January 2012 - galaxy-user - lists.galaxyproject.org

Data files for FunDO tool in Human Genome Variation?
by Paniagua, Eric 18 Jan '12

18 Jan '12

Hi, I'm trying to get the HGV tools set up on our local instance, and I've hit a stumbling block. I can't find where to get a copy of the data files that FunDO uses. They must exist because the tool seems to work fine on the main PSU instance, but after scouring the project's web page and online supplementary material for the related publications, I'm still empty handed. Anyone know where to obtain them? Is it required to build them again locally? Thanks, Eric

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SAM tools pileup in Galaxy
by Patrick Kenneth Gonzales 17 Jan '12

17 Jan '12

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Cufflinks display in ucsc
by Jennifer Jackson 17 Jan '12

17 Jan '12

Hello Rich, Without seeing your data, it sounds as if the formatting of the file is corrupted. You may try using one of Galaxy's data transformation tools (GFF-to-BED) to see if that offers any clues, or a GFF or GTF file format validator (there are several offered online, I believe that UCSC also has one in their tool kit). If this is direct output from Cufflinks, contacting the tool authors to ask if this is expected output is another good place to check. Contact information is in this section of our support wiki: http://wiki.g2.bx.psu.edu/Support#Unexpected_scientific_result If all of this checks out, you may also want to contact UCSC to ask if there are any known limitations with display of RNA-seq data. As an alternative, the Trackster visualization tool in Galaxy has become quite robust with several new features and may be what you are looking for. It has been tuned to work particularly well with RNA-seq data (with both native and custom genomes). This would probably be my first choice as a test before going further. If Trackster produced an error with the dataset, then there is definitely a problem with formatting. If Trackster will display, then the problem may be with what UCSC is expecting and what Cufflinks is producing or with some post-Cufflinks processing. Hopefully one of these will help discover the issue, but if you find that you are still stuck after working through the problem, please send a shared history link to galaxy-bugs(a)bx.psu.edu and we can try to provide feedback. Please include what you tested and the results so we are in the same place and know what is working and what isn't. Going forward, please try to send new questions as brand new threads (not as replies to old threads with new subject lines) with the "to" address directly to galaxy-user(a)bx.psu.edu (you do not need to include me as a "to" or "cc"). This ensures that questions are not lost (as this one almost was) and that our entire team and community can contribute to and benefit from replies. I am sending this email now "to" galaxy-user to start up a new thread and correct the tracking. Replies should now be sent to this message as "reply-all". Thanks for understanding! Makes it much easier for us and nothing (well, we try!) slips through. Best, Jen Galaxy tem > Hi, > I have generated a transcript file using cufflinks for the human > (hg19) or zebrafish(zv9) assemblies. When I try to display the > cufflinks "assembled transcripts" in UCSC I get this error in the UCSC > browser and it wont display the transcripts. > > human: GFF/GTF group NM_005638 on chrX+, this line is on chrY+, all > group members must be on same seq and strand > zebrafish: "GFF/GTF group vapb on chr6+, this line is on chr7-, all > group members must be on same seq and strand" > > Any ideas? > > Rich -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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universe_wsgi.ini and .htaccess file
by Sarah Maman 17 Jan '12

17 Jan '12

Dear, I would like to protect Galaxy installed on my own server , with an .htaccess file. Unfortunalty, my .htaccess file seems not to be read. Only universe_wsgi.ini seems to be read. How can I modify universe_wsgi.ini to add an .htaccess ? Thanks in advance, Sarah MAMAN

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Add Reference Genome
by Amandeep Sidhu 17 Jan '12

17 Jan '12

Hi All, We need Vicugna Pacos (http://asia.ensembl.org/Vicugna_pacos/Info/Index) added as a reference genome to run analysis using Top Hat on the public server. Thanks. Regards, Aman. ------------ Sent from Aman's iPad @biomap | http://amandeep.org/ | http://biomap.org/

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importing data to a local instance of Galaxy
by Joshua Gross 17 Jan '12

17 Jan '12

Hello all-- We have set up a local version of Galaxy on our own server. On the same computer, we have a couple ~27 GB fastq files we want to use in Galaxy, but we have not figured out how to import them. Since they are on the same HDD, we imagine that there is a way to simply copy them into a folder or something. Is there a simple way to import these files? We have been unable to locate anything in the documentation that directly addresses this issue. Thanks a lot for your time! Josh Gross

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"Alignments" tutorial now working
by Paralkar, Vikram 14 Jan '12

14 Jan '12

Hello, I was trying to figure out how to extract Alignments, and it appears that the video tutorial for that is not working (dead link). Thought I¹d report it, and I hope this is the right email address to send this report to. Thanks. Vikram The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message.

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Unable to download files from barcode splitter (from public Galaxy)
by Poh Leng Chong 13 Jan '12

13 Jan '12

Hi, I run Barcode Splitter (from public Galaxy server) and am unable to download the text files generated by the barcode splitter, got an error message which says ' Could not find 'FASTQ_Groomer_on_data_1__V1.txt' on the extra files path /galaxy/main_pool/pool2/files/003/610/dataset_3610002_files/FASTQ_Groomer_on_data_1__V1.txt. The run was Ok (green colour) but yet i was unable to download the text files. Could you please advise? Also, I wonder if you could help regarding the local Galaxy.. I used VirtualBox to install the local copy, and installed according to the instructions as in the website, command as "hg clone https://...." The setup was smooth and went OK. The problem starts when I run the local Galaxy using real data. I could upload the files, but have problems with the fastQC and barcode splitter, I could not proceed any further since these two operations could not be run...The error messages are: FastQC An error occurred running this job: Traceback (most recent call last): File "/home/Desktop/galaxy-dist/tools/rgenetics/rgFastQC.py", line 141, in <module> assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable AssertionError Barcode Splitter An error occurred running this job: /home/Desktop/galaxy-dist/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh: line 65: fastx_barcode_splitter.pl: command not found gzip: stdout: Broken pipe Can anyone help me please? I installed the local Galaxy but could not proceed further. I then used the public Galaxy but could not download the files.... Hope to hear from you. Thanks very much. Best regards Alicia

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Login error + admin rights
by sarah Maman 13 Jan '12

13 Jan '12

Dear, Galaxy is installed on our own instance and I would like to administrer Galaxy. I would like to know how could I register myself to access on admin's interface ? Moreover, I have 2 accounts : 1 - sarah.maman(a)toulouse.inra.fr 2 - sarah.maman(a)inra.toulouse.fr The second one (sarah.maman(a)inra.toulouse.fr) is a mistake. Could you please delete the second one ? Thank you in advance, Sarah MAMAN -- Sarah Maman INRA - LGC - SIGENAE Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Tax: +33(0)5.61.28.57.53

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Should I hg update a Galaxy Cloud ?
by Greg Edwards 12 Jan '12

12 Jan '12

Hi, Still experimenting with Galaxy and Cloudman on AWS EC2. The latest galaxy AMI is described as 861460482541/galaxy-cloudman-2011-03-22. How up to date is that Galaxy rev ? Should I use hg to update it before running, or saving as a customised Cloud AMI ? Thanks. -- Greg Edwards, Port Jackson Bioinformatics Consulting. gedwards2(a)gmail.com

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