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Extract Genomic DNA Problem
by Stephen Taylor 22 Jun '11

22 Jun '11

Hi, I was trying to extract FASTA sequences using the following tab separated data for Chicken on the Galaxy Main server: chr5 47258168 47259240 chr18 1938527 1939965 chr2 101973625 101974007 chr4 75653898 75674045 chr19 4258837 4263299 chr4 39330049 39372715 chr4 9606881 9610083 chr15 7264937 7265599 chr21 6659189 6667015 chr2 351239 352821 I got the following galaxy output: ==================================== 7: Extract Genomic DNA on data 6 empty format: fasta, database: galGal3 Info: 10 warnings, 1st is: Unable to fetch the sequence from '47258168' to '1072' for build 'galGal3'. Skipped 10 invalid lines, 1st is #1, "chr5 47258168 47259240" Any ideas what I am doing wrong? Thanks, Steve

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Configuring Galaxy Server
by gaurav thareja 22 Jun '11

22 Jun '11

Hi All, Thank you for last reply and links about galaxy structure. The links were helpful. But still I am uncertain about many files and their uses. To previous question, I will require further help on following issues: 1. Where all users information is stored in file structure so that i can add custom users for my galaxy server? 2. Is it possible to customize left purple panel? My real aim is to customize the galaxy browser instance as per my needs and use for internal development, which i think is possible?. So, if you guys have any development documents which can be shared to provide further insights about file and directory structure will be really helpful. Regards Gaurav Thareja

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aspera install on cloud install
by Joseph Hargitai 22 Jun '11

22 Jun '11

Hi, anyone tried to install an aspera server for a galaxy cloud instance? The goal would be to feed some local data faster to the instance. best, joe

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Re: [galaxy-user] cuffcompare error in galaxy (Carlos Javier Borroto)
by 吳正華 22 Jun '11

22 Jun '11

Hi Carlos: After I replaced cuffcompare_wrapper.py & cuffcompare_wrapper.xml with code provided by Jeremy, now I can execute cuffcompare on my local galaxy. You can check following link: https://bitbucket.org/galaxy/galaxy-central/changeset/f4b98c453389 hope this helps. Best John Wu 1. Re: cuffcompare error in galaxy (Carlos Javier Borroto) ---------------------------------------------------------------------- Message: 1 Date: Mon, 20 Jun 2011 14:01:15 -0400 From: Carlos Javier Borroto <carlos.borroto(a)gmail.com> To: ??? <johnwu(a)ibms.sinica.edu.tw> Cc: galaxy-user(a)lists.bx.psu.edu Subject: Re: [galaxy-user] cuffcompare error in galaxy Message-ID: <BANLkTi=jtR88L_X5-SZpgnU4=oVqao=epQ(a)mail.gmail.com> Content-Type: text/plain; charset=UTF-8 Hi John, I'm finding the exact same error while going through Jeremy's tutorial in a local instance of galaxy-dist. I was wonder if you found the solution. I see cuffcompare wrapper outputs these files: cc_output.combined.gtf cc_output.input1.refmap cc_output.input1.tmap cc_output.loci cc_output.stats cc_output.tracking and in the logs I'm seing this: galaxy.jobs DEBUG 2011-06-20 13:34:49,902 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output to /home/galaxy/galaxy_dist/database/files/000/dataset_68.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,917 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.tmap to /home/galaxy/galaxy_dist/database/files/000/dataset_69.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,932 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.refmap to /home/galaxy/galaxy_dist/database/files/000/dataset_70.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,948 finish(): Moved /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output.combine d.gtf to /home/galaxy/galaxy_dist/database/files/000/dataset_71.dat as directed by from_work_dir Only cc_output.combined.gtf is correctly being moved, the rest aren't being call by the correct filenames. Thanks, -- Carlos Borroto Baltimore, MD 2011/6/10 ??? <johnwu(a)ibms.sinica.edu.tw>: > Dear galaxy team: > > > > I was testing local galaxy of our lab by analyzing RNA-seq data in > Jeremy?s RNA-seq tutorial. > > > > http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise > > > > I could run TopHat, cufflinks, and cuffdiff and got results correctly, > > but when I executed cuffcompare through galaxy, the following error > occurred: > > > > Tool execution generated the following error message: > > Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output' > > The tool produced the following additional output: > > cuffcompare v1.0.3 (2403) > > cuffcompare -o cc_output? -s > /home/galaxy/data/galaxy_data/sam_index/hg19.fasta ./input1 > > > > and error messages in log file (galaxy.log) are: > > > > galaxy.jobs INFO 2011-06-10 14:02:15,161 job 130 dispatched > > galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:15,466 executing: > python > /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py > ????????????????????????????-s ????????????????????--ref_file="None" > ????????????????--dbkey=hg19 > --index_dir=/home/galaxy/software/galaxy_dist/tool-data > /home/galaxy/software/galaxy_dist/database/files/000/dataset_398.dat > > > > galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:27,834 execution finished: > python > /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py > -s???????????????????? --ref_file="None" > ??--dbkey=hg19 > --index_dir=/home/galaxy/software/galaxy_dist/tool-data > /home/galaxy/software/galaxy_dist/database/files/000/dataset_398.dat > > > > galaxy.jobs DEBUG 2011-06-10 14:02:27,943 finish(): Could not move > /home/galaxy/software/galaxy_dist/database/job_working_directory/130/c > c_output to > /home/galaxy/software/galaxy_dist/database/files/000/dataset_399.dat > as directed by from_work_dir > > galaxy.jobs DEBUG 2011-06-10 14:02:27,971 finish(): Could not move > /home/galaxy/software/galaxy_dist/database/job_working_directory/130/i > nput1.tmap to > /home/galaxy/software/galaxy_dist/database/files/000/dataset_400.dat > as directed by from_work_dir > > galaxy.jobs DEBUG 2011-06-10 14:02:27,999 finish(): Could not move > /home/galaxy/software/galaxy_dist/database/job_working_directory/130/i > nput1.refmap to > /home/galaxy/software/galaxy_dist/database/files/000/dataset_401.dat > as directed by from_work_dir > > galaxy.jobs DEBUG 2011-06-10 14:02:28,027 finish(): Moved > /home/galaxy/software/galaxy_dist/database/job_working_directory/130/c > c_output.combined.gtf to > /home/galaxy/software/galaxy_dist/database/files/000/dataset_402.dat > as directed by from_work_dir > > galaxy.jobs DEBUG 2011-06-10 14:02:28,174 > > > > job 130 ended > > > > > > I?ve tried to manually execute cuffcompare to analyze dataset_398.dat > (which is the output of tophat) and I could get correct cuffcompare output. > > > > $ cuffcompare -o cc_output? -s > /home/galaxy/data/galaxy_data/sam_index/hg19.fasta dataset_398.dat > > > > It seems that the coffcompare_wrapper might have something to do with > this error? > > > > Thanks in advance for your help! > > > > > > Best > > John Wu _______________________________________________ galaxy-user mailing list galaxy-user(a)lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user End of galaxy-user Digest, Vol 60, Issue 21 *******************************************

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Displaying MACS Peaks at UCSC
by Steven Okino 21 Jun '11

21 Jun '11

Hello, I am new to Galaxy and am trying to analyze some ChIP-Seq data. I groomed illumina FASTQ data and used Bowtie to map it to hg18. I then used MACS to call ChIP-Seq peaks; over 13,000 were identified. Analysis of individual peaks shows good consistency with ENCODE data sets on UCSC, so I know the ChIP-Seq worked. However, when I try to display the results at UCSC main I get the following error message on the UCSC browser: What am I doing wrong? Please advise. Thank you, Steven Okino

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Re: [galaxy-user] cuffcompare error in galaxy
by Carlos Javier Borroto 20 Jun '11

20 Jun '11

Hi John, I'm finding the exact same error while going through Jeremy's tutorial in a local instance of galaxy-dist. I was wonder if you found the solution. I see cuffcompare wrapper outputs these files: cc_output.combined.gtf cc_output.input1.refmap cc_output.input1.tmap cc_output.loci cc_output.stats cc_output.tracking and in the logs I'm seing this: galaxy.jobs DEBUG 2011-06-20 13:34:49,902 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output to /home/galaxy/galaxy_dist/database/files/000/dataset_68.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,917 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.tmap to /home/galaxy/galaxy_dist/database/files/000/dataset_69.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,932 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.refmap to /home/galaxy/galaxy_dist/database/files/000/dataset_70.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,948 finish(): Moved /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output.combined.gtf to /home/galaxy/galaxy_dist/database/files/000/dataset_71.dat as directed by from_work_dir Only cc_output.combined.gtf is correctly being moved, the rest aren't being call by the correct filenames. Thanks, -- Carlos Borroto Baltimore, MD 2011/6/10 吳正華 <johnwu(a)ibms.sinica.edu.tw>: > Dear galaxy team: > > > > I was testing local galaxy of our lab by analyzing RNA-seq data in Jeremy’s > RNA-seq tutorial. > > > > http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise > > > > I could run TopHat, cufflinks, and cuffdiff and got results correctly, > > but when I executed cuffcompare through galaxy, the following error > occurred: > > > > Tool execution generated the following error message: > > Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output' > > The tool produced the following additional output: > > cuffcompare v1.0.3 (2403) > > cuffcompare -o cc_output -s > /home/galaxy/data/galaxy_data/sam_index/hg19.fasta ./input1 > > > > and error messages in log file (galaxy.log) are: > > > > galaxy.jobs INFO 2011-06-10 14:02:15,161 job 130 dispatched > > galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:15,466 executing: python > /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py > -s --ref_file="None" > --dbkey=hg19 > --index_dir=/home/galaxy/software/galaxy_dist/tool-data > /home/galaxy/software/galaxy_dist/database/files/000/dataset_398.dat > > > > galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:27,834 execution finished: > python > /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py > -s --ref_file="None" > --dbkey=hg19 > --index_dir=/home/galaxy/software/galaxy_dist/tool-data > /home/galaxy/software/galaxy_dist/database/files/000/dataset_398.dat > > > > galaxy.jobs DEBUG 2011-06-10 14:02:27,943 finish(): Could not move > /home/galaxy/software/galaxy_dist/database/job_working_directory/130/cc_output > to /home/galaxy/software/galaxy_dist/database/files/000/dataset_399.dat as > directed by from_work_dir > > galaxy.jobs DEBUG 2011-06-10 14:02:27,971 finish(): Could not move > /home/galaxy/software/galaxy_dist/database/job_working_directory/130/input1.tmap > to /home/galaxy/software/galaxy_dist/database/files/000/dataset_400.dat as > directed by from_work_dir > > galaxy.jobs DEBUG 2011-06-10 14:02:27,999 finish(): Could not move > /home/galaxy/software/galaxy_dist/database/job_working_directory/130/input1.refmap > to /home/galaxy/software/galaxy_dist/database/files/000/dataset_401.dat as > directed by from_work_dir > > galaxy.jobs DEBUG 2011-06-10 14:02:28,027 finish(): Moved > /home/galaxy/software/galaxy_dist/database/job_working_directory/130/cc_output.combined.gtf > to /home/galaxy/software/galaxy_dist/database/files/000/dataset_402.dat as > directed by from_work_dir > > galaxy.jobs DEBUG 2011-06-10 14:02:28,174 > > > > job 130 ended > > > > > > I’ve tried to manually execute cuffcompare to analyze dataset_398.dat (which > is the output of tophat) and I could get correct cuffcompare output. > > > > $ cuffcompare -o cc_output -s > /home/galaxy/data/galaxy_data/sam_index/hg19.fasta dataset_398.dat > > > > It seems that the coffcompare_wrapper might have something to do with this > error… > > > > Thanks in advance for your help! > > > > > > Best > > John Wu > > > > > > > > > > ___________________________________________________________ > 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/ >

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Fwd: uploading error
by Assaf Gordon 20 Jun '11

20 Jun '11

Hello Rubina, I've forwarding your email to the galaxy public mailing list, where the Galaxy team can further help you with your upload. Generally speaking, uploading big FASTQ using the web interface is prone to errors. The Galaxy team added a new upload method, using FTP, which is more reliable. Detailed instructions are available here: https://bitbucket.org/galaxy/galaxy-central/wiki/UploadViaFTP Regards, -gordon -------- Original Message -------- Subject: uploading error Date: Mon, 20 Jun 2011 18:10:57 +0000 From: <rdalvi01(a)students.poly.edu> To: <gordon(a)cshl.edu> Hi, My name is Rubina. I am using Galaxy to convert fastq files to fasta format. I tried to upload fastq file on the following link. http://main.g2.bx.psu.edu/ However I am not able to upload. Its been a week, but it still shows uploading. Thank You, Rubina

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How to delete multiple items in libraries?
by Louise-Amélie Schmitt 20 Jun '11

20 Jun '11

Hello everyone In the admin panel > Manage data libraries section I have an issue with deleting datasets. When I click on each dataset's triangle menu and ask for deletion, everything is fine. But whenever I select datasets and ask for deletion with the drop down menu at the bottom of the page, Galaxy tells me I don't have the rights to delete them. I get the following message: "You are not authorized to delete any of the selected datasets." Did I miss anything? Thanks, L-A

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Small RNA Mapping
by Shayne Bellingham 20 Jun '11

20 Jun '11

Dear Galaxy Team, I was recently pointed to your website to analyse my NGS data, my primary interest is in mapping small RNA reads to microRNA. After following the tutorials (which are excellent) I am able to upload and map with Bowtie by small RNA data set produced from the SOLID platform. From this point I am completely lost with what to do next to obtain small RNA/microRNA mapped to the genome and a count of the tags etc as the RNA Analysis seams to be dedicated to transcript assembly and quantitation rather than microRNA from mirBase. I have been also looking at the DARIO websever http://dario.bioinf.uni-leipzig.de/index.py for doing the mapping, but I need to convert my BOWTIE SAM output to either BED or BAM file format and remain under 60MB in size. They suggest that the converting the mapping results to BED file be done with map2bed.pl (does Galaxy have a tool for this). For conversion of the mapping to BAM, I can use SAM to BAM with SAMTOOLS with header file intact as this is required for DARIO calculations. This also seems a problem as I dont think I have the header information intact. Any help or suggestions would be appreciated. Shayne A. Bellingham Department of Biochemistry and Molecular Biology Bio21 Molecular Science and Biotechnology Institute The University of Melbourne 30 Flemington Road Parkville VICTORIA 3010 AUSTRALIA

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Question please -manhattan plots
by Sagi 20 Jun '11

20 Jun '11

Dear sir, I was looking through your Galaxy Wiki, but could not find an answer to my question. I would most appreciate any help regarding the following issue: I'm conducting a GWAS study in horses. Up until now I've been using PLINK for my association analysis, and now I wish to generate a Manhattan plot. I've been looking through your online version of Galaxy-Tool under SNP/WGA: QC; LD; Plots <http://main.g2.bx.psu.edu/root/tool_menu#> --> Manhattan/QQ:<http://main.g2.bx.psu.edu/tool_runner?tool_id=rgManQQ1> link, and I've read all the instructions. I think I have an appropriate file ready to run this on your online version, but I was hoping you can send me an example file of how exactly the data should look like (and not just brief explanations about the syntax), and in what format exactly should I upload it? If you have a tutorial about this, even better. Many thanks! Sincerely, Sagi Polani Molecular Evolution Lab Koret School of Veterinary Medicine The Hebrew University of Jerusalem Israel

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