[galaxy-user] Errors when using 'Export to File' option in history pane
Hello, I am experiencing the same issues as described in Bug #588: https://bitbucket.org/galaxy/galaxy-central/issue/588/errors-when-using-export-to-file-option-in Are there more people with the same issue or is there a solution available? Thanks! Mattias -- Bioinformatician Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, the Netherlands ___ 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/
[galaxy-user] tailoring backend SGE submission requests to specific applications
Hi, is there a best practices, to replace general SGE requests with requests specific to applications - did anyone actually build such request options to be part of the selectable items in the apps menus? best, joe ___ 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/
Re: [galaxy-user] BAM files loading and mandatory grooming
Hello L-A, Would you be able to help with a bit more detail and testing? #2 sounds like it may be the issue, but without knowing more right now, I'll provided the next troubleshooting steps. 1 - this is in your own install and it is current with the latest -dist or are you using -central (which pull?). Did something change between the last successful BAM load and the new problem? 2 - without copying them means maybe that you are using a symbolic link at your own site? This load is into a Library (this is how to move data transferred outside of the Galaxy mechanisms into a history, i.e. around a local file system by direct copy or similar). Load into a Library first, then copy to history. Instruction in wiki here: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files 3 - or do you mean without copying by using the FTP method set up locally, followed by a load into a history? 4 - BAM file metadata (pencil icon - Edit options) looks OK? Or, this is the problem? 5 - SAMTools is loaded into your instance? Tools function on other BAM files or all? Some simple SAMTools commands (that work with BAM files) function line command OK on these (to rule out problem with BAM files themselves - missing .bai index could be a problem). 6 - if you start with the same data and convert SAM-BAM within Galaxy, does the SAM load and is the resulting BAM file OK? 7 - If you load the BAM file at the public Galaxy web site (using FTP), the load is successful and the BAM file once imported into a history appears OK? Please share link from this test in case we need to examine. (Options - Share or Publish, generate link, email to me and I can share with dev team if needed). Thanks for providing more info or perhaps you will find that one of these uncovers the issue, Best, Jen Galaxy team On 7/18/11 2:05 AM, Louise-Amélie Schmitt wrote: Hello everyone Whenever we try to load BAM files without copying them, we get an error stating the files need grooming, and can't use them at all. Is it this serious? Would there be a way to bypass that? Thanks! L-A ___ 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://usegalaxy.org/ http://galaxyproject.org/ ___ 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/
Re: [galaxy-user] using files produced by Barcode Splitter
Jeremy, The files need to be groomed using the FastQ Groomer so that they will end up in the fastqsanger state. Then your files will show up in the pull-down menus. David From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Jeremy Coate Sent: Monday, July 18, 2011 1:44 PM To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] using files produced by Barcode Splitter I used the Barcode Splitter tool to split multiplexed RNA-Seq libraries into separate files. I would now like to map the reads from each of these fastq files to a reference genome. However, the fastq files generated by Barcode Splitter don't appear in the Fastq File pull-down menus within the the BWA or Bowtie launch pages. I'm probably missing something obvious, but what is the trick for making these files available for the mapping tools? Do I need to import them into my history somehow? Thanks! Jeremy ___ 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/
