- galaxy-user - lists.galaxyproject.org

Help: Mapping with Bowtie does not start
by Meike.Latz＠mdc-berlin.de 10 Mar '14

10 Mar '14

Hello, I am trying to map sequences with Bowtie for Illumina. I have been waiting for a whole day now but it still says "Job is waiting to run". Are the jobs stuck in a queue or is there any other problem? Thanks a lot in advance! Meike

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Column Join feature
by Justin Clarke 07 Mar '14

07 Mar '14

Hi, I am analysing some RNA-seq data and have two different datasets, total RNA plus enzyme and total RNA minus enzyme. I used to type in "column join" in the "Tools" menu on the Galaxy homepage after uploaded the files in Text delimited format. Column join allowed me to join two datasets by a hinge column, in this case I would choose column 1 which would be the chromosome position. I would also be allowed to fill empty columns with a value of 1. The output would give me 3 columns, chromosome number (which both datasets shared), reads for minus enzyme, and reads for plus enzyme. The function would never reject any chromosome position with reads in one dataset and not the other. However, I cannot seem to be able to find this function anymore, and the new function "Join two datasets" seems to only give me back rows where both plus and minus datasets have reads. Does anyone else have this problem or know how I could get around it? Regards, Justin ---------------------------------- Justin Clarke McDowall Laboratory Garstang 8.52/8.51 Faculty of biological sciences University of Leeds Leeds LS2 9JT

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Galaxy - error
by Flávia Aburjaile 07 Mar '14

07 Mar '14

Dear Malito, I am PhD student and I am working with a bacterial transcriptome. A few days ago, i have a problem to obtain data in DESeq and Edge-r on the plataform galaxy. I get the message "no peek" at the end of the process, even with the task g reen. Have you had this problem? I would like to find a solution... Thank you, -- Flavia Figueira Aburjaile

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Compute an expression
by Hamid Qaedi 07 Mar '14

07 Mar '14

Dear All I have a tabular file and using compute (version 1.1.0) tool under text manipulation menu, I 'm going to do a computation to find rows in which column2 and 3 (c2 and c3) are similar in values (values are A,T,C and G) . It seems the syntax for doing that is "c2==c3", but it dosent work. Can anybody help? Any help would be appreciated. Hamid

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Align many FASTA files
by Jennifer Jackson 05 Mar '14

05 Mar '14

Hi Kristen, Are these longer RNA sequences, such as transcripts? Then a tool like BLAT (or BLAST) would be a good choice. Both are wrapped for Galaxy and available in the Tool Shed for use with a local, cloud, or slipstream Galaxy. A cloud is probably the simplest choice for many users - and if the work is for research purposes, be sure to check out Amazon's grant program. http://usegalaxy.org/cloud http://usegalaxy.org/toolshed The public Main server at http://usegalaxy.org has mappers, but these are tuned for NGS reads. Other public Galaxy servers can offer mapping services, too. There are 50+ to review and what each offers changes over time. If you want to look, here is the list: https://wiki.galaxyproject.org/PublicGalaxyServers Keeping questions on the mailing lists helps us with tracking and is appreciated! https://wiki.galaxyproject.org/MailingLists Thanks, Jen Galaxy team https://wiki.galaxyproject.org/Support https://wiki.galaxyproject.org/BigPicture/Choices On 3/5/14 8:43 AM, Kristin Kernohan wrote: > Hi Jennifer > > I am wondering if there is a way on Galaxy to align to the genome a > file with many (~32000) fasta formatted sequences? > > Thanks very much > > Kristin -- Jennifer Hillman-Jackson http://galaxyproject.org

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Error message
by Heller Gerwin 05 Mar '14

05 Mar '14

Hello! I use Galaxy to convert unaligned .bam files (RNA-seq) to fastq files. That works! Then i want to align the fastq files using TopHat2 or Tophat, but the analysis does not start since yesterday. However, I received the following error message several times since yesterday: Details user username null quota_percent 30 total_disk_usage 81718693796 nice_total_disk_usage 76.1 GB email gerwin.heller(a)meduniwien.ac.at tags_used model_class User id 12477bb953a54e27 source HDACollection(9b2b9157fa89d388,193) xhr readyState 4 responseText "Error in history API at listing contents: url_for could not generate URL. Called with args: ('history_content',) {'history_id': u'9b2b9157fa89d388', 'id': 'bbd44e69cb8906b5a211f8cf18ab3f22'}" responseJSON Error in history API at listing contents: url_for could not generate URL. Called with args: ('history_content',) {'history_id': u'9b2b9157fa89d388', 'id': 'bbd44e69cb8906b5a211f8cf18ab3f22'} status 500 statusText Internal Server Error responseHeaders Server nginx/1.4.4 Date Tue, 04 Mar 2014 12:52:02 GMT Content-Type application/json Transfer-Encoding chunked Connection keep-alive Cache-Control max-age=0,no-cache,no-store options data parse true emulateHTTP false emulateJSON false Thanks for help!! With kind regards, Gerwin Heller -- Gerwin Heller, Ph.D. Medical University of Vienna Department of Medicine I Division of Oncology Währinger Gürtel 18-20 A-1090 Vienna, Austria Phone: +43 1 40400 4433 Fax: +43 1 40400 4451

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unable to find the file
by do kadya 04 Mar '14

04 Mar '14

Respected Sir / Ma'am, 'x' tool having 3 commands, 1) command takes files from path. ex perl x.pl --mode 1 file1.bam file2.bam file3.fasta --output result1.txt 2) file4 must have name of result1.txt, file1.bam, file2.bam perl x.pl --mode 2 file4.txt --output-directory ~/result2/ for this second command how can i tell galaxy that i need to see the output file name and other 2 bam file name inside single text file. whenever I try to run this command it says file not found. I am uploading bam files by linking galaxy to that file hence when I specify full path, file1.bam and file2.bam are found. But I need result of 1st command. I want its file name in file4.txt How can I do this in galaxy ? Waiting for positive reply. Thank You. -- Chetan

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Adding custom genome builds to a galaxy instance
by Norris, David 04 Mar '14

04 Mar '14

Hi Galaxy Users, I am trying to understand the process of adding new entries to the genome builds dropdown list and also ensuring these new genome entries are appropriately mapped to a reference sequence. I have been working through the code to work it out myself, but it would be helpful to get some advice from another user or possibly a developer who has experience with this process to avoid possible pitfalls. It would be a nice future enhancement to expose this functionality to administrators. Any advice would be appreciated! Thanks, -David

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bc-bio galaxy
by JPeden＠tgen.org 03 Mar '14

03 Mar '14

Brad, We are looking for some advice on going from our current Galaxy to the nglims fork of Galaxy you have created. The last post I've seen on the subject of moving to the nglims Galaxy was here: http://user.list.galaxyproject.org/add-nglims-to-galaxy-dist-td4656015.html Is it still the case that it "would best to first try it out on a separate instance before thinking about integrating with your production Galaxy. It does take a bit of tweaking …." ?? Second, when I install the nglims fork of galaxy is there a way to have galaxy use the tools and genomes in bc-bio? On our original install, before we used bc-bio, I added tools mainly via the tool shed. It would be nice be to have galaxy using the same tools. Any other advice would be greatly appreciated. Thanks Jim --

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March 2014 Galaxy Update Newsletter
by Dave Clements 28 Feb '14

28 Feb '14

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