > > Jen > Galaxy team > > > On 12/15/10 12:23 PM, vasu punj wrote: > > I have submited your email to share job 31 and 25 are the Tophat runs > > which I am trying to save as bam files from Floppy icon. > > The job is run on our University cluster. I have alos enclosed screen > > shot for your ready reference. > > vasu > > > > --- On *Wed, 12/15/10, Jennifer Jackson /<jen(a)bx.psu.edu > > Hello Asifullah, > > > > It would be helpful if you would be able to share your history. > Please > > note which exact datasets (by number) you are having problems saving. > > > > Use Options -> Share or Publish -> click on the button to Share via > > link > > and then email that to me. > > > > Thank you, > > > > Jen > > Galaxy team > > > > On 12/15/10 7:56 AM, vasu punj wrote: > > > I have done the same it gav eme bam index file when i removed the > > > extension index or as such it come out to be not right bam file > > format > > > as recognized by various tools > > > Thanks > > > Date: Wednesday, December 15, 2010, 9:52 AM > > > > > > Hello Asifullah, > > > > > > Click on the "save" icon for the dataset to initiate a > download. This > > > icon is shaped like a little purple disk on the very left side > of the > > > dataset's box in the right history pane. > > > > > > Hopefully this is helpful, > > > > > > Thank you, > > > > > > Jen > > > Galaxy team > > > > > > On 12/15/10 7:47 AM, vasu punj wrote: > > > > Hi, > > > > Can we save Bam file from Tophat out put if so how can we do that > > > please. > > > > Thanks. > > > > Date: Wednesday, December 15, 2010, 9:38 AM > > > > > > > > Hello Asifullah, > > > > > > > > The Galaxy tool "Get Data -> Upload File" has instructions for > > > > uploading > > > > data to the FTP server. We recommend using the 3rd party utility > > > > FileZilla as a desktop FTP client. > > > > > > > > http://file-zilla.com/ > > > > > > > > Hopefully this will get you started, > > > > > > > > Best! > > > > > > > > Jen > > > > Galaxy team > > > > > > > > ps: In the future, if you could send questions directly to > > > > galaxy-user(a)bx.psu.edu > > > > >> *Subject: **Need a generous help regarding uploading* > > > > >> > > > > >> Dear All, > > > > >> > > > > >> I am in trouble to upload 1.2Gb illumine data on Galaxy > page for > > > > >> subsequent assembling and analysis steps. I am basically a > > > biologist > > > > >> and new regarding utility of modern bioinformatics tools. > > some one > > > > >> have suggested to upload first your data on a http web page > > > then it > > > > >> would be easy to be uploaded on GALaxy. But it is also not > > > possible > > > > >> for me as having little computer knowledge. So could some one > > > > help me > > > > >> generously regarding these issue. I will highly appreciate > > > > his/her help. > > > > >> > > > > >> Regards > > > > >> Asifullah Khan > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > galaxy-user mailing list > > > > > galaxy-user(a)lists.bx.psu.edu -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

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upload of Zea mays genome to galaxy?
by karlerhard＠berkeley.edu 06 Mar '11

06 Mar '11

Hello, I'm interested in using the galaxy tools to analyze some transcriptome libraries I made of maize seedlings. Would it be possible to upload the maize reference genome to the galaxy browser? It's available at the following website: http://ftp.maizesequence.org/current/ Hope this can be done, would be really exciting! Thanks, Karl

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